That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there On 04/27/2017 02:55 PM, Das S. wrote: > Thanks for the reply. > It has changed some way but not showing values from my lookup table. > I was just following the convention of recon-all. > Sarbani > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 27 April 2017 19:34 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > Are you getting the same aparc+aseg.mgz or has it changed in some way, > but not the way you wanted. BTW, you can create a aparc+aseg.mgz style > output directly from the annots (not sure what the point of the gcs > stuff is) > > > On 04/27/2017 01:24 PM, Das S. wrote: >> 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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
