Comments (17)
marcelzwiers
commented on May 29, 2024
It seems to me that it couldn't find any files (that's why num_files was not assigned). Coincidentally, I fixed this the other day in my (unreleased) development version. So the file structure in your test-folder is not what was expected by bidsmapper.py, can you give a tree-view?
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dlevitas
commented on May 29, 2024
I've also been running into the same error with my subject. Here's the tree-view:
.
|-sub-1036
|---001-anat-scout_acq-localizer
|---002-anat_T1w
|---003-anat_T1w
|---004-fmap_run-01
|---005-fmap_run-02
|---006-func_task-std_run-01_SBRef
|---007-func_task-std_run-01
|---008-func_task-std_run-02_SBRef
|---009-func_task-std_run-02
|---010-func_task-std_run-03_SBRef
|---011-func_task-std_run-03
|---012-func_task-std_run-04_SBRef
|---013-func_task-std_run-04
|---014-func_task-std_run-05_SBRef
|---015-func_task-std_run-05
|---016-func_task-std_run-06_SBRef
|---017-func_task-std_run-06
|---018-func_task-std_run-07_SBRef
|---019-func_task-std_run-07
|---020-func_task-std_run-08_SBRef
|---021-func_task-std_run-08
|---022-anat_T2w
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marcelzwiers
commented on May 29, 2024
The tree looks fine, so perhaps the dicom files in the series folders are not recognized? Can you perhaps show me (a snippet of) the content of e.g. 002-anat_T1w?
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dlevitas
commented on May 29, 2024
The dicoms in that folder look like this:
001_000002_000001.dcm
001_000002_000002.dcm
001_000002_000003.dcm
....
001_000002_000208.dcm
These have come from a Siemens Prisma scanner, and there are only dicom files in the series folders.
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marcelzwiers
commented on May 29, 2024
I need more info to replicate this. I did this:
conda create -n bidscointest python==3.6
[..]
source activate bidscointest
pip install bidscoin
[..]
And I get:
(bidscointest) mentat005/tmp$ tree test
test
`-- sub-1036
`-- 002-anat_T1w
|-- 00002_1.3.12.2.1107.5.2.19.45416.2017121915051526005675150.dcm
|-- 00003_1.3.12.2.1107.5.2.19.45416.2017121915051520026075138.dcm
|-- 00004_1.3.12.2.1107.5.2.19.45416.2017121915051515689275130.dcm
|-- 00005_1.3.12.2.1107.5.2.19.45416.2017121915051518607275136.dcm
[..]
(bidscointest) mentat005/tmp$ bidsmapper.py test bidstest
2019-11-20 18:38:15 - bidscoin - INFO
2019-11-20 18:38:15 - bidscoin - INFO -------------- START BIDSmapper ------------
2019-11-20 18:38:15 - bidscoin - INFO No bidsmap file found: /home/mrphys/marzwi/.conda/envs/bidscointest/lib/python3.6/site-packages/heuristics/bidsmap.yaml
2019-11-20 18:38:15 - bidscoin - INFO Reading: /home/mrphys/marzwi/.conda/envs/bidscointest/lib/python3.6/site-packages/heuristics/bidsmap_template.yaml
2019-11-20 18:38:15 - bidscoin - INFO Parsing: /home/mrphys/marzwi/tmp/test/sub-1036 (subject 1/1)
2019-11-20 18:38:15 - bidscoin - INFO New 'extra_data' sample found: /home/mrphys/marzwi/tmp/test/sub-1036/002-anat_T1w/00002_1.3.12.2.1107.5.2.19.45416.2017121915051526005675150.dcm
2019-11-20 18:38:15 - bidscoin - INFO Writing bidsmap to: /home/mrphys/marzwi/tmp/bidstest/code/bidscoin/bidsmap.yaml
2019-11-20 18:38:18 - bidscoin - INFO Opening the bidseditor
2019-11-20 18:38:21 - bidscoin - INFO -------------- FINISHED! -------------------
2019-11-20 18:38:21 - bidscoin - INFO
2019-11-20 18:38:21 - bidscoin - INFO No BIDScoin errors or warnings were reported
2019-11-20 18:38:21 - bidscoin - INFO
2019-11-20 18:38:21 - bidscoin - INFO For the complete log see: /home/mrphys/marzwi/tmp/bidstest/code/bidscoin/bidsmapper.log
2019-11-20 18:38:21 - bidscoin - INFO NB: logfiles may contain identifiable information, e.g. from pathnames
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marcelzwiers
commented on May 29, 2024
Would it be possible to send me just 1 dicomfile (e.g. from the bottom slice, i.e. containing no identifiable data)? It seems to me that the dicomfiles are somehow not recognized as a dicomfiles. You can also test this yourself as follows:
(bidscointest) mentat005/~$ python
Python 3.6.0 |Continuum Analytics, Inc.| (default, Dec 23 2016, 12:22:00)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from bidscoin import bids
>>> bids.is_dicomfile('tmp/test/sub-1036/002-anat_T1w/00002_1.3.12.2.1107.5.2.19.45416.2017121915051526005675150.dcm')
True
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marcelzwiers
commented on May 29, 2024
Thank you @dlevitas for sending me the dicomfile. It all works fine here, so I guess there must be a problem with the path to your source-data folder:
usage: bidsmapper.py [-h] [-b BIDSMAP] [-t TEMPLATE] [-n SUBPREFIX]
[-m SESPREFIX] [-i {0,1,2}] [-v]
sourcefolder bidsfolder
Can you give me the exact command that you used?
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dlevitas
commented on May 29, 2024
Hi @marcelzwiers,
Here are the steps I took to get where I'm currently at. The dicom directory initially contains all the dicoms together, unseparated by series number. Due to this, I ran dicomsort using the following command
dicomsort.py $dicom_dir
which properly organizes the dicoms by their series number.
Next, I ran bidsmapper as follows:
bidsmapper.py $dicom_dir $testing_dir/bidscoin_testing
which produces the error that @soichih raised initially.
I can avoid this issue by specifying the --interactive 0 option, which produces this output:
2019-11-21 09:07:19 - bidscoin - INFO
2019-11-21 09:07:19 - bidscoin - INFO -------------- START BIDSmapper ------------
2019-11-21 09:07:19 - bidscoin - INFO Reading: /media/data/dlevitas/sample_data/bidscoin_testing/code/bidscoin/bidsmap.yaml
2019-11-21 09:07:19 - bidscoin - INFO Reading: /usr/local/lib/python3.6/dist-packages/heuristics/bidsmap_template.yaml
2019-11-21 09:07:19 - bidscoin - INFO Writing bidsmap to: /media/data/dlevitas/sample_data/bidscoin_testing/code/bidscoin/bidsmap.yaml
2019-11-21 09:07:20 - bidscoin - INFO -------------- FINISHED! -------------------
2019-11-21 09:07:20 - bidscoin - INFO
2019-11-21 09:07:20 - bidscoin - INFO No BIDScoin errors or warnings were reported
2019-11-21 09:07:20 - bidscoin - INFO
2019-11-21 09:07:20 - bidscoin - INFO For the complete log see: /media/data/dlevitas/sample_data/bidscoin_testing/code/bidscoin/bidsmapper.log
2019-11-21 09:07:20 - bidscoin - INFO NB: logfiles may contain identifiable information, e.g. from pathnames
However, the generated bidsmap.yaml does not contain any pertinent information. This is where we are currently running into problems. For reference, we are using python 3.6.8
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marcelzwiers
commented on May 29, 2024
I still think there is an issue with the path of your sourcefolder. The problem is that the logger statement is never reached in these lines of bidsmapper code:
# Loop over all subjects and sessions and built up the bidsmap entries
subjects = bids.lsdirs(rawfolder, subprefix + '*')
for n, subject in enumerate(subjects,1):
sessions = bids.lsdirs(subject, sesprefix + '*')
if not sessions: sessions = [subject]
for session in sessions:
LOGGER.info(f'Parsing: {session} (subject {n}/{len(subjects)})')
So the sub-# folders must be located directly under your $dicom_dir folder. It seems to me that running ls $dicom_dir/sub-* in a bash shell would give an empty result?
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dlevitas
commented on May 29, 2024
Ah yes, I was incorrectly setting the sourcefolder to the subfolder with the series numbers. I'm now able to work with the bidseditor.
Thanks for the assistance.
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marcelzwiers
commented on May 29, 2024
@soichih Is your problem fixed also? Then I can close this issue
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soichih
commented on May 29, 2024
I tried to run bidsmapper.py on one of our sample directory structure, and I couldn't get it to work.
So, the directory structure must include /ses-.. to organize it under each session?
My test directory structure looks like this.
$ ls
list mr_0004 mr_0005 mr_0006 mr_0007 raw.list README-Study.txt
$ ls *
list raw.list README-Study.txt
mr_0004:
20180918114023.json axial_epi_fmri_interleaved_i_to_s-00050.dcm axial_epi_fmri_interleaved_i_to_s-00101.dcm
20180918114023.nii.gz axial_epi_fmri_interleaved_i_to_s-00051.dcm axial_epi_fmri_interleaved_i_to_s-00102.dcm
axial_epi_fmri_interleaved_i_to_s-00001.dcm axial_epi_fmri_interleaved_i_to_s-00052.dcm axial_epi_fmri_interleaved_i_to_s-00103.dcm
Here is how I am running it now.
$ bidsmapper.py . out
2019-11-24 16:15:19 - bidscoin - INFO
2019-11-24 16:15:19 - bidscoin - INFO -------------- START BIDSmapper ------------
2019-11-24 16:15:19 - bidscoin - INFO Reading: /media/data/hayashis/test/20180918GE/out/code/bidscoin/bidsmap.yaml
2019-11-24 16:15:19 - bidscoin - INFO Reading: /usr/local/lib/python3.6/dist-packages/heuristics/bidsmap_template.yaml
2019-11-24 16:15:22 - bidscoin - INFO Writing bidsmap to: /media/data/hayashis/test/20180918GE/out/code/bidscoin/bidsmap.yaml
2019-11-24 16:15:23 - bidscoin - INFO Opening the bidseditor
Traceback (most recent call last):
File "/usr/local/bin/bidsmapper.py", line 350, in <module>
interactive = args.interactive)
File "/usr/local/bin/bidsmapper.py", line 314, in bidsmapper
gui.setupUi(mainwin, bidsfolder, rawfolder, bidsmapfile, bidsmap_new, copy.deepcopy(bidsmap_new), template, subprefix=subprefix, sesprefix=sesprefix)
File "/usr/local/lib/python3.6/dist-packages/bidscoin/bidseditor.py", line 203, in setupUi
self.set_tab_bidsmap()
File "/usr/local/lib/python3.6/dist-packages/bidscoin/bidseditor.py", line 685, in set_tab_bidsmap
samples_table.setRowCount(num_files)
UnboundLocalError: local variable 'num_files' referenced before assignment
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marcelzwiers
commented on May 29, 2024
So you did the same as @dlevitas, you are using the subject folder as the sourcefolder. Bidscoin, like BIDS, works at the study level, meaning that it will convert all your subject data into BIDS. The sourcefolder is expected to contain sub-folders where each subfolder contains data for one subject. The session subfolder is then optional. Then it is assumed that in there you have all the files of one series (a "run" in BIDS speak) in one folder. That seems to be the case for you (but if not you can run dicomsort). So what you should do is to call the bidsmapper not with the . argument but with its parent directory
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marcelzwiers
commented on May 29, 2024
I now changed the help text in:
sourcefolder: The study root folder containing the raw data in sub-#/[ses-#]/run subfolders (or specify --subprefix and --sesprefix for different prefixes)
@dlevitas and @soichih, Would that have helped sufficiently or do you have more suggestions which would have made your life easier? :-)
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soichih
commented on May 29, 2024
@marcelzwiers Thanks. I was seeing this with dicomsort.py
$ dicomsort.py 20180918GE/
>> Processing: /media/data/hayashis/test/20180918GE (0 files)
I didn't know that I had to rename the subject directory from mr_N to sub-N. I also didn't know that I can only run dicomsort.py for each subject directory (not the parent of it..) I still don't know exactly why I have to run dicomsort.py, but after running it successfully I was able to run bidsmapper.py. Thanks!
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marcelzwiers
commented on May 29, 2024
@soichih, you don't have to rename your subject directories, that is what the sub-prefix argument is for (so use something like bidsmapper.py --subprefix mr_ [..]). Also you should be able to run dicomsort on the root level as well as on the subject level.
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dlevitas
commented on May 29, 2024
@marcelzwiers the edits to the help text make things a bit clearer now; thanks for doing that. Before it sounded as if it were asking for the directory with the run sub-folders.
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