Jure Demsar

> The choice of legacy fix vs pyfix is set by $FSL_FIXDIR so even if $FSL_DIR points to a version of FSL that includes pyfix, if $FSL_FIXDIR points to legacy...

I just ran some tests with pyfix through QuNex and it is working. I am having some issues with `post_fix` though, did you test this functionality as well after pyfix?...

> I think the if statement to create the .fix file was flipped. should be fixed with latest commit. Great, thanks. I will retest everything once all issues on this...

> @demsarjure this is ready for final testing. Already testing. Will confirm that everything works in a day or two and then I think we can safely merge.

Whit the latest version, I am getting this error: ``` Mon Oct 28 08:38:07 EDT 2024:hcp_fix_multi_run: Dim: 91 Mon Oct 28 08:38:07 EDT 2024:hcp_fix_multi_run: Running MELODIC located at: /opt/fsl/fsl/share/fsl/bin/melodic Mon...

> This shouldn't be needed: --T1wTemplateBrain=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.8mm_brain.nii.gz > > Does this file exist: /opt/fsl/fsl/bin/fix? Yeah, it was a silly issue on my end. Nevermind, I think this is safe to merge.

I can test interpreted MATLAB or octave but not compiled, just give me the parameters that you want to test and I will run it.

I reviewed core scripts, besides Tim's comments and a minor thing below, I have no comments. --- https://github.com/Washington-University/HCPpipelines/blob/f992acb2dadf5221a48b1ea1b978ca10002324c2/FreeSurfer/LongitudinalFreeSurferPipeline.sh#L116-L132 Here sometimes double quotes are used for descriptions and other times single...

> I have left a number of comments. I agree with many of Tim's comments. It would be good to get feedback from Mike Harms and either Jure or Grega....

The definition of the start stage parameter says: ``` opts_AddOptional '--start-stage' 'StartStage' 'stage_id' "Starting stage [PREP-TP]. One of PREP-TP (PostFSPrepLong timepoint processing), PREP-T (PostFSPrepLong build template, skip timepoint processing), POSTFS-TP1...