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if you specify the output file name of mri_label2vol to have a .nii extension it will write NIFTI instead of .mgz. cheers, Bruce On Fri, 6 Mar 2009, Lindgren, Kristen, Ann wrote: > I don't know how to use them with TBSS, but I'm using parcellations from freesurfer as seeding points for probabilistic tractography in FDT. This is what I'm doing, although there may be an easier way if you don't need to edit the labels at all. > > In Freesurfer: > 1) Open brainmask.mgz with tkmedit > 2) File --> Load Segmentation --> select aparc+aseg.mgz > 3) For color table, choose FreesurferColorLUT > 4) Click on desired label - can verify what selecting by looking on toolbox under cursor > 5) Tools --> Segmentation --> Select Main Segmentation Label at Cursor (takes few seconds, turns label green) > 6) File --> Label --> Save Label As (I usually save in the label folder) > 7) To select a new label, unselect the last one (Edit --> Clear Selection/Label) and repeat. Also, if you want to have more than one label included in a label, just keep selecting until you're done then do step 6) > 8) Convert label to mgz using mri_label2vol --label labelyoumade --o labelyoumade.mgz --temp ../mri/brainmask.mgz (if run from labels directory) > 9) You will need to convert the mgz volume to nifti format to be read in FSL. Not sure if mri_label2vol allows you to do that. Otherwise, just use mri_convert > > In FSL: > 1) Align brainmask.mgz to DTI using registration tool in FDT > 2) In probtrackx, select the appropriate mask choice, then select seed image not in diffusion space. > 3) Select the str2diff.mat transform > 4) Add labels you just created (ones in nii format) to your list > > Of note, you will need to binarize the freesurfer labels. You should be able to do that using fslmaths. I do it a different way, but I think the command should be something like: > > fslmaths label.nii -bin binlabelname > > Hope that makes sense. Like I said, there may be a more elegant way to do this, but this is how I have to do it because of the way I'm analyzing my data. Good luck! > > Kristen > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Massieh Moayedi > Sent: Fri 3/6/2009 5:21 PM > To: [log in to unmask] > Subject: [FSL] Using FreeSurfer results as ROIs in TBSS > > Hi, > > I was wondering if there was a method of extracting results (blobs) from > FreeSurfer, and using them as ROIs (or seed regions) in FSL-FDT or TBSS. > > Thanks, > > Massih Moayedi > > >