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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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ciftify_recon_all : mris_convert prefix issue #185

Open GuillaumeCDGJ opened 7 months ago

GuillaumeCDGJ commented 7 months ago

Hello,

I am running into the following problem when running ciftify_recon_all on the freesurfer folder of a subject, which was generated with fmriprep :

Running: mris_convert -c REANALYSIS/data/derivatives/fmriprep/sourcedata/freesurfer/sub-06/surf/lh.sulc REANALYSIS/data/derivatives/fmriprep/sourcedata/freesurfer/sub-06/surf/lh.white /tmp/tmptejesxgg/MNINonLinear/native/sub-06.L.sulc.native.shape.gii
Running: wb_command -set-structure /tmp/tmptejesxgg/MNINonLinear/native/sub-06.L.sulc.native.shape.gii CORTEX_LEFT
cmd: wb_command -set-structure /tmp/tmptejesxgg/MNINonLinear/native/sub-06.L.sulc.native.shape.gii CORTEX_LEFT 
 Failed with returncode 255

While running:
/home/gc277172/workbench-linux64-v1.5.0/workbench/bin_linux64/../exe_linux64/wb_command -set-structure /tmp/tmptejesxgg/MNINonLinear/native/sub-06.L.sulc.native.shape.gii CORTEX_LEFT

ERROR: NAME OF FILE: sub-06.L.sulc.native.shape.gii
PATH TO FILE: /tmp/tmptejesxgg/MNINonLinear/native

File does not exist.

From what I understand after running mris_convert directly from the command line, the issue seems to stem from the fact that it this function does not actually name the output sub-06.L.sulc.native.shape.gii as instructed, but rather lh.sub-06.L.sulc.native.shape.gii, leading to the following wb-command looking for a non-existent file. Is this due to an incompatibility between the version of freesurfer I am using (7.4.1) and ciftify, or is there a work-around to this issue ?

Thank you in advance,

Guillaume

MatildeVaghi commented 4 months ago

Hi Guillaume, I am having exactly the same problem ( I have been using freesurfer v 7.2) Did you manage to find a solution? Thanks, Matilde

CODER4715 commented 3 months ago

I have the same problem,if anyone can help me? Thanks!

CODER4715 commented 3 months ago

hey，guys！i changed my freesurfer version to 7.3.2，the error disappeared and it works fine.