Hello again,
Don't mean to be a bother. I was wondering if anyone had any thoughts on
what possibly be going wrong during my retinotopic analysis that I posted.
I'm at quite a loss and would appreciate a look.
Thanks and best,
Daniel
On Fri, May 11, 2012 at 11:49 AM, Daniel Cole
Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark -
I don't see a brain at all. Is there a way to troubleshoot this?
Thanks,
Kiely
Hi Kiely - Looks like you used flirt for the intra-subject registration,
so you can look in trac-all.log for the flirt command line that registers
diffusion to anatomical and play around with the parameters.
You can also use bbregister instead of flirt for the intra-subject
registration -
Kiely, For flirt, try using corratio, cost function instead of mutualinfo
(which is the default in trac-all) to see if that solves your registration
problem.
Hi Kiely - Looks like you used flirt for the intra-subject registration,
so you can look in trac-all.log for the flirt command line that
Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?
Thanks,
Kiely
On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
Kiely, For flirt, try using corratio, cost function instead of mutualinfo
(which is the default in
No, this is something you have to try yourself on the command line. If you
want to make the change permanent, you can edit the relevant line in
$FREESURFER_HOME/bin/trac-preproc.
On Wed, 16 May 2012, Kiely Donnelly wrote:
Is this something I can change in my dmrirc file or do I need to run
you have to run flirt commandline separately to check if it solves your
problem.
Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?
Thanks,
Kiely
On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
Kiely, For
Hi Daniel, did you miss my responses from last week?
doug
Original Message
Subject:Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only
Date: Fri, 11 May 2012 12:49:32 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Thanks Bruce! Those are the main questions now (not only to V1, but
also to the rest of the Brodmann areas). I really want to be sure
where the measures come from. I want that the different measures (i.e.
cortical thickness and area are really from the same region in the
cortex), to know
I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line look something like this if I am
running it in this individuals dmri directory:
flirt -in dwi_orig.nii.gz
The .mat registration matrix should be saved under dmri/xfms/.
On Wed, 16 May 2012, Kiely Donnelly wrote:
I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line
Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
Also, please remember to copy the list so that others can see the answer
and so that others can help with the answer.
thanks!
doug
On 05/16/2012 11:56 AM, Rashmi Singh wrote:
Dough,
Yes, the stat files exist with all its
Doug,
Attached are the aseg.stat files of the two different runs (AA262.G1 and
AB054.G1) where I got the error message.
Thanks
Rashmi.
On 5/16/12 11:41 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
Also, please remember
Dear Freesurfer Friends
I have a question about cortical thickness. I do not understand why these
commands give us DIFFERENT values for average cortical thickness.
Can you please let me know if you have any idea.
Thanks a lot
mris_anatomical_stats N2207 lh
number of vertices
I was able to load both of those. Try this:
cd /opt/freesurfer/subjects/AA262.G1/stats
asegstats2table -i aseg.stats -t test.dat
doug
On 05/16/2012 01:25 PM, Rashmi Singh wrote:
Doug,
Attached are the aseg.stat files of the two different runs (AA262.G1 and
AB054.G1) where I got the error
It just loads in a single file and creates a table with one row.
On 05/16/2012 02:02 PM, Rashmi Singh wrote:
Can you also let me know what does the following command do.
Thanks,
Rashmi.
On 5/16/12 12:58 PM, Douglas N Grevegr...@nmr.mgh.harvard.edu wrote:
I was able to load both of those.
Dear All,
Could someone explain (or point me in the right direction) as to the
meaning of the dependent measures (which can be used in qdec)
- intensity_deep/intensity_superficial
- intensity_deep.mgz/intensity_superficial.mgz
- white K/H
What do they represent ?
Thanks.
Mahinda
Dear FS experts,
How can I flip hemispheres? I read the mail list and Doug said that (2010):
The problem with this is that you will get different results when you
use the left hemi and the right-flipped-to-left hemi as compared to the
right hemi and the left-flipped-to-right hemi. You'll
Hi Tadeu, It will be available in 5.2. If you can't wait until then,
then follow the instructions here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html
doug
On 05/16/2012 03:51 PM, Tadeu Kubo wrote:
Dear FS experts,
How can I flip hemispheres? I read the mail list and
Hi Doug
Thank you!
Tadeu
On Wed, May 16, 2012 at 5:02 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Tadeu, It will be available in 5.2. If you can't wait until then,
then follow the instructions here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html
doug
Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill
tool to relabel the *entire* left hippocampus segmentation to
'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left
hippocampus volume from the original aseg.stats be identical to the volume
of
Hi Joshua
probabilities are computed internally, but not stored nor used in volume
calcualtions. Are you actually doing a 3D fill? I don't think the
hippocampus label is guaranteed to be connected. Can you try instead
replacing every voxel in matlab with the hippocampus index to your new one?
Hey Doug,
Sorry I did miss your response last time, thank you for the advice.
I tried running the analysis again and this time it did create the angle
file. However, now I'm running into a different problem.
I can get the angle map to show up on the surface of my subject's brain but
I can't get
Hi Bruce,
First, let me add that if I run the mri_segstats without the --pv flag, the
two will have identical volumes. This indicates to me that we captured all
the voxels into the new label.
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain
Department of Psychology
University of
hmmm, that is convincing. I don't think there's anything in mri_segstats
that knows about the meaning of any of the indices, but maybe Doug can
correct me?
On Wed, 16 May 2012, Joshua Lee wrote:
Hi Bruce,
First, let me add that if I run the mri_segstats without the --pv flag, the
two will
Hi all:
I'm a little confused about the DODS model and DOSS model. I have two
groups (patient and control) and one covariate (age), and I want to compare the
diffirence of thickness between the groups with age as the covariate. In DODS
model, is the process the analysis of variance
I'm having a problem in building FreeSurfer from the source codes (both
'stable5' and 'release_5_1_0') downloaded from the CVS repository.
When I run 'make', it stopped with the following error message:
mri_convert.c:39:40: error: unwarpGradientNonlinearity.h: No such file
or directory
Oops i just realized I only sent this to Bruce:
Thanks! It looks like this involves some manual intervention. Matt., I
assume you're not manually making control points on 1000s of subjects (I
imagine this is for the human connectcome project). Is your code public
somewhere?
Cheers,
Michael
Only because I was lazy! You can use surfaces for normalization too. I think
the script I gave Matt probably had that in it
On May 16, 2012, at 9:21 PM, Michael Waskom mwas...@stanford.edu wrote:
Oops i just realized I only sent this to Bruce:
Thanks! It looks like this involves some
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