Hello freesurfer experts,
I am keen on generating vertexwise intra-class correlation maps for a group
of subjects with paired measurements - similar to that in Wonderlick et al
in Neuroimage 2009. Reliability of MRI-derived cortical and subcortical
morphometric measures: Effects of
pulse sequence,
Thanks Doug,
On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote:
>> I'm using:
>> freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
>>
>> Q1)
>> If I don't want to use any thresholding for ROI analysis, can I use "-sign
>> abs -thresh 0" with funcroi-config?
>>
> Even easier: just don't specif
Hello,
I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am
doing this by issuing the "recon-all -make all -s subject" command. It
stops right away with the message:
make: Nothing to be done for `all'.
There exists the wmparc.stats file from the fs450 recon, but there is
no la
I've never seen a .raw format. Where does it come from? I don't think
mri_convert will handle it, but you can just try something like
mri_convert your.raw your.nii
(or your.mgz).
doug
Alan Francis wrote:
> Hi FSL and FreeSurfer folk:
>
> Does anyone know how to convert *.raw files to analyze
Hi FSL and FreeSurfer folk:
Does anyone know how to convert *.raw files to analyze, nifti or mgz format?
thanks much,
Alan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The inf
Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
> Hello FreeSurfer group,
>
> I am unable to run asegstats2ta
Hi Doug,
Alright. I'll try doing that.
Thanks for the information.
Best,
Lisa
__
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
Portage Bay Building, BOX 357988
Seattle, WA 98195-7988 U.S.A.
E-mail:
Yes, fix the pons cutting plane. I've modified the text in that link to
be clearer. Let me know if you still have trouble.
doug
Yang Liu wrote:
> Hi Doug,
>
> Thanks for replying!
> I checked the filled.mgz. The cerebellum is still attached.
> How can I fix the problem? I am a new user of Frees
Hi Doug,
Thanks for replying!
I checked the filled.mgz. The cerebellum is still attached.
How can I fix the problem? I am a new user of Freesurfer.
My guess is to select the correct pons cutting plane. But I found that the
instruction on
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Trouble
Hi Tyler,
by mapping the DTI to the anatomical space, you will automatically
account for partial voluming in the DTI space. The partial volume
correction in mri_segstats is for correcting within the 1mm3 anatomical
voxel, which seemed excessive given the large DTI voxel sizes (but maybe
it's n
Hi,
I have two questions about using mri_segstats. First, I notice that on the
individual dti tutorial, you don't use the --pvol option to correct for partial
voluming. Is there a reason for this? Second, would there be any disadvantage
to using mri_segstats with aparc+aseg.mgz to get volume/ t
Have you looked at the filled.mgz volume to make sure that cerebellum is
not attached?
doug
Yang Liu wrote:
> Hi,
>
> I am processing the anatomical monkey brain now.
> When recon-all runs, it stops at the step of "mris_fix_topology"
>
> I inserted the last part of my recon-all.log below:
>
> It
There's no easy way to do it. You can convert to a volume and then use
the --slice-crop option in mri_convert to extract out individual slices.
doug
Lisa F. Akiyama wrote:
> Hello,
>
> I have a large number of slice files in ima format.
> I would like to convert each of these ima files into eith
Hi Yuko, answers below
Yuko Yotsumoto wrote:
> Hi all,
>
> I'm using:
> freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
>
> I've posted two questions (Q1 & Q2 below) in my previous email regarding ROI
> analysis, and I'd like to add one more (Q3).
>
> Q1)
> If I don't want to use any thresholdin
Hi Qizhu,
1. These files do not directly contain geometry information, but there
are other files that do (eg, lh.white). You can use the mri_surf2vol
program to convert them into a standard volume file like nifti.
2. You can use mris_convert to convert to ascii. The values are listed
in the ver
Dear Ørjan,
With SUMA you can convert freesurfer's anatomically correct images to
.ply format.
Uri
2010/12/6 Ørjan Bergmann :
> Dear all
>
> I am interested doing some visualization of my cortical FreeSurfer results
> in other software.
>
> In order to do so I need to some information about how
take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/
Hi Ørjan,
yes, you can either use our matlab functions for reading surfaces, or use
mris_convert with an output surface with an extension .asc to create an
ascii file.
cheers
Bruce
On Mon, 6 Dec 2010, [UTF-8]
Ørjan Bergmann wrote:
Dear all
I am interested doing some visualization of my
Dear all
I am interested doing some visualization of my cortical FreeSurfer results
in other software.
In order to do so I need to some information about how the cortical surface
is defined. Usually these surfaces consists of a set of 3D coordinates which
gives the position of the vertices (16384
Hi all,
I'm using:
freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
I've posted two questions (Q1 & Q2 below) in my previous email regarding ROI
analysis, and I'd like to add one more (Q3).
Q1)
If I don't want to use any thresholding for ROI analysis, can I use "-sign abs
-thresh 0" with funcr
20 matches
Mail list logo
