Dear Freesurfer experts,
I would like to get your help. I extracted cortical thickness values
from each vertex from each of my individual subjects (example:
path/subject_id/surf/lh.thickness.fsaverage.mgh).
I then ran a covariance analysis over the whole group and identified
"modules" or group
Hi Freesurfer experts,
I'm working on analyzing longitudinal data using the longitudinal 2-stage
model. When running the data through long_mris_slopes, I was getting the
following error message: ERROR 1 : mris_calc compute sym. pct. change (spc)
problem?
I saw in previous messages that this is th
Hi Andreia,
You probably have lGI values that correspond to earlier versions of your
surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces
and reprocessed them, but forgot to recalculate lGI for this new surfaces).
If you simply reprocess lGI now, that should solve the p
Hello,
I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a
new error message while running "recon-all" with .nii file inputs
(details below). From the error message I believe the problem might be
that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for
previo
Hello,
Only after sending the email below I noticed that now the stats file
generated give only 0,00 were the LGI values should be, even though
they appear in the terminal.
How can I solve this issue? And, again, are all the measures (cortical
thickness, surface area, aseg) invalidated? As
Hello,
I have created an instruction guide for building freesurfer on OSX
platforms. This guide is applicable for OSX 10.6, 10.7, and 10.8.
Unfortunately I have not yet been able to successfully build on the
latest version of OSX (Mavericks) due to changes in the most recent
version of the gcc
Dear All,
As suggest, I am reposting a previous question.
I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148,
for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’
with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is
b
btw, you are strongly encouraged NOT to use FS 5.2. For TRACULA it is
probably fine, but we found some small but systematic problems with the
anatomical analysis in 5.2
doug
On 05/16/2014 11:51 AM, McGinnity, Colm wrote:
> Hi Anastasia,
>
> Many thanks for your help.
> I did reply but don't see
Dear Martin and FreeSurfer experts,
Thanks for your response.
I have just finished re-running some subjects from scratch in 5.3 and it
appears that the edits from brain.finalsurfs.manedit.mgz are not being applied
to the longitudinal subject directories.
Just to clarify, I have been doing ALL
Hi Anastasia,
Thanks for your reply.
Oh, of course, sorry I didn't realise I was looking at the bvecs after the
rotation. Now it makes sense.
Best wishes,
Colm.
> On 16 May 2014, at 16:59, "Anastasia Yendiki"
> wrote:
>
>
> Hi Colm - The final version used is bvecs. The eddy current corre
Hello Alejandra,
I've seen this error before when people have tried to run freesurfer on
cluster machines. The error indicates that the necessary X-libs are not
installed. Google tells me that if you or your sys admin can install
libXScrnSaver onto your machine it *should* fix it.
Best,
-Zeke
Hi Colm - The final version used is bvecs. The eddy current correction
step registers each DWI to the first b=0 image, and the same
transformation is applied to the corresponding gradient vector. This is a
standard procedure when doing eddy current correction by registration.
Hope this helps
Hi Anastasia,
Many thanks for your help.
I did reply but don't see the email on the forum.
I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit
confused - I've created a 3-column bvecs format file (I had been using for
version 5.2.0).
After running several I've noticed the
Hello,
i'm trying to setup freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
I think i've done downloading properly but i'm having some trouble with
installation. I can set up enviroment and when testing freesurfer with some
of the scripts from the page, sometimes it works but sometimes i get an
Hi Pedro - Looks like the mri_convert command has trouble reading your
dicoms. Have you searched for that error message in the archives of the
freesurfer list? If nobody has encountered it before, then you can post
this as an mri_convert question so that the appropriate people look at it.
a.y
> H
Dear all,
I would like to follow up on several posts that have already been made
regarding how to restrict the search volume (i.e. do a small volume correction)
to a particular region (e.g. to a freesurfer label) within qdec. As far as I
can see this query was not answered on the list:
https
Hi,
Thank you a lot! It now ran, but exited with errors: ERROR: fMRIframe: frame >=
n frames
Can you help me?
Regards,
Pedro Rosa
[server:~/Desktop] pedrogomesrosa% trac-all -corr -c config
INFO: SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop
INFO: Diffusion root is /Users/pedrogomesrosa/Deskt
Hi Pedro - Your config file needs to be a plain text file, not a rich text
format (rtf) file. If you run the cat command on your file, you'll see
that there are some formatting strings that were added by your text editor
in the beginning of the file and they include the curly brackets that give
you
Hi Doug,
I tried to load the annotation and it gave an error. I look in the
archives and I found someone with the same problem and the advice was
to run:
recon-all -s -sd -make all
I did that and tried to run again mris_anatomical_stats as previously
and still have this warning
subj/st
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