I used following code to run freesurfer step without using up sampling to 0.7 mm,
export HCPPIPEDIR=/home/all9kt/CINEPS2/CINEPS2Pipeline_N
. /home/all9kt/CINEPS2/CINEPS2Pipeline_N/Examples/Scripts/SetUpHCPPipeline.sh
export SUBJECTS_dIR=/home/all9kt/CINEPS2/studyfolder
export HCPPIPEDIR_Global=/home/all9kt/CINEPS2/CINEPS2Pipeline_N/global/scripts
export HCPPIPEDIR_Templates=/home/all9kt/CINEPS2/CINEPS2Pipeline_N/global/templates
export CARET7DIR=/home/all9kt/workbench/bin_linux64
source ${HCPPIPEDIR}/Examples/Scripts/SetUpHCPPipeline.sh
#SUBJECTS_dIR="/home/all9kt/CINEPS2/studyfolder"
SUBJECT_ID="sub-130" # Change this to your subject ID
SUBJECT_Id="sub-130k1mm"
${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh \
--subjectDIR="${SUBJECTS_dIR}" \
--subject="${SUBJECT_Id}" \
--t1="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore.nii.gz" \
--conf2hires=FALSE \
--t2="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T2w_acpc_dc_restore.nii.gz" \
--t1brain="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore_brain.nii.gz"
but I faced to this Error:
~/CINEPS2/studyfolder/sub-130k1mm/mri ~
Mon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: While running '/home/all9kt/CINEPS2/CINEPS2Pipeline_N/FreeSurfer/FreeSurferPipeline.sh --subjectDIR=/home/all9kt/CINEPS2/studyfolder --subject=sub-130k1mm --t1=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T1w_acpc_dc_restore.nii.gz --conf2hires=FALSE --t2=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T2w_acpc_dc_restore.nii.gz --t1brain=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T1w_acpc_dc_restore_brain.nii.gz':
Mon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: ERROR: Expected t2w_input_file: rawavg.T2.prenorm.mgz DOES NOT EXISTMon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: ABORTING
how can I solve this error?
I have to say when conf2hires is true, I won't face this issue.
Thanks in advance
Armin