Can you send the log file?
On 2/10/2021 10:26 AM, Bohorquez Montoya, Luisa wrote:
External Email - Use Caution
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.*
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