mgxd
commented
5 years ago @dkp can you share a few things?
- heudiconv version
- heuristic
- conversion log
- dicominfo
Thanks!
Open dkp opened 5 years ago
mgxd
commented
5 years ago @dkp can you share a few things?
Thanks!
mgxd
commented
5 years ago hi @dkp is this still a problem?
dkp
commented
5 years ago Hi Mathias, Thanks for asking. I check the heudiconv container with docker pull before I run anything, so I was running the latest in December, and it has updated several times between Dec and now. I am still reverse engineering to try to understand what overwrite does. I generally leave it on. I'd love it if you could further explain the behavior of this tag. Most recently, I see that with overwrite, my ASL image writes as two images with one component each. Without overwrite, my ASL image has 2 components and then heudiconv errors out without writing the rest of the images.
Here's an example with only 2 dicom datasets: run-01 and run-02, just a few days ago with heudiconv version 0.5.4.dev1
overwrite ON:
– sub-219_ses-itbs_acq-asl_run-01.json
– sub-219_ses-itbs_acq-asl_run-01.nii.gz
– sub-219_ses-itbs_acq-asl_run-02.json
– sub-219_ses-itbs_acq-asl_run-02.nii.gz
overwrite OFF:
– sub-219_ses-itbs_acq-asl_run-01.json
– sub-219_ses-itbs_acq-asl_run-01.nii.gz
Okay, if overwrite is OFF, then the 2 images are combined into an ASL with 2 components.
If overwrite is ON then we get 2 images with one component each AND the post images are written as well.
A runtime error is generated: RuntimeError: was asked to convert into /base/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_acq-asl.nii.gz but destination already exists
– make: [run] Error 1*
Thanks for your time. Great tool. Here's my documentation on it, BTW: https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html
-Dianne
On Wed, Mar 13, 2019 at 7:49 AM Mathias Goncalves notifications@github.com wrote:
hi @dkp https://github.com/dkp is this still a problem?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nipy/heudiconv/issues/288#issuecomment-472454035, or mute the thread https://github.com/notifications/unsubscribe-auth/AA66QFLW-iA-8zKn_4ltip55HQKrKnomks5vWQ_XgaJpZM4ZW9gk .
mgxd
commented
5 years ago The --overwrite flag is intended to facilitate re-conversions (@yarikoptic feel free to chime in, I know we have pushed and pulled on this before) - without it, heudiconv will not write to file if it already exists. Here is the logic
What I suspect is happening in your case is 2 (or more) scans are being classified for the same key. This will be caught and rightfully throw an error (stopping any further conversion). This is generally the case when excluding or hardcoding run-<number> in your key. An easy workaround would be to use the {item} formatting key, which is the index of a scan for a given info key. Here's an example
https://github.com/nipy/heudiconv/blob/5b7c33ecfb9f93c547fa5d0a38cbd22e05ea0ebd/heudiconv/heuristics/bids_ME.py#L23
Otherwise, if you could share your heuristic + dicominfo.tsv, we could track down the problem.
And awesome documentation! We were going to write up a readthedocs page, and yours checks off a lot of the boxes! Would you mind if we forked yours as a starting point?
dkp
commented
5 years ago Please, fork away! And thank you for the insights, it may take a while to digest.
-Dianne
On Wed, Mar 13, 2019 at 10:30 AM Mathias Goncalves notifications@github.com wrote:
The --overwrite flag is intended to facilitate re-conversions (@yarikoptic https://github.com/yarikoptic feel free to chime in, I know we have pushed and pulled on this before) - heudiconv will not write to file if it already exists. Here is the logic
What I suspect is happening in your case is 2 (or more) scans are being classified for the same key. This will be caught and rightfully throw an error (stopping any further conversion). This is generally the case when excluding or hardcoding run-
in your key. An easy workaround would be to use the {item} formatting key, which is the index of a scan for a given info key. Here's an example Otherwise, if you could share your heuristic + dicominfo.tsv, we could track down the problem.
And awesome documentation! We were going to write up a readthedocs page, and yours checks off a lot of the boxes! Would you mind if we forked yours as a starting point?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nipy/heudiconv/issues/288#issuecomment-472521332, or mute the thread https://github.com/notifications/unsubscribe-auth/AA66QMUGa5jpR9D89-81mZc23ZSz1t3Cks5vWTL4gaJpZM4ZW9gk .
I believe you may have dealt with similar topics, so sorry if this is a repetition... I don't see this explicitly in the issues. If I have 2 runs to convert, I expect to get: sub-220_ses-foo_task-rest_run-01_bold.json sub-220_ses-foo_task-rest_run-01_bold.nii sub-220_ses-foo_task-rest_run-01_bold.nii.gz sub-220_ses-foo_task-rest_run-01_events.tsv sub-220_ses-foo_task-rest_run-02_bold.json sub-220_ses-foo_task-rest_run-02_bold.nii sub-220_ses-foo_task-rest_run-02_bold.nii.gz sub-220_ses-foo_task-rest_run-02_events.tsv
BUT, if I run without --overwrite, then heudiconv complains that it would have to overwritedata and generates only: sub-220_ses-foo_task-rest_run-01_bold.json sub-220_ses-foo_task-rest_run-01_bold.nii sub-220_ses-foo_task-rest_run-01_bold.nii.gz sub-220_ses-foo_task-rest_run-01_events.tsv
This is not the behavior I expect. That is, it seems that I have to run with --overwrite or not everything will be converted. Am I missing something?