Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures.
Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja
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