Hi Bruce, thanks for the reply. I only have one acquisition per subject. I guess I can make a separate text file with a list of paths to dicoms and then somehow try to pair the path and the subject name in the recon-all command.
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] defining input images in a for-loop in > recon-all > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1803291007011.1...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Darko > > sorry, you need to sort this out yourself as there is no way for us to > know where the dicoms are. An alternative is to create each subject dir, > create the 00?.mgz files (if you have more than one acquistion) in the > <subject>/mri/orig dir, then run recon-all without the -i flag. If you use > -i you need to figure out a way to find one slice in the correct dicom > series for each subject. > > cheers > Bruce > > > On > Thu, 29 Mar 2018, Darko Komneni? wrote: > >> Dear experts, >> I would like to run a for-loop in FreeSurfer 5.1. so that I can have >> multiple subjects analyzed over >> the holiday, without having to come to the lab and start each of them >> myself. I searched the >> previous emails in this list and know that I can make a file with a >> subject list, and then have the >> loop go through that file. >> I was wondering, however, how to handle the -i part of recon-all command? >> Each subject in a loop >> needs to have one brain image assigned - I don't think FreeSurfer will >> know where to look for images >> just by telling it what the subject name is. >> Thanks in advance for any help! _______________________________________________ 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.
