GRE-ME conversion fails: "cannot find sSUM scan" (Prisma dataset)

DPappFMRIB commented 5 years ago

Acq details: Prisma scanner, VE11C software, protocol imported via EXAR file (recent as of Dec 2018), no problems during acquisition. Conversion via DCM2NIIX2, or SPM/DICOM convert runs without error.

However, conversion using the provided code fails with the following warning. "WARNING: Detected multiple GRE-ME scans. Only keeping the file which contains "sum". WARNING: Cannot find sSUM scan."

Yet, only one GRE-ME dataset is present.

Full terminal dump: https://pastebin.com/1Vzu9wrS

jcohenadad commented 5 years ago

@DPappFMRIB thank you for the feedback. Are you using the latest version (i.e. commit 52c3d6798c593a4c9610a2886a681992a772dc01)?

If so, do you mind sending me the Dicom folder so I can try to reproduce the issue on my end?

DPappFMRIB commented 5 years ago

@jcohenadad

I am using the most recent version, yes, and I have sent you the folder.

jcohenadad commented 5 years ago

@DPappFMRIB I tried with your data and cannot reproduce the bug. Could you please copy/paste the content of the script so i can double check you are running the latest version of the script?

DPappFMRIB commented 5 years ago

@jcohenadad Pasted in the link below. As far as I can tell, it is identical to your latest commit (52c3d67), as per text comparison. Sorry for taking up your time.

https://pastebin.com/9vuDGS9Y

jcohenadad commented 5 years ago

@alexfoias can you please try to reproduce the issue using the exact same version of dcm2niix (MacOS)?

Chris Rorden's dcm2niiX version v1.0.20171215 (OpenJPEG build) Clang8.1.0 (64-bit MacOS)

alexfoias commented 5 years ago

@jcohenadad I used the same dcm2niiX version as @DPappFMRIB but I couldn't reproduce the bug.

Here is my terminal output: https://pastebin.com/m4Gmv56P

jcohenadad commented 5 years ago

in that case let's fix https://github.com/neuropoly/bids_neuropoly/issues/4, and then we can properly address this issue.

jcohenadad commented 5 years ago

@DPappFMRIB could you please try doing the following:

go to the bids_neuropoly repository then run:
```
git pull
pip install -e .
```
then re-run convert_dcm2nii.py in the same dataset that produced the issue described in this thread.
in the output, a log file called bids_neuropoly_logger.log should be created. Please dump it in pastebin (or equivalent). thanks!

DPappFMRIB commented 5 years ago

@jcohenadad

Sadly, the same issue arises. I had a colleague of mine try and run the conversion on the same data, it worked for them. I suspect the issue lies with my system. Thank you for your help!

Terminal and logger output: https://paste.ee/p/61zxL#UiZBhvBznlsKmB9TUUnQdFEkuzbHsnSU

jcohenadad commented 5 years ago

@DPappFMRIB thanks for the feedback. I've added more verbose to help us figure out what's happening on your system. Could you please try again with the latest version (24374d9ec8165d3260d1f5722290b0af8e8ca15d). Thanks!

DPappFMRIB commented 5 years ago

@jcohenadad

Sad to say the issue still applies.

Log here: https://paste.ee/p/GAvAk#SSsySPHq2lTDgbnxJOfAyD1aiiVRfHEm

jcohenadad commented 5 years ago

@DPappFMRIB yes this was expected as I didn't touch the code-- i only added verbose to understand what was happening on your end. And we made progress :-)

Interestingly, dcm2niix forces output file names to be datax.*:

INFO:root:List of converted files:
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datab.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/data.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datah.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datad.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/dataf.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datac.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/dataa.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datae.nii.gz
/var/folders/ff/px4nh9y56fb6kxfmwdks37bc0000gr/T/tmpfVF2Vg/datag.nii.gz

Whereas on our end it looks more like this:

INFO:root:List of converted files:
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_GRE-MT1_20190116164758_16.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_GRE-T1w_20190116164758_18.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_T2w_20190116164758_13.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_DWI_b0_20190116164758_14.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_T1w_20190116164758_12.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_GRE-ME_20190116164758_19.nii.gz
/var/folders/6f/wy6ljmx9453cgth2qwv5l1s80000gn/T/tmpWLNCUf/001_GRE-MT0_20190116164758_17.nii.gz

Maybe it is related to your OS version (18.2.0). @alexfoias Can you try to reproduce with that OS version?

alexfoias commented 5 years ago

@jcohenadad I tried on Darwin 18.0. It worked, I had no issue. I'm doing the system update to get to 18.2.0.

Here is my output: https://paste.ee/p/ZDshZ

jcohenadad commented 5 years ago

@alexfoias any update?

alexfoias commented 5 years ago

I tried it Darwin 18.2.0 and everything seems to work well.

Here is my output: https://pastebin.com/GC7JxFcu

jcohenadad commented 5 years ago

OK, I'm out of ideas. Sorry @DPappFMRIB but we are not able to reproduce this error, making it difficult to find a fix for it.

neuropoly / bids_neuropoly

GRE-ME conversion fails: "cannot find sSUM scan" (Prisma dataset) #5