Dear Douglas,
Thanks for your reply. The reason I want to use mri_vol2surf in Matlab is that
I have a huge dataset saved in cell arrays of Matlab i.e. multiple subjects,
multiple datasets for each subject, multiple ROIs for each of these datasets,
multiple surfaces for each of these ROIs, and etc. Therefore the most
convenient way for me is to save my data in cell arrays: in Matlab some thing
like "data {sub,tval}{hem,roi}{s,1} = MRIread ([tvalss{tval} hemphh{hem}
roiss{roi} depth{s} 'p_surf.nii']);.
As far as I know multidimensional arrays are not supported in shell scripting.
How, in a shell script, I can use mri_vol2surf with it's input variables stored
in cell arrays? In a shell I wrote some thing like the following, but it does
not work!
# freesurfer project directory
export PATH=$PATH:/Volumes/DATA/projects/ret_obj_purs_recon/subjects
# subjects:
SUBJ=(“ 2_MzBOLD02_GB15042014_UnMasked_Mp2rage_1_0”
“4_MzBOLD04_US14082015_Masked_Mp2rage_1_0”
“5_MzBOLD05_MW14082015_Masked_Mp2rage_1_0”
“7_MzBOLD07_HG21082015_Masked_Mp2rage_1_0”
“8_MzBOLD08_SN21082015_Masked_Mp2rage_1_0”
“9_MzBOLD09_AS28082015_Masked_Mp2rage_1_0”
“10_MzBOLD10_CS28082015_Masked_Mp2rage_1_0” )
# smp directory
SPMDIR=/spm/
# smoothness:
SMOOTH=( “0_8mm” “1_2mm” “1_6mm” )
# t-values
TVALS=( “ret_tval_” “obj_tval_” “purs_tval_” “v3a_tval_” )
# hemispheres 1
HEMPH=( “_lh_” “_rh_” )
# hemispheres 2
HEM=( “lh” “rh” )
# rois 1
ROIS=( “v3aroi” “v6roi” “v7roi” )
# rois 2
ROISS=( “v3a” “v6” “v7” )
# depth line:44
DEPTH=( “000” “001” “002” “003” “004” “005” “006” “007” “008” “009” “010” )
# ==============================================================
for sub in ${SUBJ[@]} ; do
for sm in ${SMOOTH[@]} ; do
cd /Volumes/DATA/projects/ret_obj_purs_recon/subjects/ “${SUBJ[sub]}”
“${SMOOTH[sm]}“
echo “current directory:
/Volumes/DATA/projects/ret_obj_purs_recon/subjects/ ${SUBJ[sub]} ${SMOOTH[sm]}“
for tval in ${TVALS[@]} ; do
for h in ${HEMPH[@]} ; do
for roi in ${ROIS[@]} ; do
mri_vol2surf --src
$SUBJECT_DIR/${SUBJ[1]}/spm/${SMOOTH[1]}/"spmT_000${TVALS[tval]}.nii" --srcreg
register.dat --hemi ${HEMPH[h]} --surf depth ${DEPTH[s]} --mask
"${HEM[h]}.${ROISS[roi]}.label" --out ./"${TVALS[tval]}
${HEM[h]}_${ROIS[roi]}_depth ${DEPTH[s]}_surf.nii" --out_type nii
done
done
done
done
done
I would really appreciate it if you could please let me know what you think.
All the Best,
Fatemeh
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