Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
2. Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
3. Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
4. then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das