kul-radneuron/kul_vbg

A workflow to allow Freesurfer recon-all to run on brain image with gliomas

kul_vbg's Issues

Execution time

Hello,
I would like to know the approximate execution time for a 111 mm image in uVBG with a medium size tumor.
Best Theo

No overlap between lesion and parcellated lobe

Hi! This is part of the error message I receive. Could you kindly advise me how to interpret this? Many thanks

Image Exception : #63 :: No image files match: /mounts/auto/p2108glia/VBG_output/output_VBG/sub-BI_01/ROIs/LT_Hippocampus_bin
Image Exception : #22 :: Failed to read volume /mounts/auto/p2108glia/VBG_output/output_VBG/sub-BI_01/ROIs/LT_Hippocampus_bin.nii.gz
Error : No image files match: /mounts/auto/p2108glia/VBG_output/output_VBG/sub-BI_01/ROIs/LT_Hippocampus_bin
Failed to read volume /mounts/auto/p2108glia/VBG_output/output_VBG/sub-BI_01/ROIs/LT_Hippocampus_bin.nii.gz
Error : No image files match: /mounts/auto/p2108glia/VBG_output/output_VBG/sub-BI_01/ROIs/LT_Hippocampus_bin

• The LT_Hippocampus label is voxels in total, with a volume of cmm volume.
  No overlap between the lesion and LT_Hippocampus lobe.

mrstats ERROR

Error Calculating Overlapping Volumes and Writing to Text File

Hello,

Thank you creating this software and for making it relatively easy to implement for a novice (took me a few tries to realized my GPU memory of 2GB was not sufficient to run fastsurfer with cuda and that I needed to downgrade from freesurfer v7 to v6).

After running on a test subject I received the follow error in error log:
"mghRead(/home/prism/Desktop/Sub001//output_VBG/sub-JW001/sub-JW001fastsurfer/sub-JW001/mri/aparc+aseg.mgz, -1): could not open file"

Sure enough, there was no aparc+aseg.mgz in the mri directory. I assume this error also caused the script to fail to write overlapping volumes to the text file, "percent_lobes_lesion_overlap_report.txt" which was empty (except for the prefilled templated text with blanks for number of voxels).

Any idea what is cause this error and how to fix it?

PS: KUL_VBG_prep_log_2022-02-23_10-57-08.txt

Thanks,

Travis

Script doesn't find the data files

Hi,

Here is the running command I tried:
~/KUL_VBG/KUL_VBG.sh -p pat001 -a sub-pat001.nii.gz -l sub-01_ses-001_roCFM.nii.gz -z T1 -o uVBG -t -F -n 6 -B 1

I ran the script in the directory where I had the data. I also tried to give the full path and it gave the same error below:

Inputs are -p pat001 -lesion sub-01_ses-001_roCFM.nii.gz -lesion_space T1
/root/KUL_VBG/KUL_VBG.sh: line 283: : No such file or directory
T1 images provided as sub-pat001.nii.gz
/root/KUL_VBG/KUL_VBG.sh: line 398: : No such file or directory
Preproc dir is <fullpath>/VBG_out/proc_VBG/sub-pat001 and output dir is uVBG/output_VBG/sub-pat001
You are using KUL_VBG.sh version 0.48_08022021

You have specified HD-BET for brain extraction, please make sure it is called correctly from within KUL_VBG
In case of BET problems see lines 1124 - 1200

update function path to reflect funciton name line 514

Ideas how to fix this? I should have all the prerequisites installed and I also tried with -B 2 but it gave again the same error expect for the HD-BET part.

Lesion mask and T1 volumes are identical so that shouldn't be the problem.

Query regarding the lesion filled image

@KUL-Radneuron @Rad-dude Very interesting work. I have a query regarding the lesion filled sub-JW001_T1_nat_filled_brain.nii.gz image. We can see large black regions in the image as attached here (a similar black region was detected when I ran 100+ subjects). Is it some sort of bug in the pipeline? Could you talk a bit more in regard!!!

One more query is, should the lesion be connected for smooth lesion filling? Let's say a lesion has several connected components (4+) at both laterals (LT & RT). Will the lesion filling be smooth under the circumstances?

error: mghRead(/[...]/mri/brain.mgz, -1): could not open file

Hello!

I got this error when running the mri_convert command under the "=====Creating orig and rawavg from input=======" section:

mri_convert -rl /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/real_T1.mgz
Started @ 2022-10-11_21-56-11
pid = 98958 basicPID = 1957
mri_convert -rl /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/real_T1.mgz
error: mghRead(/Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz, -1): could not open file
error reading from volume /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz
reading from /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz...
niiRead(): detected input as 64 bit double, reading in as 32 bit float
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 0, -1)
k_ras = (-0, 1, 0)
reading template info from volume /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz...
Success
Finished @ 2022-10-11_21-56-17

And this resulted in a bunch of other errors onward. I checked and found that the brain.mgz file is indeed missing in the mri folder, and I am attaching a screenshot of what my mri folder contains. I am not sure what is missing because the script prior to this part seemed to have run fine. And this is the command I input:
KUL_VBG.sh -S LS -a sub-LS_T1w.nii.gz -n 1 -l LesionMask_T1.nii.gz -z T1 -B 1 -P 2 -v

Please let me know if you have any insights! Thank you in advance.

Yuqi

MNI masks normalization

Dear Ahmed

I'm using your code for brain tumor normalization to MNI with ANTs-BET for intra-axial lesions

./KUL_VBG.sh -p subj001 -b -n 6 -l tumor_bin.nii.gz -z T1 -o subj001_norm -B 2

For every subject my segmentation mask have several values, ranging from 1 to 4. For the normalization I used the largest binary mask (voxels>1).

Results look fine. I guess that subj001_T1_brain_bk2anat1_Warped.nii.gz is my final normalized image, but there are several outputs and I'm quite confused how to normalize my original segmentation masks considering the different values.

Do you have any suggestions?
Thanks,
Lorenzo

Function_path editing

Dear developers,

Congratulations for this pipeline!
I would like to use with my data. I tried with a subject (sub-01):

./KUL_VBG.sh -p 01 -l $dir/KUL_VBG-master/lesion.nii.gz -z T1 -b -B1

This is my output:

Preproc_ dir is $dir/KUL_VBG-master/lesion_wf/proc_LWF/sub-01 and output dir is $dir/KUL_VBG-master/lesion_wf/output_LWF/sub-01
You are using KUL_VBG.sh version 0.47 - 02-01-2021
Inputs are -p 01 -lesion $dir/KUL_VBG-master/lesion.nii.gz -lesion_space T1
we have one session in the BIDS dir, this is good.
We found T1 WIs $dir/KUL_VBG-master/BIDS/sub-01/sess1/anat/sub-01_T1w.nii.gz

You have specified HD-BET for brain extraction, please make sure it is called correctly from within KUL_VBG
In case of BET problems see lines 1124 - 1200

update function path to reflect funciton name line 514

To solve this problem I changed the following:
function_path=($(which KUL_VBG.sh | rev | cut -d"/" -f2- | rev))
to
function_path=($(which pwd/KUL_VBG.sh | rev | cut -d"/" -f2- | rev))

Could this edit modify the results?

Thanks a lot!
Lorenzo