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 <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!
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