Hi,
Is there a way to address or account the effects of partial voluming
when sampling grey matter intensity (mri_vol2surf)?
In particular, where there is cortical thinning, I'm also finding
intensity changes that could either be due to changes in the amount of
partial voluming or a change in
I put it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/isxconcat-sess
If you just want to concatenate the vertex values, then just do
something like
mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz
sess2/bold/analysis/contrast/ces.nii.gz ...
On
can you send the two command lines you ran?
On 04/27/2015 02:53 PM, Alshikho, Mohamad J. wrote:
Hi Doug,
I am working on a GLM for functional connectivity analysis. I made simple
FSGD file for two groups + NO covariates then I ran the following command
line on the right hemisphere and the
You can mri_concat the cesvar files. For the dof, just add up the dofs
in each run.
On 04/27/2015 05:08 PM, Reza Rajimehr wrote:
If I use mri_concat instead of isxconcat-sess, will I have all the necessary
files for fixed-effects averaging by mri_glmfit? Specifically, can I generate
If I use mri_concat instead of isxconcat-sess, will I have all the
necessary files for fixed-effects averaging by mri_glmfit?
Specifically, can I generate cesvar.nii for --yffxvar and ffxdof.dat
for --ffxdofdat in mri_glmfit?
Reza
I put it here:
I ran only one command line :
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C
Contrast1group.diff.mtx --C Contrast2group1.mtx --C Contrast3group2.mtx --C
Contrast4g1g2.intercept.mtx --surface fsaverage lh --glmdir glm-fsgd-2G0C.wls
--nii.gz
This command ran smoothly on the right
Hi,
editing the long does not really introduce much bias I think. It is
usually not necessary and it is not recommended, because often it
problems in the long are caused by earlier problems in the base or even
cross, so it is best to fix it there. Your case seems to be different
(problems
Hi Konrad
if you read Rebecca Shafee's recent paper:
http://www.ncbi.nlm.nih.gov/pubmed/25449739
you can see what we do about this kind of thing. The stream is largely
undocumented but you are welcome to try it out if you like.
cheers
Bruce
On Mon, 27 Apr 2015, K. Wagstyl wrote:
Hi,
Is
Hi Bruce,
Thanks for this. I did see this paper and would like to try the
correction method - is it included in a new release of freesurfer or is
it a separate script?
If it's separate, would it be possible to try it?
Many thanks,
Konrad
On 2015-04-27 13:43, Bruce Fischl wrote:
Hi Konrad
Thanks Doug! Could you clarify a bit more on how to add up the dofs
in each run?
You can mri_concat the cesvar files. For the dof, just add up the dofs
in each run.
On Monday, April 27, 2015, Reza Rajimehr rajim...@gmail.com wrote:
If I use mri_concat instead of isxconcat-sess, will I have
Eachoutput.nii.gz sess1/bold/analysis folder will have a dof.dat file
with a number in it. Add up all those numbers, create a files with the
sum in it, and pass that file to mrI_gomfit.
On 04/27/2015 06:18 PM, Reza Rajimehr wrote:
Thanks Doug! Could you clarify a bit more on how to add up the
Hi Doug,
I am working on a GLM for functional connectivity analysis. I made simple FSGD
file for two groups + NO covariates then I ran the following command line on
the right hemisphere and the left hemisphere.
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd fsgd --C
Thanks Doug! Could you put the updated isxconcat-sess script in an ftp
server and provide a link so that I can download it? I do not have
access to the dev environment.
Now I should run the command with the flag -trgsubject F99, right?
My analysis is on the surface, and I only want to
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