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.