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Hello Freesurfer
I have been trying to run this subject 3 times (with different walltime) and I am having the same error. Would you mind please to explain me what I am doing wrong?
Thank you
subject="$1"
echo $subject
cd /scratch/global/lbohorquez/Freesurfer/"$subject"
export SUBJECTS_DIR=/scratch/global/lbohorquez/Freesurfer/"$subject"
ANATDIR=/scratch/global/lbohorquez/Freesurfer/
OPENMP=12 export OMP_NUM_THREADS=12
recon-all \ -autorecon2 -autorecon3 -subject "$subject" \ -no-isrunning -parallel -openmp 12 \
####SUMA-ize with AFNI echo "Before Suma"
@SUMA_Make_Spec_FS -NIFTI \ -fspath ${SUBJECTS_DIR}/"$subject" \ -sid "$subject" echo "After Suma"
######## registration TO MNI cd ${SUBJECTS_DIR}/"$subject"/SUMA/ @SSwarper -input "$subject"_SurfVol.nii -base MNI152_2009_template_SSW.nii.gz -subid ssWarp
Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin.