ciftify_recon_all : mris_convert prefix issue #185
Description
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