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 fischl@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.2.20.1803291007011.1834@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!
yes, that would work cheers Bruce
On Thu, 29 Mar 2018, Darko Komnenić wrote:
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 fischl@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.2.20.1803291007011.1834@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!
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Darko Komnenić