If you just want to check the orientation, then you can run mri_info. It
will not tell you whether the orientation is correct or not, but neither
will fslhd
doug
On 6/19/13 11:18 AM, Bruce Fischl wrote:
Hi Brigette,
not sure how you could do this except visually. Bring the images up
and v
If you want to use it as a mask in FSFAST, you can do that at the higher
level when you run mri_glmfit. You would then extract the label for
fsaverage only and pass it to mri_glmfit with the --label option
doug
On 6/19/13 11:22 AM, Bruce Fischl wrote:
Hi Daniel,
have you run recon-all on yo
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the
commands “long_mris_slopes” or “long_qdec_table” I just get
“command not found” as an answer. When I try to look up a package that might
include the command, by typing “cnf long_m
Hi Catherine,
what does mris_preproc --version give you?
Thanks, Martin
On Jun 20, 2013, at 4:27 AM, Catherine Bois wrote:
> Hi!
>
> I am running 5.3...Typing freesurfer into the command window leads to;
>
> You are running this version of FreeSurfer:
>
> freesurfer-Linux-centos6_x86_64-st
Hi Peter,
can you run any free surfer command at all? Looks to me that you did not source
free surfer. What happens if you type
freesurfer
into the terminal window? It should print the version.
Best, Martin
On Jun 20, 2013, at 5:17 AM, Peter Bohn wrote:
>
>
>
>
> Dear Freesurfer experts,
Dear Doug,
I just installed 5.3 version and now I have the Xhemi. I need to study
asymmetry of the brains -processed with FS 5.1- comparing right and left
hemispheres for each subject individually and between male and female
groups including 40 subjects each. Would you please let me know the
proced
Hi,
Thank you for your response. I am actually using two random effects
(time and intercepts), and have fixed my design matrix to incorporate
this. We are actually running R2011b Matlab, however I just realised
that we do not have the Statistics toolbox. Could this be what is
causing the e
Yes, those scripts are available since 5.2. You need to update to a newer
version.
Best Martin
Peter Bohn wrote:
>Hi Martin,
>
>thanks a lot fort he quick reply! When I type freesurfer into the
>window it shows me v5.0.0 as the version. Sorry for my prior mistake
>concerning the version’s name
Hi
Strange error in tracula 5.1. When I use a dmric file that have worked
before I now get
subj: Undefined variable.
I may have uppgrade tcsh. Is there any fix to get tracula-preproc to use
the id from dmric files
Knut J
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Hi Peter
we use semething similar, although we've extended it and made it
significantly more accurate. If you want to contact the CMA you can try:
Dave Kennedy
cheers
Bruce
On
Thu, 20 Jun 2013, Peter Bohn wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis
Dear Doug, dear freesurfers,
thank you very much! If I'd like to change the orientation (from PSR to
LAS), is there a way in Freesurfer to do it?
Thanks again!
Best,
Brigitte
2013/6/20 Douglas Greve
>
> If you just want to check the orientation, then you can run mri_info. It
> will not tell y
Dear Doug,
Thank you for your e-mail.
As you suggested, we changed tnullmax to 6 sec and run the following code
in Optseq:
--ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0
--ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0
--ev Loss4 4.0 8.0 --ev
Not totally sure with 5.0, but I don't think it requires same voxel space for
all time points (since 5.1), so it should work to run the analysis with 5.3 on
that data.
Cheers Martin
Peter Bohn wrote:
>Thanks a lot! Do I have to repeat
>creating the base and the longitudinal runs once I use the
Hello all,
Thank you very much for your comments and sorry for not being too
precise with my problem before.
It seemed at the begining to me very strange that the same image
processed in crossectional or longitudinal had different results in
registration and I thought it was something related to
Which one failed?
Bruce
On Jun 20, 2013, at 10:29 AM, Daniel Garcia
wrote:
> Hello all,
>
> Thank you very much for your comments and sorry for not being too
> precise with my problem before.
>
> It seemed at the begining to me very strange that the same image
> processed in crossectional or
The longitudinal one, about 20 mm out of the good registration
Le jeudi 20 juin 2013 à 10:36 -0400, Bruce Fischl a écrit :
> Which one failed?
> Bruce
>
> On Jun 20, 2013, at 10:29 AM, Daniel Garcia
> wrote:
>
> > Hello all,
> >
> > Thank you very much for your comments and sorry for not bein
Hi Tudor,
Looking at the log files for the 4 subjects, it seems to me that the left
hemisphere was finished and that it is currently processing the right
hemisphere. So, either it's still running, or some external instance killed the
process, but it's definitely not an error in the lGI process
Hi all,
Is there a rule that let me avoid having the error message could not force
null max?
-- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3 15
--ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4.5 ..
Thanks
AS
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Dear FreeSurfers,
I have been using FreeSurfer for editing for the past year now and I have
recently come across an issue that I have not seen before in a new dataset.
The pial surfaces are missing in the right hemisphere following the first
run of Freesurfer (before any edits). There are also som
Dear FreeSurfers,
It seems that the tutorial sample data needs correction for
skull strip, too. I am just curious why it only serves a sample for control
points.
Thank you very much!
Sincerely,
Ye
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Hi Doug and Freesurfers,
I realized that I hadn't updated my group levels to one group. However, when I
do that..the qdec complains about group.level having at minimum two levels. How
can I run (using QDEC) single group regression?
Thanks,
Manish
From: Mani
Dear Doug,
Is there a way to use the Freesurfer and Tracula output to compute
connectivity maps?
Thanks!
Sal
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The information in th
Hi there,
I was wondering if the cortical thickness values of the ROIs in
?h.aparc.a2009s.stats or ?h.aparc.stats have been corrected based on the
subject's whole brain volume or the template volume or if it is just the
thickness measures without correction.
Thanks,
Jack
_
Do you structural or functional con maps? If structural, then you will
have to ask Anastasia.
doug
On 6/20/13 12:36 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Is there a way to use the Freesurfer and Tracula output to compute
> connectivity maps?
>
> Thanks!
>
> Sal
>
_
you might need to reduce the number of TRs
On 6/20/13 10:34 AM, A a wrote:
Hi all,
Is there a rule that let me avoid having the error message could not
force null max?
-- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3
15 --ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4
Was there an error? Look in the recon-all.log file to see
doug
On 6/20/13 10:36 AM, Deirdre O Shea wrote:
Dear FreeSurfers,
I have been using FreeSurfer for editing for the past year now and I
have recently come across an issue that I have not seen before in a
new dataset. The pial surfaces
here you go
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
doug
On 6/20/13 2:25 AM, amirhossein manzouri wrote:
Dear Doug,
I just installed 5.3 version and now I have the Xhemi. I need to study
asymmetry of the brains -processed with FS 5.1- comparing right and
left hemispheres for each subje
Try
mri_convert file.nii --out_orientation LAS file2.nii
doug
On 6/20/13 5:30 AM, Brigitte Dahmen wrote:
Dear Doug, dear freesurfers,
thank you very much! If I'd like to change the orientation (from PSR
to LAS), is there a way in Freesurfer to do it?
Thanks again!
Best,
Brigitte
2013/
On 6/20/13 5:55 AM, Laura Dekkers wrote:
Dear Doug,
Thank you for your e-mail.
As you suggested, we changed tnullmax to 6 sec and run the following
code in Optseq:
--ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0
8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.
I thought it would have worked with a single group. Maybe Nick knows of
the top of his head.
doug
On 6/20/13 12:36 PM, Manish Dalwani wrote:
Hi Doug and Freesurfers,
I realized that I hadn't updated my group levels to one group.
However, when I do that..the qdec complains about group.leve
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