micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Home Page: http://micapipe.readthedocs.io
License: GNU General Public License v3.0
mrinfo -dwgrad $file.Original bvals
0 500 500 500 500 500 500 500 500 500 500 500 501 500 500 500 1000 1000 1000 1000 1000 1000 1001 1000 1000 1001 1000 1001 1000 1001 1000 4000 4001 3999 3999 3999 3999 4002 4000 3999 4002 4002 4006 3998 4003 4001
Original bvecs
0.000 0.354 0.227 0.091 0.263 0.058 -0.281 0.269 -0.179 0.236 0.045 -0.063 0.090 -0.120 -0.283 0.119 0.500 0.322 0.129 0.372 0.082 -0.398 0.381 -0.253 0.334 0.064 -0.089 0.128 -0.170 -0.401 0.168 1.000 0.643 0.258 0.745 0.164 -0.796 0.761 -0.506 0.667 0.128 -0.178 0.255 -0.340 -0.801 0.336
0.000 0.000 0.271 0.109 -0.210 -0.179 -0.113 0.151 0.295 -0.056 -0.339 -0.317 -0.209 -0.260 0.116 0.015 0.000 0.383 0.153 -0.297 -0.254 -0.161 0.213 0.416 -0.079 -0.479 -0.449 -0.295 -0.368 0.165 0.021 0.000 0.766 0.307 -0.594 -0.507 -0.321 0.427 0.833 -0.158 -0.959 -0.898 -0.590 -0.736 0.329 0.043
0.000 0.000 0.000 0.324 0.107 0.299 0.181 0.173 0.079 0.257 0.090 -0.142 -0.271 0.207 0.177 -0.333 0.000 0.000 0.458 0.151 0.423 0.257 0.244 0.112 0.364 0.127 -0.202 -0.384 0.292 0.251 -0.470 0.000 0.000 0.916 0.303 0.846 0.513 0.489 0.224 0.728 0.254 -0.403 -0.767 0.585 0.501 -0.941
"New" bvals
0 62.658 62.485 62.56899999 62.35900001 62.403 62.2455 62.54550001 62.6535 62.4405 62.52299999 62.311 62.736222 62.4245 62.437 62.6375 250 250.373 249.814 249.394 250.169 250.374 250.316066 249.609 250.293 249.915666 250.326 251.115865 249.588 251.278027 249.565 4000 4001.820205 3998.476131 3997.68033 3997.644339 3998.304174 4004.285142 4000.404 3998.348163 4004.325162 4003.988994 4011.664484 3996.084958 4006.374529 4001.904226
Freesurfer recon_all takes a long time to run, and occupies a fair bit of space. It'd be great if you could specify an existing freesurfer directory that micapipe could use. qsiprep and fmriprep both now implement this capability.
In 02_proc-dwi.sh, this:
str_dwi_affine="${dir_warp}/${idBIDS}_space-dwi_from-dwi_to-nativepro_mode-image_desc-"
mat_dwi_affine="${str_dwi_affine}0GenericAffine.mat"
Was changed to:
str_dwi_affine="${dir_warp}/${idBIDS}_space-dwi_from-dwi_to-nativepro_mode-image_desc-affine_"
mat_dwi_affine="${str_dwi_affine}0GenericAffine.mat"
However, 03_SC.sh still looks for:
str_dwi_affine="${dir_warp}/${idBIDS}_space-dwi_from-dwi_to-nativepro_mode-image_desc-"
mat_dwi_affine="${str_dwi_affine}0GenericAffine.mat"
And throws an error at this line:
if [ ! -f "$mat_dwi_affine" ]; then Error "Subject $id doesn't have an affine mat from T1nativepro to DWI space:\n\t\tRUN -proc_dwi"; exit; fi
Because I have this file in my xmf/ directory:
sub-05423_space-dwi_from-dwi_to-nativepro_mode-image_desc-affine_0GenericAffine.mat
and not this one:
sub-05423_space-dwi_from-dwi_to-nativepro_mode-image_desc-0GenericAffine.mat
This prevents SC from running.
str_dwi_affine="${dir_warp}/${idBIDS}_space-dwi_from-dwi_to-nativepro_mode-image_desc-affine_"mat_dwi_affine="${str_dwi_affine}0GenericAffine.mat"What is the current behavior?
Even when the DWI was processed successfully, the Sankey diagram of DWI is orange (INCOMPLETE)
Please provide the steps to reproduce and if possible a minimal demo of the problem
mica-pipe -QC_subj -sub -bids -out
What is the expected behavior?
The color of the sankey diagram should be blue for a complete DWI process
Currently the documentation recommends installation via container:
https://micapipe.readthedocs.io/en/latest/#reproducibility:
To encourage reproducibility and robustness of investigations using micapipe, we provide a fully containerized version of the pipeline in the form of a Docker container. Step-by-step tutorials are provided for bare metal and containerized installations. We encourage users to use containerized versions, offered through Docker and Singularity, given the large number of software dependencies used by the pipeline to handle multiple MRI data modalities.
https://micapipe.readthedocs.io/en/latest/pages/01.install/index.html:
We offer three installation options for micapipe: two containerized versions (Docker and Singularity) as well as a bare-metal installation.
But no such container exists: the Docker instructions attempt to pull from an invalid source, and the Singularity instructions are a placeholder.
I'm not super-familiar with Docker in execution (I'm more familiar with Singularity), but here's what I get when I try to run the recommended Docker command on a fresh Ubuntu 20.04.1 system:
$ sudo docker pull MICA-MNI/micapipe:latest
invalid reference format: repository name must be lowercase
# In case it's only that the case is a problem:
$ sudo docker pull mica-mni/micapipe:latest
Error response from daemon: pull access denied for mica-mni/micapipe, repository does not exist or may require 'docker login': denied: requested access to the resource is denied
# In case it's relevant:
$ docker --version
Docker version 20.10.6, build 370c289
Is it just that it's planned but no one's managed to get to it yet? I didn't see a Dockerfile in the repo or nearby in GitHub.
(To make the documentation correct and the containers available.)
(Probably not relevant, but, Singularity and RHEL 7.6, with SGE.)
(Happy to provide on request.)
I am testing micapipe in a sigularity container in a cluster grid.When I look at the logs in several steps (e.g dwi_proc) there are several error messages related to missing python dependencies such as nilearn. I clip an example of this error. Am I doing something wrong? how should I prevent/solve this error?
Thanks in advance
PD: Here is an example of the way I run the code. I followed the tutorial example of the sudemex_conn database depicted in the documentation
singularity run --cleanenv -B /mnt:/mnt -H $PWD singularity/micapipe_29092021.simg \
-bids /mnt/MD1200B/egarza/afajardo/sudmex_conn/ds003346-download -sub 010 \
-out /mnt/MD1200B/egarza/afajardo/sudmex_conn -proc_structural -proc_freesurfer -post_structural \
-GD -Morphology \
-proc_dwi \
-dwi_main /mnt/MD1200B/egarza/afajardo/sudmex_conn/ds003346-download/sub-010/dwi/sub-010_dwi.nii.gz \
-dwi_rpe /mnt/MD1200B/egarza/afajardo/sudmex_conn/ds003346-download/sub-010/fmap/sub-010_dir-PA_run-01_epi.nii.gz -SC -proc_rsfmri \
-mainScanStr task-rest_bold \
-fmri_rpe /mnt/MD1200B/egarza/afajardo/sudmex_conn/ds003346-download/sub-010/fmap/sub-010_dir-PA_run-02_epi.nii.gz
-regress_WM_CSF \
-GSR \
-QC_subj |& tee micapipe_prueba/prueba4_logs.txt |& tee micapipe_prueba/prueba4_logs.txt \
might be great to add a task fmri stream to micapipe at one point in early 2022. We discussed this with some of you already and it may be a slight variation of the already existing rest fmri stream, and perhaps include afni's 3dDeconvolve to get beta time series that would then be mapped to the surfaces (instead of / or in addition to the preprocessed task based time series). https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html
When running the micapipe container with the MPC module it appears that for some subjects and sessions my surface are not ordered correctly resulting in wrong lateralised correlation matrices, see the attached screenshots of the intensity profiles and resulting correlation matrices for two sessions of the same subject. This does not always happen in the same manner (i.e., the misordering of surfaces isn't consistent in the same way across subjects).
My suspicion is that the surfaces are not created in the proper temporal order (or at least something is failing in line 158 of 03_MPC.sh). Unfortunately as I am running the containerised default version all individual surface files are removed so I can't check that assumption without running the code step by step.
If there is an easy fix that could be plugged into the already run data (i.e., all freesufer and other registrations look totally fine and I would hate to rerun) then that would be much appreciated.
Hi - I am trying to run mica-pipe via Docker. It has completed 'proc_structural', but will not let me run 'proc_dwi' due to the following error:
rorypiper@MS00048528 mica-pipe-test % docker run -ti --rm
-v /Users/rorypiper/Desktop/mica-pipe-test/bids:/bids_dataset:ro
-v /Users/rorypiper/Desktop/mica-pipe-test/out:/output_directory
-v /Users/rorypiper/Desktop/mica-pipe-test/tmp:/tmp
-v /Applications/freesurfer/license.txt:/opt/freesurfer-6.0.0/freesurfer_license_file.txt
micalab/micapipe:latest
-out /output_directory
-sub 01
-bids /bids_dataset
-proc_dwi -ses 01
-nocleanup \
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
INFO: /root/matlab/startup.m does not exist ... creating
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.0
MICA pipeline - (Version v0.1.1 'Roadrunner')
Subject: 01 Session: ses-01
[ WARNING ]..... fix was not found, ICA-FIX will be skipped
[ INFO ]..... micapipe will use 6 threads for multicore processing
[ INFO ]..... Subject 01 directory exist
[ INFO ]..... Inputs of proc_dwi:
tmpDir : /tmp
dwi_main : DEFAULT
dwi_rpe : DEFAULT
rpe_all : FALSE
Affine only: FALSE
Processing : LOCAL
**-------------------------------------------------------------
[ ERROR ]..... Subject 01 doesn't have T1_nativepro warp to MNI152.
Run -proc_structural
-------------------------------------------------------------**
I have been able to run the entire structural leg of the pipeline without issues, -proc_dwi without issues, (-SC not without issues) and I am now trying to run -proc_rsfmri
I am getting the error that the main rsfMRI scan cannot be found, even after manually specifying the scan via -MainScanStr. The file exists, and I have tried using both uncompressed (.nii) and compressed (.nii.gz) files.
I would expect the command to be able to at least find the scan, as it exists, e.g.:
I am running the pipeline through a singularity wrapper, on my university's computing cluster e.g.
$SINGULARITY_PULLFOLDER/micapipe_latest.sif -sub 001 -bids rawdata -out derivatives -ses 0
I am using MobaXterm as a terminal, and running this from a Windows computer.
Could anyone help me figure out what's going wrong here?
[ucjucrs@login12 dataset]$ $SINGULARITY_PULLFOLDER/micapipe_latest.sif -sub 001 -bids rawdata -out derivatives -ses 0 -proc_rsfmri -mainScanStr task-rest_run-1_bold.nii.gz
WARNING: Bind mount '/home/ucjucrs => /home/ucjucrs' overlaps container CWD /home/ucjucrs/Scratch/dataset, may not be available
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.0
-------------------------------------------------------------
MICA pipeline - (Version v0.1.1 'Roadrunner')
Subject: 001 Session: ses-0
-------------------------------------------------------------
[ WARNING ]..... fix was not found, ICA-FIX will be skipped
[ INFO ]..... micapipe will use 6 threads for multicore processing
[ INFO ]..... Subject 001 directory exist
[ INFO ]..... Inputs:
Topup Config : DEFAULT
ICA fix training : DEFAULT
Main scan : task-rest_run-1_bold.nii.gz
Phase scan : DEFAULT
Reverse Phase : DEFAULT
Smoothing : 0
Perform NSR : 0
Perform GSR : 0
No FIX : 0
Longitudinal ses : FALSE
[ INFO ]..... Using user provided main scan: /scratch/scratch/ucjucrs/dataset/rawdata/sub-001/ses-0/func/sub-001_ses-0_task-rest_run-1_bold.nii.gz
[ INFO ]..... No run number specified for phase reversals and did not find more than one phase reversal scan - all good!
-------------------------------------------------------------
[ ERROR ]..... Couldn't find 001 main rsfMRI scan :
ls
-------------------------------------------------------------
Erasing temporal directory: /tmp/*_micapipe*_001
OLD_PATH is unset or empty
-------------------------------------------------------------
GLOBAL micapipe running time with LOCAL processing: 0.017 minutes
-------------------------------------------------------------
Hi all,
I believe this conditional allows the code to advance & the file names to be changed before run_first_all is complete.
run_first_all does the following:
(1) calls first_flirt
(2) calls run_first & first_boundary_corr for each subcortical region
(3) calls fslmerge twice. Once to compile all the corr files into the 4D firstseg file, and again to compile all the first files into the 4D origsegs file.
(4) calls to first_mult_bcorr to convert firstseg into a 3D file with all subcortical segmentations together. This is the final version of firstseg that is later copied in line 115 of post_structural and eventually used to compute subcortical connectomes.
(5) calls to imrm to remove all of the individual segmentation files (corr & first)
The intermediate 4D version of firstseg created by the first call to fslmerge has the same name. This allows the code to advance prematurely and run_first_all to be interrupted before the final version is computed. At least on the BIC cluster this is happening.
Thanks for the great pipeline!
Mark
Hi,
I am running the conteinerized version of micapipe with singularity CE 3.5.3 in a cluster grid. It is worth noting that I pulled the container from the dockerhub : singularity pull micapipe.sif docker://micalab/micapipe:latest.
At some point of the freesurfer_proc crashes because the path to the license.txt file is missing (I clip a screenshot of the logs), and therefore all the subsequent steps fail. I have a freesurfer license but I don't know how to get it into the container. Is there a way to achieve this? Thanks in advance
Hi MicaPipe team. Really excited to use this, but hit a problem with the output from the proc_sructural (and therefore cannot run the post_structural past step 3.
The proc_structural leaves me with an empty a Conte69 directory and therefore causes these issues in post_structural:
rorypiper @ MS00048528 Tue 15 Feb 2022 00:22:10 GMT:
COMMAND --> wb_command -surface-resample /tmp/790_micapipe_post-struct_sub-385_ses-01preop/rh.white.surf.gii /Users/rorypiper/Desktop/sub-385/ses-01preop/out/micapipe/sub-385/ses-01preop/anat/surfaces/conte69/sub-385_ses-01preop_rh_sphereReg.surf.gii /Users/rorypiper/Documents/software/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /Users/rorypiper/Desktop/sub-385/ses-01preop/out/micapipe/sub-385/ses-01preop/anat/surfaces/conte69/sub-385_ses-01preop_space-conte69-32k_desc-rh_white.surf.gii
While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -surface-resample /tmp/790_micapipe_post-struct_sub-385_ses-01preop/rh.white.surf.gii /Users/rorypiper/Desktop/sub-385/ses-01preop/out/micapipe/sub-385/ses-01preop/anat/surfaces/conte69/sub-385_ses-01preop_rh_sphereReg.surf.gii /Users/rorypiper/Documents/software/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /Users/rorypiper/Desktop/sub-385/ses-01preop/out/micapipe/sub-385/ses-01preop/anat/surfaces/conte69/sub-385_ses-01preop_space-conte69-32k_desc-rh_white.surf.gii
ERROR: NAME OF FILE: rh.white.surf.gii
PATH TO FILE: /tmp/790_micapipe_post-struct_sub-385_ses-01preop
File does not exist.
Please can you help?
What is the current behavior?
-proc_dwi without -autotract and without -keep_tck. (Exit successfully)-proc_dwi with -autotract.tck tractogramSuggested fix
tck tractogram if not detected before -autotract call.What is the current behavior?
The call to nifti_capture.py during dwi processing, in 02_proc-dwi.sh at lines 285 and 304 fails (file not found).
What is the expected behavior?
Call to nifti_capture.py should run smoothly, which can probably be solved by adding the full path to this script, as this was done in release 0.1.1 for micapipe_qc:
Do_cmd ${MICAPIPE}/functions/nifti_capture.py ...
Hi all,
I have gotten everything to run except for the MPC stage. I am not sure what the input should be. I have a t1 weighted image, but no t2w.
The environment I'm using is Linux 16.04 LTS (xenial) with 24 processors.
Thanks,
Matt
Suggest adding 1 comma at the end of lines 2 & 38 (L & R medial wall) to fix
dwi_reverse=($(ls "${subject_bids}/dwi/${subject}${ses}"_dir-PA_*dwi.nii* 2>/dev/null))*_dir-PA_*dwi.nii* and should not cause issues or errors down the road (although I might be wrong about that...)Traceback (most recent call last): File "/fellows/fellows2/gabrielp/micapipe/functions/nifti_capture.py", line 33, in <module> from nilearn import plotting ModuleNotFoundError: No module named 'nilearn'Firstly, thank you all for creating this phenomenal resource! I'm excited to use it!
I was looking through the LUT files for the Schaefer parcellations, and I noticed that the final entry (1002) for the Schaefer-1000 atlas is missing. I also noticed that the penultimate entry was listed as the control network, which broke from the general pattern of having default network regions last.
Any clarification on these network labels here would be greatly appreciated!
I successfully ran these modules: -proc_structural, -proc_freesurfer, -post_structural, -GD, -Morphology, -proc_dwi
When I run -QC_subj, I am missing the following in my report:
1- the Freesurfer native surfaces in the -proc_freesurfer section.
2- the output parcellations and the conte69 surfaces in the -post_structural section.
3- the registration of T1w in DWI space in the -proc_dwi section.
4- the surfaces in the Cortical morphology section.
When I check the QC log , this error stood out:
INFO ]..... Creating matrices and Sankey diagram ๏ฟฝ[0m
Loading required package: viridisLite
Attaching package: โviridisโ
The following object is masked from โpackage:scalesโ:
viridis_pal
Error in library("plotly") : there is no package called โplotlyโ
Execution halted
๏ฟฝ[38;5;75m
[ INFO ]..... Create surface visualizations ๏ฟฝ[0m
๏ฟฝ[0m๏ฟฝ[31m2022-03-10 17:45:47.620 ( 2.349s) [ 2D806C0] vtkPythonAlgorithm.cxx:112 ERR| vtkPythonAlgorithm (0x4044235fc0): Failure when calling method: "ProcessRequest":๏ฟฝ[0m
๏ฟฝ[0m๏ฟฝ[31m2022-03-10 17:45:47.628 ( 2.356s) [ 2D806C0] vtkExecutive.cxx:752 ERR| vtkCompositeDataPipeline (0x4042cb61c0): Algorithm vtkPythonAlgorithm(0x4044235fc0) returned failure for request: vtkInformation (0x4041f3fbe0)
Debug: Off
Modified Time: 174
Reference Count: 2
Registered Events: (none)
Request: REQUEST_DATA
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
๏ฟฝ[0m
๏ฟฝ[0m๏ฟฝ[31m2022-03-10 17:45:47.635 ( 2.363s) [ 2D806C0] vtkPythonAlgorithm.cxx:112 ERR| vtkPythonAlgorithm (0x4043a68740): Failure when calling method: "ProcessRequest":๏ฟฝ[0m
๏ฟฝ[0m๏ฟฝ[31m2022-03-10 17:45:47.637 ( 2.366s) [ 2D806C0] vtkExecutive.cxx:752 ERR| vtkCompositeDataPipeline (0x4041f31850): Algorithm vtkPythonAlgorithm(0x4043a68740) returned failure for request: vtkInformation (0x40458a3fc0)
Debug: Off
Modified Time: 306
Reference Count: 2
Registered Events: (none)
Request: REQUEST_DATA
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
๏ฟฝ[0m
๏ฟฝ[0m๏ฟฝ[31m2022-03-10 17:45:57.786 ( 12.514s) [ 2D806C0]vtkXOpenGLRenderWindow.:448 ERR| vtkXOpenGLRenderWindow (0x40458a6660): bad X server connection. DISPLAY=๏ฟฝ[0m
qemu: uncaught target signal 6 (Aborted) - core dumped
/opt/micapipe/functions/micapipe_qc: line 189: 634 Aborted ${MICAPIPE}/functions/qc_surf.py -subBIDS "$idBIDS" -subDir "$subject_dir"
๏ฟฝ[38;5;118m
Current line will only remove shells with b values exactly equal to 0, and will return error on non-integer values. Wouldn't be able to handle the following case:
$ shells=($(mrinfo "$dwi_n4" -shell_bvalues))
$ echo ${#shells[@]}
4
$ for i in "${!shells[@]}"; do echo ${shells[i]}; done
5
299.5
699.875
1996.61
Suggest replacing line 187 with:
$ thr=15
$ for i in "${!shells[@]}"; do if [ ${shells[i]%.*} -le $thr ]; then unset 'shells[i]'; fi; done
$ echo ${#shells[@]}
3
I am running micapipe on my university's cluster, and I am getting a 'cannot stat' error when running proc-structural. This happens during the ANTs step. Running proc_structural therefore results in an error. I am trying to run proc_structural to completion.
I am using MobaXterm v20.3 build 4396 to tunnel into my university cluster from my work computer.
dataset/
rawdata/
sub-001/
ses-0/
anat/
sub-001_ses-0_run-1_T1w.nii
sub-001_ses-0_run_1_T1w.json
dwi/...
fmap/...
func/...
ses-1/...
derivatives/
freesurfer/
sub-001_ses-0/
label/
mri/
...
sub-001_ses-1/...
micapipe/
Because I am not allowed to run sudo command on the cluster,
# Create a .singularity directory in Scratch
mkdir $HOME/Scratch/.singularity
# Create cache subdirectories we will use / export
mkdir $HOME/Scratch/.singularity/tmp
mkdir $HOME/Scratch/.singularity/localcache
mkdir $HOME/Scratch/.singularity/pull
# Set all the Singularity cache dirs to Scratch
export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity
export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull
# Bind the data directory in Scratch so it is accessible from inside the container and the temporary storage jobs are allocated
# add after $USER
export SINGULARITY_BINDPATH=/scratch/scratch/$USER,/tmpdir
# to pull docker image
singularity pull docker://micalab/micapipe:latest
# Prints micapipe version / test commands can be used (this is equivalent to running mica-pipe command)
$SINGULARITY_PULLFOLDER/micapipe_latest.sif -v
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_BINDPATH=/scratch/scratch/$USER/Struct_MRI/MICA_BIDS/,/tmpdir
[ucjucrs@login12 MICA_BIDS]$ $SINGULARITY_PULLFOLDER/micapipe_latest.sif -bids /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS/rawdata -out /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS/derivatives -sub 001 -ses 0 -proc_structural
WARNING: Bind mount '/home/ucjucrs => /home/ucjucrs' overlaps container CWD /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS, may not be available
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.0
-------------------------------------------------------------
MICA pipeline - (Version v0.1.1 'Roadrunner')
Subject: 001 Session: ses-0
-------------------------------------------------------------
[ WARNING ]..... fix was not found, ICA-FIX will be skipped
[ INFO ]..... micapipe will use 6 threads for multicore processing
[ INFO ]..... Subject 001 directory exist
[ INFO ]..... sub-001 directory structure:
/scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
โโโ anat
โย ย โโโ first
โย ย โโโ surfaces
โย ย โย ย โโโ conte69
โย ย โโโ volumetric
โโโ dwi
โโโ func
โโโ logs
โโโ QC
โย ย โโโ png
โโโ xfm
11 directories
-------------------------------------------------------------
Structural processing
micapipe v0.1.1 'Roadrunner', LOCAL
-------------------------------------------------------------
[ INFO ]..... MICA pipe - Software versions
MRtrix3..... 3.0.1
/opt/miniconda-latest/envs/micapipe/bin/mrinfo
FSL......... 6.0
/opt/fsl-6.0.0
ANFI........ Aug 22 2021 (Version AFNI_21.2.05 'Nerva')
/opt/afni-latest/3dresample
ANTS........ 2.3.3.dev168-g29bdf
/opt/ants-2.3.4
WorkBench... 1.3.2
/usr/bin/wb_command
FreeSurfer.. freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/opt/freesurfer-6.0.0
fix.........
/opt/fix
python...... Python 3.7.10
/opt/miniconda-latest/envs/micapipe/bin/python
R........... 3.6.3
/usr/bin/R
[ INFO ]..... mica-pipe inputs:
id = 001
BIDS = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata
out = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe
ses = ses-0
[ INFO ]..... BIDS naming:
subject_bids = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0
bids_T1ws = N-1, e.g. /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0/anat/sub-001_ses-0_run-1_T1w.nii
bids_dwis = N-0, e.g.
subject = sub-001
subject_dir = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
proc_struct = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat
dir_warp = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/xfm
logs = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/logs
[ INFO ]..... Processing directories:
subject_dir = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
proc_struct = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat
dir_conte69 = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69
dir_volum = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/volumetric
dir_warp = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/xfm
dir_logs = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/logs
dir_QC = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/QC
dir_freesurfer = /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/freesurfer/sub-001_ses-0
[ INFO ]..... Utilities directories:
scriptDir = /opt/micapipe/functions
util_MNIvolumes = /opt/micapipe/MNI152Volumes
util_lut = /opt/micapipe/parcellations/lut
util_parcelations = /opt/micapipe/parcellations
util_surface = /opt/micapipe/surfaces
util_mics = /opt/micapipe/MICs60_T1-atlas
[ INFO ]..... Saving temporal dir: FALSE
[ INFO ]..... ANTs will use 6 threads
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND --> mkdir -p /tmp/30415_micapipe_proc_struc-vol_001
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND --> 3dresample -orient LPI -prefix /tmp/30415_micapipe_proc_struc-vol_001/obl-001_ses-0_run-1_T1w.nii -inset /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0/anat/sub-001_ses-0_run-1_T1w.nii
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND --> fslreorient2std /tmp/30415_micapipe_proc_struc-vol_001/obl-001_ses-0_run-1_T1w.nii /tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND --> cp -v /tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz
cp: cannot stat '/tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii': No such file or directory
[ INFO ]..... T1w_nativepro biasfield correction and intensity rescaling
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND --> N4BiasFieldCorrection -d 3 -i /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz -r -o /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz -v
Running N4 for 3-dimensional images.
file /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz does not exist .
Mask not read. Using the entire image as the mask.
/opt/micapipe/functions/utilities.sh: line 584: 95445 Segmentation fault $l_command
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND --> ImageMath 3 /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w.nii.gz RescaleImage /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz 0 100
file /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz does not exist .
terminate called after throwing an instance of 'itk::ExceptionObject'
what(): /src/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1340:
itk::ERROR: RescaleIntensityImageFilter(0x43cfa80): Input Primary is required but not set.
/opt/micapipe/functions/utilities.sh: line 584: 95486 Aborted $l_command
-------------------------------------------------------------
[ ERROR ]..... sub-001_ses-0_space-nativepro_t1w was not generated
-------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND --> exit
Erasing temporal directory: /tmp/*_micapipe*_001
OLD_PATH is unset or empty
-------------------------------------------------------------
GLOBAL micapipe running time with LOCAL processing: 0.083 minutes
-------------------------------------------------------------
Hi Raul/Jess - together with Casey, we were discussing to incorporate the JuBrain parcellation into the default parcellations that are used for connectome generation in a future release of micapipe. She has already the parcellation in MNI152 but also fsaverage and conte69. The parcellation is partial (ie not all brain regions have a label) but this may nevertheless be useful to link micapipe with some of the julich projects for hiball etc. - what do you think?
Hi!
I ran micapipe by docker with the following commands:
docker run -ti --rm
-v /my_path/bids:/data:ro
-v /my_patht/micapipe/derivatives:/out
-v /my_path/micapipe/working_directory:/tmp
-v /my_path/license.txt:/opt/freesurfer/license.txt
micalab/micapipe:latest -bids /data -out /out
-proc_structural -sub 03 04 -threads 10 -tracts 10M
It seems that it ran successfully but there is no results generated under derivative and working_dirctory except these. The folders of freesurfer and sub-03 can not be opened or deleted. My input data is in BIDS format which can be used to fmriprep (so I guess it might not result from my data).
micapipe
โโโ derivatives
โย ย โโโ freesurfer [error opening dir]
โย ย โโโ micapipe
โย ย โโโ micapipe_processed_sub.csv
โย ย โโโ pipeline-description.json
โย ย โโโ sub-03 [error opening dir]
โโโ working_directory
Thank you so much if you can give me any idea to deal with this. Happy holiday!
Hello everyone,
I am trying to run micapipe_cleanup using a linux machine with docker.
However I keep getting the error that the repository does not exist.
I have been using the following command:
docker run -it micalab/micapipe:latest micapipe_cleanup (arguments...)
The following command also did not work for me:
docker run -it micalab/micapipe:latest /opt/micapipe/functions/micapipe_cleanup (arguments...)
Could anyone help me with constructing a proper Docker command? Thank you in advance!
What is the current behaviour?
Freesurfer is slow and fix_topology is a problem.
What is the motivation / use case for changing the behaviour?
Speedup, no vertex correction issues in fix_topology
Other information
FastSurfer https://deep-mi.org/research/fastsurfer/ would be a great alternative to Freesurfer cortical parc. and segmentation.
https://github.com/deep-mi/FastSurfer
Drawbacks: It resamples T1w images to 1mm iso if they are hires - could include an option for choosing either stream (free vs fastsurfer)
singularity run --cleanenv \
-B /xdisk/adamraikes/cornell/nifti:/nifti:ro \
-B /xdisk/adamraikes/cornell/derivatives/freesurfer-7.3.1:/fs_input \
-B /xdisk/adamraikes/cornell/derivatives/micapipe:/output \
-B /tmp:/tmp \
-B /groups/adamraikes/license.txt:/opt/freesurfer-6.0.0/license.txt \
/groups/adamraikes/singularity_images/micapipe-v0.1.4.simg
-bids /nifti \
-out /output \
-sub 087 \
-threads 8 \
-proc_structural
This is the output when I do so:
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.3
[ WARNING ]..... DEPRECATION: mica-pipe is deprecated and will be removed from upcoming versions (use micapipe instead)
micapipe -bids /nifti -out /output -sub 087 -threads 8 -proc_structural
-------------------------------------------------------------
MICA pipeline - (Version v0.1.4 'Roadrunner')
Subject: 087 Session: SINGLE
-------------------------------------------------------------
[ WARNING ]..... fix was not found, ICA-FIX will be skipped
[ INFO ]..... micapipe will use 8 threads for multicore processing
[ INFO ]..... Subject 087 directory doesn't exist
adamraikes @ r4u11n1.puma.hpc.arizona.edu Mon Nov 21 12:30:26 MST 2022:
COMMAND --> mkdir -p /output/micapipe/sub-087/logs /output/micapipe/sub-087/xfm /output/micapipe/sub-087/dwi /output/micapipe/sub-087/func /output/micapipe/sub-087/anat/first /output/micapipe/sub-087/anat/volumetric /output/micapipe/sub-087/anat/surfaces/conte69 /output/micapipe/sub-087/QC/png
adamraikes @ r4u11n1.puma.hpc.arizona.edu Mon Nov 21 12:30:26 MST 2022:
COMMAND --> ln -s /opt/freesurfer-6.0.0/subjects/fsaverage5/ /output/freesurfer
adamraikes @ r4u11n1.puma.hpc.arizona.edu Mon Nov 21 12:30:26 MST 2022:
COMMAND --> mkdir -p /output/freesurfer/conte69/surf
[ INFO ]..... sub-087 directory structure:
/output/micapipe/sub-087
\u251c\u2500\u2500 anat
\u2502ย ย \u251c\u2500\u2500 first
\u2502ย ย \u251c\u2500\u2500 surfaces
\u2502ย ย \u2502ย ย \u2514\u2500\u2500 conte69
\u2502ย ย \u2514\u2500\u2500 volumetric
\u251c\u2500\u2500 dwi
\u251c\u2500\u2500 func
\u251c\u2500\u2500 logs
\u251c\u2500\u2500 QC
\u2502ย ย \u2514\u2500\u2500 png
\u2514\u2500\u2500 xfm
11 directories
/opt/micapipe/micapipe: line 666: /opt/micapipe/functions/01_proc-struc_volumetric.sh /nifti 087 /output/micapipe SINGLE FALSE 8 /tmp DEFAULT: No such file or directory
/opt/micapipe/micapipe: line 949: [: too many arguments
-------------------------------------------------------------
GLOBAL micapipe running time with container-micapipe v0.1.4 processing: 0.000 minutes
-------------------------------------------------------------
It generates the relevant file tree as expected but fails after creating the folders. The same command works for my v0.1.2 singularity image.
I assume those two missing files are related to why the workflow line is orange (everything else in the QC reports look fine).
I think I see the "missing" files in my dwi folders (so they're not actually missing), but I'm not certain these are what it wants:
For example:
sub-02E_ses-01_space-dwi_desc-t1w_nativepro_SyN.nii.gz
sub-02E_ses-01_space-dwi_model-DTI_map-FA.mif
What is the expected behavior?
Screenshots of these two files should appear in the QC report and the workflow line should not be orange.
Please tell us about your computing environment:
I'm running micapipe v0.1.2 in the provided singularity container.
Other information
The terminal output while running QC is not informative when it gets to each of these missing files:
This is the terminal output when QC gets to the missing T1w in DWI space:
[ INFO ]..... Registration: T1w in DWI space
And this is the terminal output when QC gets to the missing FA atlas image:
[ INFO ]..... Registration: FA atlas in native dwi
Erasing temporal directory: /tmp
OLD_PATH is unset or empty
What is the current behaviour?
*micapipe currently do not support this QC
What is the motivation / use case for changing the behaviour?
It will improve the subject QC
If relevant, please tell us about your computing environment:
not relevant
Hi, I'm using auto_tract standalone pipeline to do bundle segmentation with whole-brain tractogram we estimated before.
Tractograms were estimated with matrix3 iFOD2.
When I run auto_tract pipeline, however, there were no streamline counted as Fornix of both hemisphere.
I think it is weird because when I open tractogram files, there were streamlines on the Fornix
Are there any tips or cautions I need to know for running auto_tract pipeline?
Hi all,
when trying to run micapipe on my MacOS Monterey (12.2.1) with M1, I get an error relating to arm-based system of Mac since micapipe requires a linux/amd64 platform.
One solution suggested on the net is to build micapipe before using it and so I have run docker build https://github.com/MICA-MNI/micapipe.git --platform linux/amd64
It started to build nicely installing several dependencies, but got stuck on step 6/23 when building FSL python environment:
[ 6/23] RUN bash -c 'bash /opt/fsl-6.0.0/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.0':
#8 8.533 Stage 1
#8 8.533 By installing this python distribution you agree to the license terms in
#8 8.533 /opt/fsl-6.0.0/fslpython/LICENSE.txt
100%.758
#8 42.70 Stage 2
100%5.15
#8 882.4 /opt/fsl-6.0.0/etc/fslconf/fslpython_install.sh: line 203: 759 Killed FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -f "${script_dir}/fslpython_environment.yml" 2>> "${miniconda_install_log}"
#8 882.4 761 Done | ${script_dir}/progress.sh 133 ${quiet} >> "${miniconda_install_log}"
#8 882.4 Failed to create FSL Python environment - see /tmp/fslpythonesRS/fslpython_miniconda_installer.log for details
------
executor failed running [/bin/sh -c bash -c 'bash /opt/fsl-6.0.0/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.0']: exit code: 4
M1 users, any suggestions on how to make micapipe build/run?
Thank you,
Dominika
3Tissue/bin/ss3t_csd_beta1, on response functions generated using the dhollander algorithm.tckgen.Since the program is still experimental, it may be best to turn on this functionality using a flag, e.g. -do_ss3t_csd (name taken from QSIprep).
fmriprep uses fieldmaps (magnitude and phasediff) to correct distortion in bold images. It also allows a simple RPE image of the main bold data. Could you implement some of these alternatives?
Thank you!
Currently:
singularity run --cleanenv /my_images/micapipe-.simg
-B path/to/your/bids_dataset:/bids_dataset:ro
-B path/to/your/bids_dataset/derivatives:/output_directory
-B path/to/your/working_directory:/tmp
-B path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/freesurfer_license_file.txt
micapipe.simg
-bids /bids_dataset
-out /output_directory
-all -ses 01
-threads 10 -tracts 10M
Should be changed to:
*singularity run --cleanenv *
-B path/to/your/bids_dataset:/bids_dataset:ro
-B path/to/your/bids_dataset/derivatives:/output_directory
-B path/to/your/working_directory:/tmp
*-B path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt *
*/path/to/container/micapipe.simg *
-bids /bids_dataset
-out /output_directory
-all -ses 01
-threads 10 -tracts 10M
:)
As we talked about in the preprocessing meeting, PyBIDS doesnโt recognize these file names with lower case ยซย tย ยป
Hi all,
I'm trying to use mica-pipe on some of my data (especially the -SC, -Morphology, and -MPC modules). I am running into a problem, however. I am getting the Freesurfer license error, and I can't figure out why. I've moved it to my home directory and pointed to it, but no luck. I am running Ubuntu 16.04.4 LTS and have current versions of all of the software I need.
The bigger problem seems to be that I can't do anything involving the conte69 surfaces. Proc_structural works fine, and for freesurfer, I copied a prior run (from outside mica-pipe) to my derivatives/freesurfer subdirectory. In the subdirectory, I now see conte69, fsaverage, fsaverage5 and my subject directory. However, within the conte69 directory, I see only a surf subdirectory (surf) which contains lh.conte69.gii and rh.conte69.gii. I have a feeling that this is a problem, but I'm not sure. In any event, it seems that the connectome modules are dependent on proper processing of the conte69 surfaces and registration of images to them. So I'm stuck.
Any help is appreciated!
Best wishes,
Matt
2.6.32), posting the error: "KERNEL TOO OLD", indicating 2.6.32 is not supported by Ubuntu 18.04's version of glibc.ubuntu:xenial or an earlier version of debian will allow researchers with older HPC environments to deploy and use the micapipe container.2.6.32, Distro: CentOS 6.10We have two runs of rsfmri in a single session:
tree inputs/sub-219/ses-itbs/func
inputs/sub-219/ses-itbs/func
โโโ sub-219_ses-itbs_task-rest_run-01_bold.json
โโโ sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
โโโ sub-219_ses-itbs_task-rest_run-01_events.tsv
โโโ sub-219_ses-itbs_task-rest_run-02_bold.json
โโโ sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
โโโ sub-219_ses-itbs_task-rest_run-02_events.tsv
I'd like to process them separately, so I specified and ran two separate docker commands:
docker run -ti --rm \
-v ${PWD}/inputs:/bids_dataset:ro \
-v ${PWD}/outputs:/output_directory \
-v ${PWD}/working:/tmp \
-v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
micalab/micapipe:latest \
-bids /bids_dataset \
-out /output_directory \
-sub 219 -ses itbs \
-proc_rsfmri \
-mainScanStr task-rest_run-01_bold -mainScanRun 1
and
docker run -ti --rm \
-v ${PWD}/inputs:/bids_dataset:ro \
-v ${PWD}/outputs:/output_directory \
-v ${PWD}/working:/tmp \
-v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
micalab/micapipe:latest \
-bids /bids_dataset \
-out /output_directory \
-sub 219 -ses itbs \
-proc_rsfmri \
-mainScanStr task-rest_run-02_bold -mainScanRun 2
Only the first run claims to have completed. How can I get separate output for each run?
UPDATE: I have tried making the Freesurfer license accessible to the container by adding '''-B /path/to/your/local/freesurfer-license:/opt/freesurfer-6.0.0/license.txt''' when running -post_structural, but this didn't help. I also tried mounting a file using docker run -v, but this also did not work.
BTW, I pulled the container into a singularity wrapper, and I run commands like this:
$SINGULARITY_PULLFOLDER/micapipe_latest.sif (and then enter commands)
Original post:
I am trying to run the post_structural part of the pipeline. I have previously quality-controlled FreeSurfer files that I would like to include in this step.
I have run -proc_structural without errors prior to this, and I think my FreeSurfer files are in the right location.
My dataset looks like this:
dataset/
---/rawdata
------/sub-001
---------/ses-0
---------/ses-1
------/sub-002
---------/ses-0
....
---/derivatives
------/freesurfer
---------/license.txt
---------/sub-001_ses-0
------------/mri
------------/surf
....
------/micapipe
---------/sub-001
------------/ses-0
....
When I run -post_structural, I get the output below. Would anyone know what is causing this?
[ucjucrs@login12 dataset]$ $SINGULARITY_PULLFOLDER/micapipe_latest.sif -sub 001 -ses 0 -out derivatives -bids rawdata -post_structural -atlas aparc
WARNING: Bind mount '/home/ucjucrs => /home/ucjucrs' overlaps container CWD /home/ucjucrs/Scratch/dataset, may not be available
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /opt/freesurfer-6.0.0
FSFAST_HOME /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects
MNI_DIR /opt/freesurfer-6.0.0/mni
FSL_DIR /opt/fsl-6.0.0
-------------------------------------------------------------
MICA pipeline - (Version v0.1.1 'Roadrunner')
Subject: 001 Session: ses-0
-------------------------------------------------------------
[ WARNING ]..... fix was not found, ICA-FIX will be skipped
[ INFO ]..... micapipe will use 6 threads for multicore processing
[ INFO ]..... Subject 001 directory exist
[ INFO ]..... Selected parcellations: aparc, N=1
-------------------------------------------------------------
POST-structural processing
micapipe v0.1.1 'Roadrunner', LOCAL
-------------------------------------------------------------
[ INFO ]..... MICA pipe - Software versions
MRtrix3..... 3.0.1
/opt/miniconda-latest/envs/micapipe/bin/mrinfo
FSL......... 6.0
/opt/fsl-6.0.0
ANFI........ Sep 27 2021 (Version AFNI_21.2.09 'Nerva')
/opt/afni-latest/3dresample
ANTS........ 2.3.3.dev168-g29bdf
/opt/ants-2.3.4
WorkBench... 1.3.2
/usr/bin/wb_command
FreeSurfer.. freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/opt/freesurfer-6.0.0
fix.........
/opt/fix
python...... Python 3.7.10
/opt/miniconda-latest/envs/micapipe/bin/python
R........... 3.6.3
/usr/bin/R
[ INFO ]..... Structural processing output variables:
T1 nativepro = /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w.nii.gz
T1 5tt = /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w_5TT.nii.gz
T1 fast_all = /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/first/sub-001_ses-0_space-nativepro_t1w_all_fast_firstseg.nii.gz
T1 resolution = 1.0
[ INFO ]..... Saving temporal dir: FALSE
[ INFO ]..... ANTs will use 6 threads
[ INFO ]..... wb_command will use 6 threads
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mkdir -p /tmp/16979_micapipe_post-struct_sub-001_ses-0
[ INFO ]..... Subject 001 has a T1 on FreeSurfer space
[ INFO ]..... Cerebellum parcellation to T1-nativepro Volume
[ INFO ]..... Subject 001 has a Cerebellum parcellation on T1-nativepro
[ INFO ]..... Subcortical parcellation to T1-nativepro Volume
[ INFO ]..... Subject 001 has a Subcortical parcellation on T1-nativepro
[ INFO ]..... fsaverage5 annnot parcellations to T1-nativepro Volume
[ INFO ]..... Running surface lh aparc_mics.annot to sub-001
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mri_surf2surf --hemi lh --srcsubject fsaverage5 --trgsubject sub-001_ses-0 --sval-annot lh.aparc_mics.annot --tval /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/lh.aparc_mics.annot
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
Setting mapmethod to nnf
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
setenv SUBJECTS_DIR /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer
cd /opt/micapipe/parcellations
mri_surf2surf --hemi lh --srcsubject fsaverage5 --trgsubject sub-001_ses-0 --sval-annot lh.aparc_mics.annot --tval /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/lh.aparc_mics.annot
sysname Linux
hostname login12.myriad.ucl.ac.uk
machine x86_64
user ucjucrs
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-0
trgval = /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/lh.aparc_mics.annot
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/fsaverage5/surf/lh.sphere.reg
[ INFO ]..... Running surface rh aparc_mics.annot to sub-001
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mri_surf2surf --hemi rh --srcsubject fsaverage5 --trgsubject sub-001_ses-0 --sval-annot rh.aparc_mics.annot --tval /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/rh.aparc_mics.annot
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
Setting mapmethod to nnf
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
setenv SUBJECTS_DIR /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer
cd /opt/micapipe/parcellations
mri_surf2surf --hemi rh --srcsubject fsaverage5 --trgsubject sub-001_ses-0 --sval-annot rh.aparc_mics.annot --tval /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/rh.aparc_mics.annot
sysname Linux
hostname login12.myriad.ucl.ac.uk
machine x86_64
user ucjucrs
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-0
trgval = /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/label/rh.aparc_mics.annot
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = rh
trghemi = rh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/fsaverage5/surf/rh.sphere.reg
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mri_aparc2aseg --s sub-001_ses-0 --o /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc.mgz --annot aparc_mics --new-ribbon
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
SUBJECTS_DIR /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer
subject sub-001_ses-0
outvol /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.white
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mri_label2vol --seg /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc.mgz --temp /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/mri/T1.mgz --o /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc_in_T1.mgz --regheader /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/mri/aseg.mgz
Number of labels: 0
Annot File: (null)
Template Volume: /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/mri/T1.mgz
Outut Volume: /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc_in_T1.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: (null)
Hemi: (null)
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-1.00000 -0.00000 -0.00000 128.00000;
-0.00000 -0.00000 -1.00000 128.00000;
-0.00000 1.00000 -0.00000 128.00000;
-0.00000 -0.00000 -0.00000 1.00000;
Template Voxel Volume: 1
nHits Thresh: 0
Computing registration based on header
RegMat: --------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Label RAS-to-Vox: --------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 -1.00000 128.00000;
0.00000 1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> mrconvert /tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc_in_T1.mgz /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz -force
mrconvert: [WARNING] existing output files will be overwritten
mrconvert: [ERROR] cannot access file "/tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc_in_T1.mgz": No such file or directory
mrconvert: [ERROR] error opening image "/tmp/16979_micapipe_post-struct_sub-001_ses-0/aparc_in_T1.mgz"
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> fslreorient2std /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz
ERROR: Could not find image /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> fslmaths /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz -thr 1000 /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz
Image Exception : #63 :: No image files match: /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc
terminate called after throwing an instance of 'armawrap::AWException'
what(): No image files match: /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc
/opt/micapipe/functions/utilities.sh: line 584: 79209 Aborted $l_command
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:00 GMT 2021:
COMMAND --> antsApplyTransforms -d 3 -i /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz -r /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w.nii.gz -n GenericLabel -t /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/xfm/sub-001_ses-0_from-fsnative_to_nativepro_t1w_0GenericAffine.mat -o /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/volumetric/sub-001_ses-0_space-nativepro_t1w_atlas-aparc.nii.gz -v -u int
Using double precision for computations.
Input scalar image: /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz
file /tmp/16979_micapipe_post-struct_sub-001_ses-0/sub-001_ses-0_space-fsnative_t1w_aparc.nii.gz does not exist .
Reference image: /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order):
1. /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/xfm/sub-001_ses-0_from-fsnative_to_nativepro_t1w_0GenericAffine.mat (type = AffineTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LabelImageGenericInterpolateImageFunction
terminate called after throwing an instance of 'itk::ExceptionObject'
what(): /src/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1340:
itk::ERROR: ResampleImageFilter(0x3242580): Input Primary is required but not set.
/opt/micapipe/functions/utilities.sh: line 584: 79218 Aborted $l_command
[ INFO ]..... Native surfaces to conte69-64k vertices (lh hemisphere)
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_shortcuts -freesurfer-resample-prep /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.white /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.pial /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.sphere.reg /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.midthickness.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-lh_midthickness.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_lh_sphereReg.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> mris_convert /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.pial /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.pial.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.pial.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_lh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-lh_pial.surf.gii
While running:
wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.pial.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_lh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-lh_pial.surf.gii
ERROR: NAME OF FILE: lh.pial.surf.gii
PATH TO FILE: /tmp/16979_micapipe_post-struct_sub-001_ses-0
File does not exist.
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> mris_convert /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/lh.white /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.white.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.white.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_lh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-lh_white.surf.gii
While running:
wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/lh.white.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_lh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-lh_white.surf.gii
ERROR: NAME OF FILE: lh.white.surf.gii
PATH TO FILE: /tmp/16979_micapipe_post-struct_sub-001_ses-0
File does not exist.
[ INFO ]..... Native surfaces to conte69-64k vertices (rh hemisphere)
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_shortcuts -freesurfer-resample-prep /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.white /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.pial /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.sphere.reg /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.midthickness.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-rh_midthickness.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_rh_sphereReg.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> mris_convert /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.pial /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.pial.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.pial.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_rh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-rh_pial.surf.gii
While running:
wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.pial.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_rh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-rh_pial.surf.gii
ERROR: NAME OF FILE: rh.pial.surf.gii
PATH TO FILE: /tmp/16979_micapipe_post-struct_sub-001_ses-0
File does not exist.
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> mris_convert /scratch/scratch/ucjucrs/dataset/derivatives/freesurfer/sub-001_ses-0/surf/rh.white /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.white.surf.gii
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer-6.0.0/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
ucjucrs @ login12.myriad.ucl.ac.uk Tue Nov 16 22:07:01 GMT 2021:
COMMAND --> wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.white.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_rh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-rh_white.surf.gii
While running:
wb_command -surface-resample /tmp/16979_micapipe_post-struct_sub-001_ses-0/rh.white.surf.gii /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_rh_sphereReg.surf.gii /opt/micapipe/surfaces/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii BARYCENTRIC /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69/sub-001_ses-0_space-conte69-32k_desc-rh_white.surf.gii
ERROR: NAME OF FILE: rh.white.surf.gii
PATH TO FILE: /tmp/16979_micapipe_post-struct_sub-001_ses-0
File does not exist.
-------------------------------------------------------------
Post-structural processing ended in 0.033 minutes :
Steps completed : 03/08
Status : INCOMPLETE
Check logs : /scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/logs/post_structural_11-11-2021.txt
/scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/logs/post_structural_12-11-2021.txt
/scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/logs/post_structural_15-11-2021.txt
/scratch/scratch/ucjucrs/dataset/derivatives/micapipe/sub-001/ses-0/logs/post_structural_16-11-2021.txt
-------------------------------------------------------------
Erasing temporal directory: /tmp/16979_micapipe_post-struct_sub-001_ses-0
OLD_PATH is unset or empty
Erasing temporal directory: /tmp/*_micapipe*_001
OLD_PATH is unset or empty
-------------------------------------------------------------
GLOBAL micapipe running time with LOCAL processing: 0.067 minutes
-------------------------------------------------------------A docker command that uses
-v path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/freesurfer_license_file.txt \
as specified in the documentation fails immediately saying that the freesurfer license.txt cannot be found.
The correct bind mount appears to be as follows:
-v path/to/your/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
What is the current behaviour?
Micapipe uses default behavior of mrconvert, which includes bvalue scaling.
What is the motivation / use case for changing the behaviour?
For ABCD multishell RSI sequences, bvalue-scaling leads to incorrect DTI estimation. Allowing for an option to not scale bvalues in mrconvert would make the DTI pipeline much more flexible.
Currently the circle ci workflow is what looks like a hello world.
Given that we display the result of this workflow on the bids app dash, it would be better for users if this information reflected the results of some actual tests.
https://bids-apps.neuroimaging.io/apps/
I will remove the badge on the dashboard until this is fixed.
Ahoi hoi folks,
mica-pipe currently takes a -bids and a -out argument and subsequently creates a new directory with the name of the participant specified via -sub within -out. While it's kinda "BIDS-y", it's not BIDS-conform. Following the BIDS derivatives, a new pipeline specific directory should be created under derivatives and within that a folder for each participant. Furthermore, a pipeline description and json sidecar files need to be generated. For example:
bids_dataset
derivatives
mica-pipe
pipeline-description.json
sub-001
sub-001_T1w_desc-preproc.nii.gz
sub-001_T1w_desc-preproc.json
dataset_description.json
participants.tsv
participants.json
sub-001
sub-002
bids_dataset_root_folder/derivatives/micapipepipeline_description.jsonjson sidecar files-out as BIDS derivatives specify where things should go and thus only -bids is neededHappy to provide further information for any of this.
Cheers, Peer
Pulled and built a docker/singularity image for 0.1.5. Structural and Freesurfer appear to run fine. However, running into issues with -proc_dwi
Call:
singularity run --cleanenv -B ${PWD}/nifti:/nifti:ro -B ${PWD}/derivatives/micapipe:/output -B /groups/adamraikes/license.txt:/opt/freesurfer-6.0.0/license.txt -B /tmp:/tmp /groups/adamraikes/singularity_images/micapipe_0.1.5.sif -bids /nifti -out /output -sub 00228190 -ses 00 -proc_dwi -dwi_main /nifti/sub-00228190/ses-00/dwi/sub-00228190_ses-00_dir-AP_dwi.nii.gz -b0thr 61
Error:
COMMAND --> mrdegibbs /tmp/10672_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif -nthreads 6
mrdegibbs: [ERROR] Expected exactly 2 arguments (1 supplied)
mrdegibbs: [ERROR] Usage: mrdegibbs in out
mrdegibbs: [ERROR] Yours: mrdegibbs /tmp/10672_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif
mrcalc: [ERROR] Could not interpret string "" as either an image path or a numerical value
mrcalc: [ERROR] As image:
mrcalc: [ERROR] no name supplied to open image!
mrcalc: [ERROR] As numerical value:
mrcalc: [ERROR] cannot convert empty string to complex float
mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
mrmath: [ERROR] error opening image "-"
Looks like $dns_dwi is never defined
micapipe/functions/02_proc-dwi.sh
Line 198 in 23a5215
proc_structural on a uint16 or float32 T1-weighted image using the default micapipe docker container, the artifact from below is produced. Eventually, the workflow terminates due to segmentation faults in fslmaths and fsl-FIRST.-dwi_main.acq- tag from the original filename
sub-01_acq-multishell_space-dwi_preproc.mif instead of sub-01_space-dwi_desc-dwi_preproc.mifmicapipe v0.1.1 'Roadrunner'In my case, would proc_dwi need to be ran on each independent DWI sequence?
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