Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put?
Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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 < >> fis...@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 >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
