list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
no! Don't delete those files - we need them. Just don't include them in your
for loop
cheers
Bruce
On Mon, 3 Aug 2015,
Lim, Lena wrote:
Thanks, Bruce. So do I delete that files and run recon-all -qcache -subjid $i
for all
have
so far ?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I think you
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
no! Don't delete those files - we need them. Just don't include them in your
for loop
cheers
Bruce
On Mon, 3 Aug
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I think you should be all set. I meant don't delete fsaverage and all
On
Mon, 3 Aug 2015, Lim, Lena wrote:
Sorry, I don’t understand. Those files are now in the directory. What exactly
should I run next?
-Original Message
...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I think you should be all set. I meant don't delete fsaverage and all
On
Mon, 3 Aug 2015, Lim, Lena wrote:
Sorry, I don’t
,
Lena
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 30 July 2015 18:02
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
you
with Freesurfer preprocessing pls
Hi Lena
you need to run the hippocampal subfield code. Depending on what version you
are running it could mean adding something like:
-hippocampal-subfields-T1/T1T2/T2
and removing the -autorecon-all
cheers
Bruce
On Thu, 30 Jul 2015, Lim, Lena wrote
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
those aren't files that you need to recreate - they are distributed with FS
(which is also why you don't have permission to write into their directories).
You should leave them out of the list that you
: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 15:38
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
those aren't files that you need to recreate
Hi Lena
you need to run the hippocampal subfield code. Depending on what version
you are running it could mean adding something like:
-hippocampal-subfields-T1/T1T2/T2
and removing the -autorecon-all
cheers
Bruce
On Thu, 30 Jul 2015, Lim, Lena wrote:
Dear Freesurfer experts,
My
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