Dear Freesurfer experts,
We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain.
Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 9389 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label...
Why does it say that 0 nonzero vertices have been found, yet it selects 9389 vertices? Is there an additional option that we should be utilizing? Is a label the correct way to create what we are looking for, or would an overlay be more appropriate? If the latter is the case, should we be using mri_vol2surf?
Thank you in advance for your assistance!
Best,
Sarah Weiss and Robert Kim