Is this a volume label that is supposed to be on the cortical ribbon? An
you wan to do a surface-based dilation? Or do you just want to dilate it
in 3D?


On 12/04/2018 08:28 PM, Mareike Grotheer wrote:
>
>         External Email - Use Caution
>
> 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
>
>
>
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