Dear all,
I would like to make amendments to the FSL dtifit call during trac-preproc.
In which way can I edit the call in trac-preproc?
# LS tensor estimation
set cmd = dtifit
set cmd = ($cmd -k $dwidir/dwi.nii.gz)
set cmd = ($cmd -m $brainmask)
set cmd = ($cmd -r $dwidir/bvecs)
set cm
Dear all,
I'd like to convert the aparc+aseg.mgz to nifti and use it in the space of
the original MR image. The basic conversion from mgz to nifti works fine
"mri_convert aparc+aseg.mgz aparc+aseg.nii". However if I reslice it in the
space of the original MRI than something fails and even negative
Hi Anastasia or anyone,
Are there any other groups of labels which are, by default, produced in
comparable less vs more restrictive ways?
For instance, is there a way to produce lh.aparc.thresh.annot with comparably
constrained labels?
And does it make sense to do so?
Regards,
Don
I found the problem and would like to report a bug here. The problem
is related to the faulty configure.in file produced during
setup_configure. The faulty snippet is
202 ac_have_gcc_44="no"
203 if test "${CC}" = "gcc"; then
204 gcc --version | head -n 1 | awk '{print $2 $3}' | grep
"GCC(4.4
Hi, all.
I want to convert a freesufer label to diffusion mask with the following
approach.
# tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg
register.dat
# mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation
aparc.a2009s
tkregister2 --mov S000
Hi Don
no, it doesn't make sense for the aparc since it is a complete tiling of
the surface. Each point is assigned the most likely label with no holes,
so no thresholding is needed.
cheers
Bruce
On Thu, 11 Sep 2014, Krieger, Donald N. wrote:
Hi Anastasia or anyone,
Are there any other
Thanks for getting back, Bruce.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.e
Hi Gabor
try adding:
-odt int
to the mri_convert command line. Because the rawavg.mgz is type uchar it
wants to convert to uchar otherwise, which is messing things up.
cheers
Bruce
On Thu, 11 Sep 2014, Gabor
Perlaki wrote:
> Dear all,
>
> I'd like to convert the aparc+aseg.mgz to nifti and
Dear Freesurfer expert,
I am trying to normalized for ICV subcortical volume (Buckner et al. 2004)
using the following:' mri_label_volume [options]...'
where options are either '-atlas_icv ' or '-eTIV
'.
My version of freesurfer is 5.3.0.
But I get this problem:
$ mri_label_volume -atla
Abel,
Is this still an issue for you? If so please type the following 3
commands to the command terminal and send me the output.
Also, lets take this conversation offline, so please just send the
output directly to my email address directly, not the list.
setenv FREESURFER_HOME Desktop/freesur
See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 09/11/2014 05:12 AM, Gabor Perlaki wrote:
> Dear all,
>
> I'd like to convert the aparc+aseg.mgz to nifti and use it in the
> space of the original MR image. The basic conversion from mgz to nifti
> works fine "mri_convert apa
Usually, the register.dat is generated with bbregister. What you have
may work if the DTI was acquired in the same session as the anatomical
and the subject did not move between the two.
doug
On 09/11/2014 08:16 AM, Xiang-zhen Kong wrote:
> Hi, all.
> I want to convert a freesufer label to diff
HI freesurfer experts
We were wondering if it is possible to restrict the Monte Carlo analysis run by
mri_glmfit-sim to a specific region fo the surface , instead of the whole
surface, by using a mask or label to specify the ROI?
I didn't see a --mask or --label option in mri_glmfit-sim
Thank
You do this by specifying a mask or label to mri_glmfit, then
mri_glmfit-sim will automatically use this mask. Note that you have to
run the simulation (ie, you cannot use --cache). In this case you may
want to run mri_mcsim. See
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Jenny,
May I ask were you got those list of binaries... Was is from the Release
Notes page? I ask because we link to some "official" patches on the
release notes page but we also frequently give people "dev" versions of
some binaries to help solve a particular issue that they may be having.
Th
Hi Jenny, I have no idea what is in the HCP release (probably no one
else here does either, but Nick and Zeke might want to chime in).
Unfortunately, we don't keep a simple list of patch files. I also don't
know about the dynamic vs statics linking (Nick/Zeke?)
doug
On 09/09/2014 01:09 PM, Gu
thanks, but we are using qdec to do the inital analysis , not mri_glmfit
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Thursday, September 11, 2014 9:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
You'll have to use mri_glmfit to do this. QDEC is very limited when it
comes to doing something special. QDEC will generate the fsgd file and
contrast files for you. You can even look in the QDEC output folder for
the mri_glmfit.log file which gives the mri_glmfit command. You'll just
need to
thanks, I'll try that
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Thursday, September 11, 2014 10:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim montecarlo analysis with mask
Y
Thanks for the update. We will examine your patch and possibly include
it, or some form of it, into the development tree.
-Zeke
On 09/11/2014 07:54 AM, Arman Eshaghi wrote:
> I found the problem and would like to report a bug here. The problem
> is related to the faulty configure.in file produce
Hi Anastasia,
I am probably doing something wrong with the syntax of the dmrirc file.
I get this error message
trac-all -prior
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
ERROR: flag
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_d
Hi Michele,
Don't think there is anything wrong with the attached dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path to your
configuration file.
Right now it reads the path to your file as a flag, which is of course
not what you want.
Best,
Barbara
On 11/09/
Thanks! it's running...
On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp
wrote:
> Hi Michele,
>
> Don't think there is anything wrong with the attached dmrirc.tutorial file.
> You definitely need to add the '-c' flag infront of the path to your
> configuration file.
> Right now it reads the p
I think it must have gotten contaminated as an attachement. Try using
this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
> Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under
>
Ok. Then, I'm not sure if everything is correct with the command lines
since I use 5.0.
Any thought on this Freesurfer team?
Thanks,
Andreia
Citando will brown :
Thanks again, for the record, I'm using freesurfer version 5.3.0 on
Centos 6.
On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
So, I re-ran the case with the set reinit option. It "half" worked!...in
the sense that the new results show the left uncinate right, but the
right-side one is still a dot (see screenshot of the brain view from the
bottom).
Any further suggestion?
Thanks.
[image: Inline image 2]
On Thu, Sep 1
You can try just re-running "trac-prep -prior" and "trac-paths" for the
L uncinate and no other tracts
On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I re-ran the case with the set reinit option. It "half"
worked!...in the sense that the new results show the left uncinate
right, but the
sorry, this thread has gotten too deep. Can someone summarize the question?
On Thu, 11 Sep 2014, _andre...@sapo.pt wrote:
Ok. Then, I'm not sure if everything is correct with the command lines since
I use 5.0.
Any thought on this Freesurfer team?
Thanks,
Andreia
Citando will brown :
Thanks Doug! It seems to be working this time. I will keep you posted on the
results.
Best,
Hamdi
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thu
Hey everyone,
i have tried to run the trac-all command (Tracula), but it returned an error (bvecs and bvals don't have the same number of entries).
I'm using the latest freesurfer and Tracula update.
I have attached the log-file and my files with the corresponding bvecs and bvals.
Ben
Sure. We'd like to know how to find the surface area of the cortical grey
matter from the pial surface. So specifically, what is the surface area of
the pial/grey matter boundary of the cortex for each hemisphere?
We're using Freesurfer v5.3 on Centos 6.
Thanks,
Will Brown
On Fri, Sep 12, 2014
Thanks very much, Douglas.
This is very helpful.
Best,
Xiang-zhen
【小孔成像】http://www.conxz.net
From: Douglas N Greve
Date: 2014-09-11 22:48
To: freesurfer
Subject: Re: [Freesurfer] from freesufer label to diffusion mask
Usually, the register.dat is generated with bbregister. What you have
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