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Minor changes to coordinate delimiter, ciftify container binding #28

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Minor changes to coordinate delimiter, ciftify container binding #28

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4 changes: 3 additions & 1 deletion modules/cifti_mesh_wf.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,8 @@ process ciftify{
-v !{params.bids}:/bids \
-v $(pwd):/output \
-v $(pwd)/work:/work \
-v $(pwd)/fmriprep:/fmriprep \
-v $(pwd)/freesurfer:/freesurfer \
Comment on lines +111 to +112
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@jerdra jerdra Oct 21, 2022

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Suggested change
-v $(pwd)/fmriprep:/fmriprep \
-v $(pwd)/freesurfer:/freesurfer \

Your invocation file is probably mis-specified here if you need to bind to the root directory of the container!

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@jerdra jerdra Oct 21, 2022

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Make sure that in ciftify that your fmriprep workdir is set to /output

-v !{params.license}:/license \
-v !{params.resources}:/resources \
!{params.ciftify_descriptor} $(pwd)/!{json} \
Expand Down Expand Up @@ -470,7 +472,7 @@ workflow cifti_meshing_wf {

mri2mesh(
fmriprep_anat_wf.out.preproc_t1.map { s, t1 ->
[ s, t1, try_fetch_t2("${params.bids}/${s}/**/*T2w.nii.gz") ]
[ s, t1, try_fetch_t2("${params.bids}/${s}/*/*/*T2w.nii.gz") ]
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@jerdra jerdra Oct 21, 2022

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Ok this one is strange cause I tested it w/the double star to recursively check directories. Mind if I test this real quick?

Only asking because I'd prefer ** since it removes dependencies on how the directory under subject is organized

})

// Full fmriprep/ciftify pipeline
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2 changes: 1 addition & 1 deletion modules/transformation.nf
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Expand Up @@ -107,7 +107,7 @@ process format_for_ants {
import numpy as np

# Read in RAS, convert to LPS
coords = np.loadtxt('${coords}', delimiter=',')
coords = np.loadtxt('${coords}', delimiter=' ')
coords[0] = -coords[0]
coords[1] = -coords[1]

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