pipeline doesn't run fMRI subpipe

[shen4brains]

Likely case-sensitive search mismatch for raw fMRI data by file manager. Currently investigating

[noahfl]

i have a fix for this. the pipeline automatically capitalizes all filenames but misses the fMRI files in func for some reason. i'll push it up in a moment

[shen4brains]

seems to be finding fMRI data now, but has an issue with "print" in python, and also not sure why it's calling the wrong FSL directory:

PATT: ['/liberatrix/mcintosh_lab/kshen/ukbb/sub-002S0413/ses-1/func/sub-002S0413_ses-1_task-rest_acq-TR3000_bold.nii.gz'] MAYBE HERE key: rfMRI, fileConfig: fMRI/rfMRI.nii.gz File "/opt/fsl/bin/imglob", line 78 print "Usage: $0 [-extension/extensions] " ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Usage: $0 [-extension/extensions] ")? File "/opt/fsl/bin/imglob", line 78 print "Usage: $0 [-extension/extensions] " ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Usage: $0 [-extension/extensions] ")? File "/opt/fsl/bin/imglob", line 78 print "Usage: $0 [-extension/extensions] " ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Usage: $0 [-extension/extensions] ")? File "/opt/fsl/bin/imglob", line 78 print "Usage: $0 [-extension/extensions] " ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Usage: $0 [-extension/extensions] ")? cat: scores.txt: No such file or directory

[noahfl]

That's weird. I ran a subject through and didn't get this error. What does it say when you type which python?

[noahfl]

also, what does echo $FSLDIR return?

[shen4brains]

/liberatrix/mcintosh_lab/kshen/ukbb/software/env/bin/python

but:

/opt/fsl

[noahfl]

Okay so it seems like $FSLDIR was overwritten somehow between the last time you sourced init_vars and now. I think you might have to do it again

I think for sourcing init_vars, it's best to cd to the main UK_biobank_pipeline_v_1 directory and then run . init_vars directly from there. I've started doing it that way and haven't had issues in a while

[shen4brains]

Hmm... I've tried sourcing init_vars directly from its own directory and I'm still not getting the right $FSLDIR:

(base) [kshen@gateway UK_biobank_pipeline_v_1]$ echo $FSLDIR /opt/fsl (base) [kshen@gateway UK_biobank_pipeline_v_1]$ . init_vars (/liberatrix/mcintosh_lab/ukbb/software/env) [kshen@gateway UK_biobank_pipeline_v_1]$ echo $FSLDIR /opt/fsl

I'm trying to determine now whether any of the subsequently sourced items in init_vars rewrites $FSLDIR

[noahfl]

that's so weird. i just sourced the init_vars script in your UK_biobank_pipeline_v_1 directory and ran echo $FSLDIR and it returned the correct fsl directory. i'll try some other stuff out

[noahfl]

if you do

source ~/.bashrc and then

. /liberatrix/mcintosh_lab/kshen/ukbb/UK_biobank_pipeline_v_1/init_vars

does $FSLDIR show correctly?

[shen4brains]

Finally got it to work by getting rid of this in my .bashrc

source /opt/source/afni_fsl.sh

Double checked this several times by toggling it on and off in .bashrc. I didn't trace why afni_fsl.sh overrides $FSLDIR but it's something we should note in case other users on gateway have this issue

editing to add I'm not entirely sure this actually fixes the issue It works with my ssh connection but not with a vnc connection despite killing the vncserver and restarting several times as well as sourcing .bashrc several times; Is there something about vnc that I'm not understanding?

[shen4brains]

In any case, the original issue, Python "print" problem have been resolved

[noahfl]

Finally got it to work by getting rid of this in my .bashrc

source /opt/source/afni_fsl.sh

Double checked this several times by toggling it on and off in .bashrc. I didn't trace why afni_fsl.sh overrides $FSLDIR but it's something we should note in case other users on gateway have this issue

editing to add I'm not entirely sure this actually fixes the issue It works with my ssh connection but not with a vnc connection despite killing the vncserver and restarting several times as well as sourcing .bashrc several times; Is there something about vnc that I'm not understanding?

I'm not really familiar with VNC so I can't speak to those issues, but I've never had any problems over ssh