Hi all:
I got some regions of interest showing significant diffencese in VBM
between two groups. Now, i attemp to compare cortical thickness of these ROIs.
However, i don't know how to map the ROIs to cortical surface and extract
cortical thickness values? I need help._
Dear Freesurfers,
I am now encountering a new error with the Hinds V1 procedure:
I am still using the same version (5.1.0) and nothing has changed, except
that I have been doing some cross-hemispheric registration for some of the
subjects (not this one).
using inflated surface for initial alignm
Dear Freesurfer list,I want to do a ROI analysis on longitudinally processed cortical thickness data in fsaverage space.I followed the steps proposed for long. processing on http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova(i.e sample each time point onto the average surface, concaten
Dear all,
I am currently running cortical thickness analysis using Freesurfer v5.2 on
a high performance computing cluster however, when I run the 'recon_all'
command I get the following error
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
Current Stamp: freesurfer-Linux-centos4
Hi Andi - You can try, but the trac-* files are just wrapper scripts that
call the executables of tracula, which are the dmri_* files. You should
also replace the entire $FREESURFER_HOME/trctrain directory with the new
version.
Hope this helps,
a.y
On Fri, 8 Mar 2013, Andi Heckel wrote:
H
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I
obtain the "Input TR, TE, FlipAngle for each subjects must match"
error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using
mri_ca_train for all subjects).
TR, TE and FlipAngle are the same for
Hi Anders
usually this means you did some editing but didn't complete the rerunning
of the recon-all process. Try running it with -make all
cheers
Bruce
On Fri, 8 Mar 2013,
Anders Hougaard wrote:
Dear Freesurfers,
I am now encountering a new error with the Hinds V1 procedure:
I am still u
what version are you running? This should never happen on the first
subject, so it's pretty puzzling.
Bruce
On Fri, 8 Mar 2013,
alexandra.cristo...@urjc.es wrote:
> Hi everybody,
>
> I'm trying to create my own atlas with the rebuild_gca_atlas script. I
> obtain the "Input TR, TE, FlipAngle for
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" escribió:
> what version are you running? This should never happen on the first
> subject, so it's pretty puzzling.
>
You'll need to register to the symmetric template and then map the label
through that
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
doug
On 03/07/2013 08:17 PM, Chao Suo wrote:
> Hi Freesurfers,
>
> I have created a label on left hemi.
> Is there a command could mirror this label to the right h
Salil, can you run fslregister with --debug as the first option, capture
the terminal output, and send it to me?
thanks
doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
>
> Hi Salil - I'm cc-ing Doug who may be able to help. The error happens
> when bbregister invokes fslregister, in this
You can use mri_segstats with the concatenated/smoothed data as the
input and the label as the --slabel option. Use --avgwf to get the
output. Also, spec --excludeid 0 so that it only gives you the data from
the label.
doug
On 03/08/2013 04:33 AM, Andreas Werner wrote:
> Dear Freesurfer list,
I would run recon-all on the VBM registration target, map the
significance map onto the surface, then use mri_surf2surf to map it to
your individual subjects.
doug
On 03/08/2013 03:16 AM, ZhiLiangLong wrote:
> Hi all:
> I got some regions of interest showing significant diffencese in
> VB
Tim, what were your vol2vol, surf2surf, and freeview commandlines?
doug
On 03/08/2013 11:10 AM, Timothy Brown wrote:
> Hi Doug,
>
> Thank you for your reply.
>
> I tried FreeView and have attached screenshots of results.
>
> freeview_native_brain.jpg - snapshot of native brain
>
> freeview_aseg.jpg
Hi, I convert my files and i get news folders with one file with the extension
.mgz in the folder orig. But , when i try to loasd the volume, I get an error
-[esther@IP132-207-67-224 ~]$ tkmedit 13A
orig.mgzmghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz,
-1)
Does that file exist? What was your command to create the mgz file?
On 03/08/2013 12:12 PM, Valtina Pouegue wrote:
> Hi,
> I convert my files and i get news folders with one file with the
> extension .mgz in the folder orig. But , when i try to loasd the
> volume, I get an error
>
I convert my set of DICOM of the folder
'Patient13A'[esther@IP132-207-67-224 ~]$ recon-all -i
$SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13ASubject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0Current Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.
You will need to run the full processing stream. You can do that from
the beginning with
recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s
13A -all
but now that you have a file there, you can run
recon-all -s 13A -all
doug
On 03/08/2013 12:31 PM, Valtina Pouegue wrote:
Try running mri_surf2surf like this (added rawavg.mgz after register.dat)
mri_surf2surf --sval-xyz pial --reg register.dat rawavg.mgz --tval
pial.native --tval-xyz --hemi lh --s 1158119_3_6
On 03/08/2013 12:38 PM, Timothy Brown wrote:
> Hi Doug,
>
> mri_vol2vol --mov brain.mgz --targ rawavg.mgz
If i'm right, the command: > recon-all -s 13A -all execute the whole
segmentation ( between 20-40 hours). So , if I just want the see the volume, I
have to to the segmentation [ absolutely] ?VP
> Date: Fri, 8 Mar 2013 12:36:34 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: pval...@hotmail.com
>
No, you can just run tkmedit -f subject/mri/orig/001.mgz
You do not need to run recon-all to get a volume, you can just run
mri_convert, eg
mri_convert /path/to/dicomfile out.mgz
tkmedit -f out.mgz
doug
On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
> If i'm right, the command: > recon-all -s 1
OK. Thanks ! ;)
> Date: Fri, 8 Mar 2013 13:16:10 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: pval...@hotmail.com
> CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
>
>
> No, you can just run tkmedit -f subject/mri/orig/001.mgz
> You do not need to
or even
freeview -v /path/to/dicomfile
On Fri, 8 Mar 2013, Douglas N Greve wrote:
>
> No, you can just run tkmedit -f subject/mri/orig/001.mgz
> You do not need to run recon-all to get a volume, you can just run
> mri_convert, eg
> mri_convert /path/to/dicomfile out.mgz
> tkmedit -f out.mgz
>
> d
VP,I try FreeView,, tit Date: Fri, 8 Mar 2013 13:39:51 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: gr...@nmr.mgh.harvard.edu
> CC: pval...@hotmail.com; freesurfer@nmr.mgh.harvard.edu;
> ni...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
>
> or even
>
> freeview -v /path/to/dicomfile
looks like you don't have permission to write to that directory (or the
disk is full)
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
VP,I try FreeView,, tit Date: Fri, 8 Mar 2013 13:39:51 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: gr...@nmr.mgh.harvard.edu
> CC: pval...@hotmail.com; freesurfe
I don't think the disk is a problem: I have a lot of space. But in resume,
here is exactly what i did ( in order):- I created a folder where I saved the
dicoms of my subject- I tried the command
recon-all -i
[-i ] -s
like recon-all -i $SUBJECTS_DIR/PatientXX/blablabla.dcm -s XX . - I got
what are you trying to do? If run a recon, your first command should have a
-all at the end of it
cheers
Bruce
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
I don't think the disk is a problem: I have a lot of space. But in resume,
here is exactly what i did ( in order):- I created a folder wh
Just a dial error. I use the all at the end.
I have 4 subjects and a set of dicom for each subjects. I would like to convert
my dicoms files to be able to make a segmentation with Freesurfer ...
Date: Fri, 8 Mar 2013 14:32:20 -0500
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: ni..
try giving it the dicoms directly as input (instead of converting first)
and make sure you have -all on the recon-all command line and see if that
works
Bruce
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
Just a dial error. I use the all at the end.
I have 4 subjects and a set of dicom for each
Dear FreeSurfer community,
I am trying to obtain subcortical segmentation masks for a group of healthy
volunteers using FreeSurfer v5.1 running on Ubuntu 12.10. I need the masks
to be in the native space of the original 1mm^3-isotropic 256*256*160
T1-weighted images. I found a helpful link which s
maybe sure you specify nearest neighbor interpolation when converting the
aseg. You will lose some accuracy with the resampling of course.
cheers
Bruce
On Fri, 8
Mar 2013, Tal, Assaf wrote:
Dear FreeSurfer community,
I am trying to obtain subcortical segmentation masks for a group of health
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