Hi,
After upgrading to FreeSurfer 5.2.0, the command with -subcortseg flag
exited with the following error.
MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white):
could not open file
The -autorecon1 stage finished without error, so I'm wondering if there
is any change in
Do you have read permission to the file? Also, you can convert straight
to mgz, not need to use nii as an intermediate.
doug
On 3/15/13 5:13 AM, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to
mgz. But I think I shoul first convert mnc to nii
Hi all,
When I run recon-all –qcache, there are a lot of Error messages saying rm:
No match. (although just this error message, no others).
I'm wondering if this is something of concern, or something I can simply ignore.
Thanks!
Daniel
___
That's correct.
On Thu, 14 Mar 2013, Mehul Sampat wrote:
Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm
flags in recon-all help and also here
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
My interpretation is when I use autorecon-pial, I only need the
Hi everyone,
I'm a very new fresurfer user and I have to understand the very simple
basis of its use yet.
So I have some maybe stupid questions about that.
I heve to work on cortical thickness, so I suppose I have to complete the
segmentation and then correcting CPs and Pial surface.
The first
I get this error-esther@m3012-04 ~]$ mri_info
$SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mncmincRead(): can't find file
/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc---I
check in the directory enad the file is right there,
Date: Fri, 15 Mar
can you run ls -l and mri_info on it?
On Fri, 15 Mar 2013, Valtina Pouegue
wrote:
I get this error-
esther@m3012-04 ~]$ mri_info
$SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
mincRead(): can't find
file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m
Hi freesurfer experts,
I'm planning to run a few different glms on surface data using glm_fit e.g.
diagnosis * age; diagnosis * age * symptoms; diagnosis * age *
somebehavioral variable etc..
Do I have to run mris_preproc using the specific fsgd file for each glm? My
data are already qcached,
it seems like the watershed failed and nothing got created after that. You
need to track down why. Usually it's either the talaraich that failed or
the volume is oriented incorrectly. Can you bring the T1.mgz up in tkmedit
and confirm that the directions it shows are anatomically correct? Then
just:
mri_convert full path to minc file volume.mgz
cheers
Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Sorry, I am also a beginner in Linux environment. Now it works.
I try :
-
esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA
total 13892
-rwxr--r-- 1 esther esther 14224696
Thanks a lot!
Date: Fri, 15 Mar 2013 13:09:41 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert problem
just:
mri_convert full path to minc file volume.mgz
cheers
Bruce
On Fri, 15 Mar 2013, Valtina
Matt,
Yes, I think the plan is to discuss this and other potential options. I had a
feeling you may know the most, but I thought I would send out the question in
case anyone else has tried. As it stands, it sounds like no method currently
exists for a Caret surface-to-Freesurfer transition?
Hi Laura, you would only need to run preproc multiple times if the
subjects changed between analyses. If it is the same subjects in the
same order, then you only need to run it once.
doug
On 3/15/13 4:42 PM, Laura M. Tully wrote:
Hi freesurfer experts,
I'm planning to run a few different
Hello all,
Which labels reside in temporal lobe? Do I look at aseg or aseg+aparc.?
I am very new to freesurfer therefore forgive me for my naive questions.
Best,
Akshay
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Freesurfer@nmr.mgh.harvard.edu
Hi, FreeSurfer experts
I have a question regarding making a volume template based on the surface
template for non-human primates. I have made a surface template using a group
of monkeys and now, we want to see the result, which is a mgh surface file, on
the coronal slices of the template. So I
Hi Longchuan
what kind of volume template do you mean?
Bruce
On Fri, 15 Mar 2013, Longchuan Li
wrote:
Hi, FreeSurfer experts
I have a question regarding making a volume template based on the surface
template for non-human primates. I have made a surface template using a
group of monkeys
Hi Neha
the vertices are indices into the surface file. You can load it in with
read_surf, and find the corresponding vertex in the surface (e.g.
?h.white). These are in surface RAS or tkreg RAS coords, which you will
then need to convert to volume coords. I believe Doug has documented this
Thanks Doug. just to be clear - I'd need to run it once per surface measure
correct? i.e. once for thickness analyses on each hemi, and once for area
analyses on each hemi?
On Fri, Mar 15, 2013 at 11:05 AM, Douglas Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Laura, you would only need to run
yep, once per measure.
doug
On 3/15/13 10:56 PM, Laura M. Tully wrote:
Thanks Doug. just to be clear - I'd need to run it once per surface
measure correct? i.e. once for thickness analyses on each hemi, and
once for area analyses on each hemi?
On Fri, Mar 15, 2013 at 11:05 AM, Douglas
Hi, Bruce
Sorry for the late reply as I was trying to figure it out by myself.
I mean the average of the subjects in the volume space that were used for
generating the surface template. Actually I kind of found a volume average in
the mri folder named as T1.mgz that seems to correspond to the
Kara,
the gifti format is used to convert between caret and freesurfer surfaces.
use mris_convert (see --help).
Nick
Matt,
Yes, I think the plan is to discuss this and other potential options. I
had a feeling you may know the most, but I thought I would send out the
question in case
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