Hello, all
I read some paper which describe " Automated cortical and subcortical parcellation was performed with FreeSurfer to define specific cortical and subcortical regions in each individual’s T1 scan, based on the Desikan-Killiany atlas. Automated segmentation results were reviewed for quality control, and were then registered to each individual’s diffusion images, and used as the seed and target regions for fiber tracking." I try to do this.
Firstly, I do " FreeSurfer Registration" as follows:
tkregister2 --mov mri/orig.mgz --targ /mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit
convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.ma
flirt -in dti_FA -ref struct_brain -omat fa2struct.mat
convert_xfm -omat struct2fa.mat -inverse fa2struct.mat
convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat
convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat
so, I get the freesurfer2fa.mat
secondly, I do the label files
mris_convert lh.white lh.white.gii
echo lh.BA44.label lh.BA45.label > listOfAreas.txt
label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txt
Thirdly, I do this command:
probtrackx2 -x lh.BA44.gii -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=freesurfer2fa.mat --meshspace=freesurfer --seedref=struct.nii.gz --forcedir --opd -s /DST.bedpostX/merged -m /DST.bedpostX/nodif_brain_mask --dir=/data_tang/result
But it fail as follows:
load seeds
read gifti
read scalar data that is float32
Errors:child killed:segmentation violation
In addition, if I want to use the Desikan-Killiany atlas as seed, how should I deal with the lh.aparc.label ? Please help me
Thank you
Yan
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