the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd <directory where you will put each subject>
cheers Bruce
On Fri, 27 May 2016, Marja Caverlé wrote:
Hi Bruce,
Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time?
Thanks,
Marja
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all
ERROR: Flag -001 unrecognized.
-001 -i AD_TM001.nii.gz -all
Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s <subject id> -i <path to input .nii.gz file> Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: 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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