-- Forwarded message --
From: Bruce Fischl [EMAIL PROTECTED]
Date: 06/08/2007 14:23
Subject: Re: [Freesurfer] Fake thickness map 2
To: Inês Souta [EMAIL PROTECTED]
they don't matter. For a real volume they would be the ras2vox transform
and the mr parameters. For your purposes
freesurfer v.3.0.5 for Linux-Centos4
2007/8/6, Bruce Fischl [EMAIL PROTECTED]:
yes, you should be able to open it in tksurfer. What version of
freesurfer do you have?
On Mon, 6 Aug 2007, Inês Souta wrote:
And after creating the mgh volume, how can I read it? Is it possible to
open
it
Sorry, I was saving it with the wrong extension. I am already able to open
it in tksurfer! Thanks a lot,
Ines
2007/8/6, Inês Souta [EMAIL PROTECTED]:
freesurfer v.3.0.5 for Linux-Centos4
2007/8/6, Bruce Fischl [EMAIL PROTECTED]:
yes, you should be able to open it in tksurfer. What
And after creating the mgh volume, how can I read it? Is it possible to open
it in tksurfer? Should I load it as an overlay?
I've used one of my already pre-processed subjects, created a 'vol' with the
same number of vertices of one of the hemisferes, and saved the output of
save_mgh file as an
yes, you should be able to open it in tksurfer. What version of
freesurfer do you have?
On Mon, 6 Aug 2007, Inês Souta wrote:
And after creating the mgh volume, how can I read it? Is it possible to open
it in tksurfer? Should I load it as an overlay?
I've used one of my already pre-processed
That looks exactly right. Are you experiencing a problem? I assume that
uS1_v01_06LOC_x001.img is a mean functional image of some sort (and not
a contrast image). Did you check the registration?
doug
Johannes Klackl wrote:
Dear all,
I'm currently trying to conduct a surface-based group
what do you mean by allowable null intervals? If you mean that there
needs to be a fixed amount of time between two stimuli, then you cannot
use optseq for this. However, you can tell optseq that there are only
two stimuli, which each stimulus is a pair. Then you'd have to go back
and recode
For #2, you can use mri_volsynth with --pdf checker to create a checker
board pattern. You'll need a new version, which I have put here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_volsynth
doug
Bruce Fischl wrote:
hmmm, not sure i understand. You can visualize any
Where is this data located? I cant find it under
/space/ventzl/1/users/SUBJECTS_DIR
Robert Levy wrote:
Hello,
I found a possible bug in mri_surfcluster, but it may be linked
specifically to average7 and no other srcsubjects (but I haven't
checked that). When I run mri_surfcluster with
I was just wondering why the banks of the superior temporal sulcus was
made into its own label on the Desikan template. Does this correspond
(roughly) to a particular functional area. I didn't see anything in the
paper about why it was chosen. Is it just easy to define given
sulcal/gyral
I think it's where Ron Killiany previously found large effects in
prodromal AD.
On Mon, 6 Aug 2007, Morgan Hough wrote:
I was just wondering why the banks of the superior temporal sulcus was made
into its own label on the Desikan template. Does this correspond (roughly) to
a particular
Hi Bruce,
I see. It just seems to be surrounded by very large parcellation units
that haven't been divided. Does it have good landmarks to place it along
the sulcus?
Cheers,
-Morgan
Bruce Fischl wrote:
I think it's where Ron Killiany previously found large effects in
prodromal AD.
On
Hi Morgan,
I'm not really sure. You could check with Ron and Rahul (ccd).
cheers,
Bruce
On Mon, 6 Aug
2007, Morgan Hough wrote:
Hi Bruce,
I see. It just seems to be surrounded by very large parcellation units that
haven't been divided. Does it have good landmarks to place it along the
I am reporting thickness values from subjects native space constrained
by mask labels using mris_anatomical_stats. I am currently getting the
average of the unsmoothed estimates. I would like to be able to get
smoothed values but the usage reports the smoothing option as -nsmooth
# where the #
Hi all,
I just wanted to ask about editing labels in tksurfer. I have
converted my annot files to labels using mri_annotation2label, and now
have all of the labels in the label directory. However when I edit
the labels, and then save them using save selected label (highlighting
the label and
Hi Sarah,
When you save the label, is there any output on the shell?
Can you load and edit a single label, save it out, exit tksurfer,
restart it, and load the label in again, with the changes you made
present in the label?
On Mon, 2007-08-06 at 14:09 -0400, Sarah J Greene wrote:
Hi all,
The easiest thing is #2. It will produce rstd.mgh as an output, and
that's what you want.
Burmicz, Ryszarda wrote:
Hi Freesurfers,
I have tried looking this up on the list, but I don't understand
exactly what to do in this scenario: I have a group of subjects (all
controls). I want to
I don't have an easy way to do this, sorry.
Robert Levy wrote:
Hi,
I was trying to figure out if there is any way to determine the exact
size at which clusters becomes significant given a specified
significance, and it appeared from the mc-corrected overlay that in
this overlay the
Hi,
I'm getting a bus error when I run mri_glmfit on my Intel Mac. When
I had this problem before, I got a development version of mri_glmfit
which solved the problem. Unfortunately I've reinstalled a newer
version of Freesurfer since then and overwrote that binary file and
it's no
Cate,
There is a current dev distribution of freesurfer for the Intel Mac
here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/macintel
Its the .dmg file, which you can drag and drop to your desktop, then
double-click to start the install GUI.
A new mri_glmfit is also in
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