Comments (13)
Looks like this is the place to point out problems with the docs and slides.
Following the tutorial in the slides produces output that fails the bids validator seemingly due to the lack of subject-specific directories. Appears to be related to issue #89 . Following satra's recommendation by modifying the heuristic file to explicitly include the subject as a directory (e.g., t1w = create_key('sub-{subject}/anat/sub-{subject}_T1w')) fixes the issue for the tutorial data (PHANTOM1_3) and for our own datasets. Assuming I'm not missing a reason why heudiconv doesn't sort files into subject directories automatically; it would be helpful to new users if the slides and heudiconv readme.md were updated. Possibly also the heuristics in the repository as well so as not to breed confusion when people poke through them!
Thanks
from heudiconv.
Thank you! Confirming that since then the test directory was dissolved and that dataset got a proper place as you pointed out
from heudiconv.
@yarikoptic could you point me to the new location? I'm updating the slides now
from heudiconv.
@mgxd, @yonestar pointed to the correct corrected one: git clone http://datasets.datalad.org/dicoms/dartmouth-phantoms/PHANTOM1_3/.git
from heudiconv.
lol ... guess i misread - thanks!!
from heudiconv.
also small note that would be good to add to tutorial: after convertall script runs, its output is in output/.heudiconv
-- this does not show up with ls
command, requires ls -a
to see the dir
from heudiconv.
Very helpful @yonestar! I've spent hours looking for the output. Any way this could be modified so the output of convertall is not hidden?
from heudiconv.
Hi,
I also found a potential error in the example slide. It's on slide #30 phantom_heuristic.py.
The error message is like this:
Traceback (most recent call last): File "/usr/local/bin/heudiconv", line 2079, in <module> main() File "/usr/local/bin/heudiconv", line 2071, in main return _main(args) File "/usr/local/bin/heudiconv", line 1934, in _main min_meta=args.minmeta) File "/usr/local/bin/heudiconv", line 1281, in convert_dicoms info = heuristic.infotodict(seqinfo_list) File "/data/phantom_heuristic.py", line 16, in infotodict info[dwi].append(s.series_number) # append if multiple series meet criteria AttributeError: 'SeqInfo' object has no attribute 'series_number'
And when I looked into seqinfo, there was a similar one, series_id. After I replaced s.series_number with s.series_id, the final code worked. It would be good to have an updated example slides soon! :)
Thanks for the great tool.
Thanks,
Wani
from heudiconv.
Thank you all for the suggestions, the documentation has been updated - if there are any parts that you feel could be improved or are not clear enough, let us know!
from heudiconv.
One question:
In your docker example slide, you used {item:01d}
to give different numbers to different number of runs (e.g., run1, run2, etc.). And item is defined using this line: info[rest].append({'item': s.series_id, 'rec': 'corrected'})
And when I see what's in series_id, series_id is string with "SeriesNumber + ProtocolName". In your example data, it's just 1, 2, 3, etc, but in my data, it's like '25-r2_460tr_xxx', which is defined as series_id = '-'.join(map(str, series_id))
in bin/heudiconv. i.e., In our data, SeriesNumber is not necessarily the run number.
Even in this case, I wonder if {item:01d}
will provide the right run numbers. I have had difficult time to figure this out, and hasn't been successful to get run1, run2, etc. as the func file names.
Could you give me some guidance on that? Given that I'm not a python master, I might miss something. Any inputs on this would be appreciated!
Thanks,
Wani
from heudiconv.
When I attempt to perform the git command on slide 4: git clone http://datasets.datalad.org/dicoms/dartmouth-phantoms/PHANTOM1_3/.git/, I get the following error message: fatal: could not create work tree dir 'PHANTOM1_3'.: Permission denied
from heudiconv.
@tjhendrickson make sure you have permission to create a new directory where you are ATM
from heudiconv.
from heudiconv.
Related Issues (20)
- Option(s) or heuristic component to augment metadata in sidecars
- Issue a warning if there fieldmaps but they were not applied to any sequence HOT 1
- idea: Produce a result record from the run
- idea: heuristic call back after converting a subject/session or dcm2niix conversion
- heudiconv produces strange filenames with _heudiconv740_Eq_1 at the end HOT 1
- [DOC] Lacking information about heudiconv commands populate-templates etc HOT 1
- support dcm2niix "Bidsguess"
- BIDSVersion in data_description.json file HOT 11
- dicominfo not reporting all information HOT 1
- Reading Phase Encoding from JSON into {dir} HOT 1
- Conda installation problem HOT 2
- Commandline --command option usage HOT 14
- ASL Support
- Issues while building the dockerfile HOT 2
- [JOSS]: Figure 2 - update with fresh data and clarify how data could be refreshed HOT 1
- [JOSS]: Add more on state of the field HOT 1
- [JOSS]: Add a figure outlining typical heudiconv "workflow"
- [JOSS]: walk through documentation to catch deficiencies HOT 2
- INFO: Need to process 0 study sessions
- Failure due to binary incompatibility in Singularity image for Heudiconv 1.0.0 HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from heudiconv.