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Hello FreeSurfer Developers,
I am trying to bring functional ROIs defined in a different program into FreeSurfer, so that I can dilate them into the white matter with –proj abs, but I am running into a problem I was hoping you could help me with. Here are the steps I am taking:
1)I am converting my ROIs, which are in nifti format, to FreeSurfer labels using:
cmd = ['mri_vol2label --c ' outFile{1} ' --id ' num2str(roiVal(roi)) ' --l ' saveLabel{1} ' --surf ' subject ' ' hemi ]; unix(cmd);
2)Next, I want to dilate the labels using this:
cmd = sprintf('!mri_label2vol --subject %s --label %s --o %s.nii.gz --hemi %s --reg %s.dat --temp %s --proj abs -7 0 .1 --fillthresh .001', fs_subject,labelFileName,niftiRoiName,hemisphere, tmpRegFile, regMgzFile); eval(cmd);
This does not work, I get the following Error Message: ERROR: label my_label.label is not a surface label.
I can circumvent this error by manually opening the label in tksurfer and saving it again. After that mri_label2vol runs without error. I assume that tksurfer automatically converts the label to a surface label. While this solves my problem in principle, I have many labels and am hoping that there may be a better way. Do you have any ideas how one could do this automatically? I am running the above code in Matlab R2015a. I am using FreeSurfer version 6.0.0 on Ubuntu 12.04 LTS.
Thank you very much,
Mareike