I’m getting some puzzling outputs of the brain mask for some (but not other) functional data, some weird “brightness” and issues with the report with the new 1.0.6 version. They might (hopefully) be all related.
Here is the history of the puzzle and what I did to try to get at it so far. Help in where to look next and what to check is appreciated!
Originally I ran some anatomical and resting state data with fmriprep version 1.0.0.rc6 from the singularity container (poldracklab_fmriprep_1.0.0-rc6-2017-10-11-cb35f5c22c6a.img). All fine.
usr/local/miniconda/bin/fmriprep /project/source/ /project/derivatives/ participant --participant-label subjx --ignore slicetiming --ignore fieldmaps --ignore-aroma-denoising-errors --output-space T1w --no-freesurfer --work-dir /project/work
Then I wanted to update all my data to the newer version of fmriprep 1.0.6-2 (poldracklab_fmriprep_1.0.6-2-2018-01-30-dc6144d544ef.img) and field maps) . Same input data otherwise.
/usr/local/miniconda/bin/fmriprep /project/source/ /project/derivatives/ participant --participant-label subjx --ignore slicetiming --ignore-aroma-denoising-errors --output-space T1w --fs-no-reconall --work-dir /project/work --fs-license-file /data/dorit/license.txt
The output report showed
- some chunks in the brain mask is missing for half of the runs (2 sessions a 4 runs),
- very bright areas in the frontal areas for all runs and
- when I try to open the report.htm file locally (working on HPC cluster) no images are shown (which is resolved by downloading the figure folder putting it in a subject-labled folder in the same directory. Maybe 3 is intended and I just missed that part in the docs.)
About 1 and 2:
I was puzzled (given that the output and reports looked normal in the older fmriprep version).
So I ran the same command, just without field maps. No change, ie. same issue 1 and 2.
Then I ran the same command, without field maps and without one of the originally affected runs (run1) (just to test if its is run dependent or some random thing). And I get different runs now affected by 1 (only 2 our of the remaining 7), as well as remaining issue 2 for all runs. In addition it ran slice time correction although I specified it shouldn’t.
/usr/local/miniconda/bin/fmriprep /project/source/ /project/derivatives/ participant --participant-label subjx --ignore slicetiming --ignore fieldmaps --ignore-aroma-denoising-errors --output-space T1w --fs-no-reconall --work-dir /project/work --fs-license-file /data/dorit/license.txt
“Slice timing correction: Applied”
I also reran the older fmriprep version again to make sure I’m running it on the same data. Again the old version does not produce issues 1-3 on the same source data.
I should mention that I did always delete/move the output directory and the working directory from that subject. The input nii data in the source folder looks fine at first glance (i.e. not crazy movements or brightness to begin with).
No html report reports any actual errors (nor any string searches in the log files).
Any idea where this might be getting off track? Maybe I’ just missing something obvious, but I don’t know what yet. Help appreciated!
Apologies for the long post. Just trying to be informative. For visualization purposed I uploaded screenshots form the epi2T1 registration onto dropbox. Let me know if there is a better way to share the images. https://www.dropbox.com/sh/4ucl7u1nv3jq605/AAB1_Iku0ERu3RHH8Ox63ro4a?dl=0
Notice that the brain is quite ‘special’, i.e. huge ventricles and no CC.