Hi Doug,
the analysis is done on the cortex surface. The following commands are used for
the analysis of the functional activation in the right hemisphere cortex:
preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305
-fwhm 0 -per-run -nosmooth
plot-twf-sess -s sessionID
Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working.I'm using currently version of FS and matlab R2009b.the following error alwais apair:INFO: FreeSurfer build stamps do not matchSubject Stamp:
Gabriel,
If I am correct, your path (fsmatlab) is pointing to the matlab folder of
freesurfer distribution (I.e. Including the matlab scripts) whereas it should
point to the matlab installation directory.
You can check using the command getmatlab.
Let me know,
Marie
On 16 oct. 2012, at
Thanks Marie,You are right is pointing to the FSmatlab directory not to the installation folder, but the wiki say so:You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script. Do I need to change that in the startup.m?I did also try the getmatlab
I do not have a question on how to use the program, the wiki covered that well.
My question is about the formula embedded in the program to calculate the
contrast.
The formula is ((wm-gm)/((wm+gm)/2))*100
This creates a dynamic range of -200 to +200. Which the last time I checked is
not
Dear Marie,I've tried to set the matlab installation path, into the tcsh path (where my FS_HOME is), but It's not working. I have no idea how to change this on the startup.m, can you help me with it?Regards,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,If I am correct,
Gabriel,
I would start by adding the path to the matlab installation directory to $PATH.
On a Mac it looks like /Applications/Matlab_R*/bin. Then the getmatlab command
should work, and LGI as well.
Marie
On 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla ggon...@upo.es wrote:
Thanks
Yes, that was actually a mistake on my part. It does go between -200 and
+200.
doug
On 10/16/2012 11:02 AM, Phil Greer wrote:
I do not have a question on how to use the program, the wiki covered that
well.
My question is about the formula embedded in the program to calculate the
Marie,I'm working on centOS 4, I'd add the path to the matlab installation folder on my PATH as:setenv MATLABPATH /root/trabajo/matlab2009
setenv PATH ${MATLABPATH}/bin:${PATH}And this is not working stillAny ideas?GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,I would
... Strange, then I would just quickly look at the following things (in a new
terminal, so that you are sure that everything is cleanly set):
1) whether the $PATH is indeed correctly set without typo. Either by verifying
the $PATH variable (type $PATH in your shell, you should see your full
If you want to do a repeated measures ANOVA with more than two time
points, I've put a page together here:
http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
doug
On 10/15/2012 08:24 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote:
Hi Martin,
If you could make available
Dear Experts,
I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean
ages that are not significantly different, though ranges/median are. I want to
compare cortical thickness between groups while allowing for age (age as
nuisance factor) but also want to see if there is
I have downloaded the FreeSurfer software onto a Mac computer.
I did the setenv/source steps and got this output:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer/
FSFAST_HOME /Applications/freesurfer//fsfast
FSF_OUTPUT_FORMAT nii.gz
Hi Julia,
I'm not certain, but I think you just need to define FREESURFER_HOME
source FS again before trying to run tkmedit or qdec. The pico
$FREESURFER_HOME .license command resulted in FREESURFER_HOME: Undefined
variable., so that environment variable needs to be set. I think after
the
Hi Everyone,
Back in May I was very excited to learn that there was some movement toward
allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some
of our structural images, which could be fantastic help in subcortical
segmentations. Is this something that is still in the works
On 10/16/2012 02:08 PM, Mahinda Yogarajah wrote:
Dear Experts,
I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean
ages that are not significantly different, though ranges/median are. I want
to compare cortical thickness between groups while allowing for age (age
can you send a pic?
On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote:
Hi Doug,
the analysis is done on the cortex surface. The following commands are used
for the analysis of the functional activation in the right hemisphere cortex:
preproc-sess -s sessionID -fsd bold -nostc -surface
Thank-you Bruce!
On 16/10/12 12:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Vanessa
I'm running some tests now
Bruce
On Oct 15, 2012, at 9:10 PM, Vanessa Louise Cropley vcrop...@unimelb.edu.au
wrote:
Dear Bruce/freesurfer community,
Thank-you for offering to take
Dear Doug,
Many thanks for reply. Given the age-group interaction, and the fact that even
when age is demeaned it simply means a difference in thickness will be tested
for at age=mean age (as opposed to age=0) can I at least interpret the findings
when using DODS model with age as a nuisance
On 10/16/12 8:27 PM, MAHINDA YOGARAJAH wrote:
Dear Doug,
Many thanks for reply. Given the age-group interaction, and the fact that
even when age is demeaned it simply means a difference in thickness will be
tested for at age=mean age (as opposed to age=0) can I at least interpret the
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