Subject: Re: [Freesurfer] Include T2 in recon-all command
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Hi William,
I wanted to use both T1 and T2 to do the recon -all -all.
Could it be:
* recon-all -subject subjectname -i invol1 <-i invol2> -all
El mié., 3 mar. 2021 17:16, Ammon, W
Hi Rosalia,
You can include T2 images by adding the flags -T2 /path/to/volume (to point to
the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).
You can read more about this
Hello Shujiro,
Our group has never used Canon scanners before, so unfortunately I don’t have
any Canon-specific protocol I can point you to. Below is the link to our
suggested T1 structural protocol as we have used/tested on Siemens scanners
before. You could try to reproduce this protocol on
Hello,
Are you still getting the error message that “atleast 1 subject must be
provided”? Or is it a different error message? The screenshot shows you are in
the directory MRI4 but the command you’ve sent indicates you want to output
aparcstats.txt to the directory team33.
Make sure to remove
Hello,
It is not advisable to mix versions of FreeSurfer as results across different
versions of FreeSurfer are expected to differ, even if by a little. We
recommend that the same version of FreeSurfer be used to process every case in
your dataset. If you were to proceed with an analysis of,
Hi Saman,
It looks like with the --subjects flag you are pointing Freesurfer to the stats
directory within a subject directory (where Freesurfer expects the subject
directory). aparcstats2table and asegstats2table assume a standard Freesurfer
directory configuration so try entering just the
