Odd output

[araikes]

Hi @fliem,

I was trying out this docker container image. I had previously run Freesurfer's longitudinal pipeline using the BIDS-Apps/Freesurfer image. TRACULA ran without any apparent issue. When I went to visualize the tracts is where it got weird. When I try to overlay the tracts on the MNI152 T1 brain, the tracts are nowhere near it. I'm not sure if this is a "me" issue or an issue with the outputs from the analyses. I'm uploading a screenshot for what I see. The command used to open that in freeview was:

freeview -v /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -w ${PWD}/*.path.mean.txt

Please let me know what else might be needed to debug this. Thanks.

[fliem]

Hi, mhh, looks interesting.

Do you see this only for this subject and session, or also for other data in your study?

How does the merged_avg33_mni_bbr.mgz file in native space look like? (freeview -tv dpath/merged_avg33_mni_bbr.mgz -v dmri/dtifit_FA.nii.gz)

[araikes]

I apologize. I should've been more specific. That image is based on the group2_tract_stats folder path mean text files.

For individual subjects/sessions, the merged_avg33 files appear fine in native space and close to ok (offset but not nearly as dramatically) in MNI152 space.

[fliem]

Hi, I wont be able to look into this for the next couple of days. I'll get back to you the week after next. Sorry

[araikes]

Not a problem.

[fliem]

Hi @araikes. I just tested this with two datasets, and my images look correct (I am using FreeView 2.0) -- like in the turorial.

Does the attached file display correctly? It might be a bit squiggly, because it's only based on two subjects, but the general position and orientation should work. lh.cst_AS.avg33_mni_bbr.path.mean.txt

Other than that, I can only point you towards the FS mailing list.