Hi,
freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
$Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $
after recon-all i ran recon-all -s $subject -qcache
this generates lh.area.fsaverage.mgh which only contains values 0 and
higher while negative values exist for the lh.area of the
Dear Freesurfer experts,
I have a question about qdec...as it is supposed to be doing whole brain
cortical analyses, how come one first has to generate statistical tables,
and chose thicknesses of different regions from these tables? Is this just
an option, rather than being necessary for qdec?
Dear Freesurfer experts,
I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some
subjects, it looks that the pipeline stucked in the middle of mri_cc and
keeps running for days (without any error message). Last time when it
occurred I thought it may be caused by some hardware-r
I've noticed this at well when something goes wrong before mri_cc. It gets
stuck in some kind of infinite loop. You might check that the linear and
nonlinear registration worked correctly.
Peace,
Matt.
From: Dawei Liu
Date: Wednesday, February 20, 2013 10:49 AM
To:
Subject: [Freesurfer]
Hi Linn,
did you ever solve this?
you need to specify a name for the base and the tp1id and tp2id are
placeholders for the id's of the corresponding 2 cross sectional time
points. Don't typ;e the '...'
So for example:
recon-all -base linn-base -tp linn1 -tp linn2 -all
linn1 and linn2 shoul
Hi Sabin,
what was the recon-all command you used for this?
Thanks, Martin
On 02/05/2013 09:51 AM, Sabin Khadka wrote:
Hi all,
I am running longitudinal processing and it keeps on crashing with no
error message whatsoever in middle of one or the other processing
steps. I am not sure if this
Hi Ziad,
Thank you so much for the suggestions. However, I'm not really sure how to
utilize any of them...So I guess more detailed help would be necessary for
me to follow these suggestions. Sorry.
I've also never actually used SUMA. Previously I was just using a 3dcalc
command to bring aseg ROIs
Hi Bruce,
After exhausting all of our options, Tali Swisher informed me that I
should contact you. I have been trying to run freesurfer on a brain and
have been running into a lot of problems. After first running:
recon-all -i nifti-files/002-t1w-realign-masked.nii.gz -autorecon1
-noskullstrip
Hello,
I recently posted on the FreeSurfer mailing list, but received no reply.
The main problem I am having is due to my virtual machine disk image, there
isn't enough space. The virtual machine allows me to store up to four
patient files, but there are some processes on FreeSurfer that require
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Anastasia,
We have a set of MR data and all have the recon-all processing done in
FreeSurfer version 5.1. Will we be able to use the results from the recon-all
FreeSurfer version 5.1 for the new TRACULA version 5.2 or will we have to run
recon-all in version 5.2 to use TRACULA version 5.2?
Tha
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
& aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033
Dear FreeSurfer experts,
I have some experience with FSL and SPM, but not a lot with FreeSurfer, so
please bear with me.
When I observe FreeSurfer segmentations, I see that images are binary (either a
voxel belongs to a tissue class, or it does not) and not probabilistic. I want
to obtain tot
Hi Cyrus - Great question! The only thing that tracula utilizes from the
freesurfer recon is the aparc+aseg, and since I'm told that there have
been no changes from 5.1 to 5.2 affecting how the aparc+aseg is generated,
you'll be fine using either 5.1 or 5.2 freesurfer recons as input for the
n
Dear Bruce and freesurfer experts,
I am trying to use mri_average_subjects, but encountered the error:
mghRead(/fullpath/surf/lh.inflated.H, -1): could not open file.
.
Then I tried
mri_info subject/surf/lh.inflated.H
, and it worked.
But when I tried
mri_info $(readlink -f subject/surf/lh.infla
If someone can send us and example of this behavior I will fix it
Cheers
Bruce
On Feb 20, 2013, at 12:23 PM, Matt Glasser wrote:
> I've noticed this at well when something goes wrong before mri_cc. It gets
> stuck in some kind of infinite loop. You might check that the linear and
> nonlinear
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