Hi Anastasia,I’m using this version of tracula.trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki ExpI’ve attached the log-file you requested.
Robby De Pauw, dra.Ghent UniversityDepartment of Physiotherapy and Rehabilitation Sciences3B3De Pintelaan 185B-9000 Ghentrobby.dep...@ugent.be
trac-all.log
Dear Freesurfers,
I am trying to run trac-all with many subjects through a configuration file.
The first subject gets processed without error, but after that I keep
getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found.
This is my command with the output (below configuration fi
Hi Doug
Thanks a lot for your answer
Cheers
Jürgen
---
-
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (
Thanks to Eugenio, for the tip!
We did look at (orig,nu,T1,brainmask,norm,nu,noneck, aseg, wm,
filled).mgz. The only one showing a difference where our white matter
error occurs is filled.mgz.
In some of the other previous images are minor differences around that
area, but not overlapping the
thank you!
Angela
>
> You can use --paired-diff-norm instead of --paired-diff, this will compute
>
> (L-R)/((L+R)/2)
>
> You can then divide the output by 2, eg,
>
> fscalc output.mgh div 2 -o output.div2.mgh
>
> doug
>
>
>
>
> On 8/24/14 9:52 AM, angela.fav...@unipd.it wrote:
>> Hi all,
>> I have
thank you!
that solved my problem!
>
> I think this has something to do with the unix LOCALE because it is
> interpreting the "2.0" as "2,0" using the comma "," instead of the "."
> I actually don't know how to fix this. If you run
>
> echo $LANG
>
> does it return
>
> en_US.UTF-8
>
> if not, as
Dear FreeSurferAs I am trying to preprocess my fMRI data through FsFast, I came across this error:ERROR: cannot find AFNI command 3dvolreg.afniI’m using a mac and bash-shell. I’ve also attached the log-file.This is the command I used:preproc-sess -s GEZ_004_HACO/ -surface fsaverage -mni305 -fwhm 5
Dear Sebastian,
Attached is the *.orig for both recon (green being
the one with wm error and red being the one with error). Unfortunately
they are not identical; a section of the dura is misclassified as wm in
the red delineation. As mentionned before, both orig.mgz are numerically
identical i
Hi Vincent,
On Aug 26, 2014, at 16:45 , Vincent Beliveau wrote:
> Dear Sebastian,
>
> Attached is the *.orig for both recon (green being the one with wm error and
> red being the one with error).
I see, what about the *.orig.nofix? I just noticed that the *.orig are
still run throug
thank you Bruce and Douglas for your reply!
Alejandra
2014-08-20 13:07 GMT+02:00 Alejandra Machado :
> Hello,
>
> I was wondering if FS has an output mask (labelled volume) for each tissue
> types (gm+wm+venctricular_csf) that I can then turn into each subject's
> native space. I understand I
how about the ?h.orig.nofix
On 08/26/2014 10:45 AM, Vincent Beliveau wrote:
>
> Dear Sebastian,
>
> Attached is the *.orig for both recon (green being the one with wm
> error and red being the one with error). Unfortunately they are not
> identical; a section of the dura is misclassified as wm
Hello,
I have 80 subjects' MRIs that were segmented in 2009 with a version of
freesurfer that included this (cvs_version $Id: mri_segstats.c,v 1.11.2.5
2006/04/13 18:57:07 nicks Exp $) in the aseg.stats output. The other 19 of my
subjects segmented in 2013 display this (cvs_version $Id: mri_seg
Hello Robby,
You can download the 3dvolreg.afni file using the following link:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/5.3.0-patch/lion/
Please download it and copy it to your "/Applications/freesurfer/bin"
directory.
-Zeke
On 08/26/2014 10:42 AM, Robby De Pauw wrote:
> Dear Fre
Dear all,
I've got a question: is the color that I get for significant clusters in
tksurfer depending on the contrast vector specified? For example: when I
get a red cluster and my question of interest would be: "is there a
difference between Males and Females regressing out the effect of age and
Freesurfer,
We have scans that have recon-all completed. Following
recon-all, we completed watershed (under the MNE toolbox) to extract skull and
scalp from the T1 scans. The outputs of this algorithm are outer brain, inner
skull, outer skull and outer scalp surfaces. We are part
And is that area outside of the brain not present in the wm.mgz or
filled.mgz on the good output? The orig.nofix should hug the boundary of
the wm.mgz
doug
On 08/26/2014 04:53 PM, Vincent Beliveau wrote:
>
> I've attached ?h.orig.nofix for both recon with and without wm error.
> They are simi
That area outside the brain is not present in both wm.mgz and
filled.mgz for the failed output but for the good output, it is present
in wm.mgz but not in filled.mgz (see attached figures). Again, given the
similarity of the inputs it is surprising that the wm.mgz and filled.mgz
end up being seg
Dear Freesurfer Experts,
I'm working on a younger population (around age 8), and I seem to have an
issue with the pial and wm surfaces grabbing dura on the images.
I've run gcut, -wsthresh at about 15, and even used the
talairach_with_skull_2.lta registration file to no avail, and I'd rather
not
In the bad output of the fill, is it hanging onto the mask by a small
thread, one that does not exist in the good wm/fill? When the wm is
analyzed to get the fill, it removes "islands". I think that
extracerebral stuff is an island in the good (and so removed) and still
connected in the bad. I
Hi Reza, if you look in preproc-sess you will see each of the commands
that gets run. You can adapt the command lines from that
doug
On 08/24/2014 07:52 PM, Reza Rajimehr wrote:
> Hi,
>
> I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis
> of monkey data. To have a better
Joel,
The 'recon-all.log' file in the 'scripts' directory of the subject
should have the version of freesurfer used. Also, the file
'build-stamp.txt' in that same directory will show the version used.
N,
On Tue, 2014-08-26 at 18:31 +, Joel R Pieper wrote:
> Hello,
>
> I have 80 subjects'
Hi all,
I am a little unclear as to how to find the cortical grey matter volume in
the stats output files. The ?.aparc.stats file shows:
Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2
What about grey?
Thanks,
Will
___
Freesurfer m
Hi,
I have got anatomicals of a subject from someone else. The anatomicals
have been processed, and the surfaces have been reconstructed. The path to
these files in my machine is obviously different from the path where data
have been analyzed. I also want to change the name of the subject and give
no, that should not affect anything. Once you do the fMRI analysis,
changing the subject name then means having to re-register (or change
the name in the registration files).
doug
On 8/27/14 12:05 AM, Reza Rajimehr wrote:
> Hi,
>
> I have got anatomicals of a subject from someone else. The ana
The volume for each structure is given as the 4th column. If you want
total GM volume, look in aseg.stats
doug
On 8/26/14 8:43 PM, will brown wrote:
Hi all,
I am a little unclear as to how to find the cortical grey matter
volume in the stats output files. The ?.aparc.stats file shows:
Me
25 matches
Mail list logo
