[Freesurfer] Overlaying a lesion map onto an inflated surface

Dear Freesurfer list, I did a group level thickness analysis in qdec with lesioned brains and I would like to overlay individual lesion map onto the group level results to check for overlap, etc. I was wondering if I could convert individual lesion maps and overlay them on the group level inflated

[Freesurfer] extracting ROIs from the freesurfer atlases in Qdec

Dear list, I would like to use specific regions from either the Destrieux Atlas (aparc.a2009s.annot), Desikan-Killiany Atlas (aparc.annot) for an ROI analysis. Is there a way to use these ROIs in Qdec (similar to WFUpicktlas)? If we need to trace them manually based on these atlases, what do we ne

[Freesurfer] recon-all error messages

Dear List, I've been encountering a series of error messages when I did recon-all on a number of subjects, using Freesurfer v5.1 Below are the error messages for 3 different subjects (all with lesions). I tried them using both dicom and nifti, and on various computers, but the same messages appea

[Freesurfer] Flipping analyze images

Dear List, I have a question regarding using .img in Freesurfer. We only have analyze images, but we can tell the orientation of the images through the patient's lesion location. Because freesurfer sometimes flips these image after recon-all, I'm now flipping the "problematic" ones using mri_con