You could run it with -label-V1
This is run at the end of recon-all and should only take a few min and
would change the recon-all.log file.
On 09/21/2017 01:57 PM, STACEY M SCHAEFER wrote:
>
> Hello,
>
>
> I want to run recon-all again on scans that have already been
> hand-edited, the appr
Hello,
I want to run recon-all again on scans that have already been hand-edited, the
appropriate recon-all flags ran, and resulting output checked and approved.
The images look good, but when the hippocampal subfield routine was later run
on the images, it crashed, leaving an error in the re
each subject is run separately through recon-all regardless of group.
For group analysis, you will run mris_preproc, mris_surf2surf (to
smooth), then mri_glmfit (after creating an appropriate FSGD file). Look
at our group analysis tutorial and exmaple FSGD page
doug
On 11/12/2013 02:10 PM,
Hello FreeSurfer experts,
I have a question regarding group analysis and running of recon all group
wise.
For example I have group A, B, and C with several subjects in each group, if
want want to compare their cortical and subcortical measurements group wise,
how do I run the recon all.
Also c
_
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, September 13, 2013 9:09 AM
> To: Rashmi Singh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] recon all question
>
> what do you want to do with the brain volume? Are you really aft
>From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>Sent: Friday, September 13, 2013 9:09 AM
>To: Rashmi Singh
>Cc: freesurfer@nmr.mgh.harvard.edu
>Subject: RE: [Freesurfer] recon all question
>
>what do you want to do with the brain volume? Are you re
use this option.
Rashmi
___
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 13, 2013 9:09 AM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] recon all question
what do you want to do
shmi
>
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, September 13, 2013 8:46 AM
> To: Rashmi Singh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] recon all question
>
> 1. I don't think I know a
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 13, 2013 8:46 AM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] recon all question
1. I don't think I know anyone who has done this, and we haven't asses
___
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 12, 2013 5:27 PM
> To: Rashmi Singh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon all question
>
> Hi Rashmi
>
> putting them in the orig folder with those numbers
, September 12, 2013 5:27 PM
To: Rashmi Singh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to
do motion correction and averaging.
cheers
Bruce
On Thu, 12 Sep 2013, Rashmi Singh wrote
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to
do motion correction and averaging.
cheers
Bruce
On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per
scan for a subject.
Hello Freesurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a
subject.
While running the FreeSurfer, if I want to use the three mprages for that
subject as an input file, may I just keep the three mgz files (001.mgz, 002
.mgz and 003.mgz) in the
Title: Recon-all question
I’ve installed Freesurfer on Mac running Tiger. Am able to run mri_convert to attain 001.mgz and view with tkmedit without a problem. Can run recon-all –help and attain the help files, but running recon-all –subjid -all (or autorecon1) –mgz does not produce any image
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