Hi,
In FreeSurferColorLUT.txt (Freesurfer 5.1), there is a label for the inferior
colliculus (7100), but this structure seems only to be labeled collectively
with other brainstem structures (16) in aparc.a2009s+aseg. It appears from
posts in the mail list that only a subset of the labels in
Fr
Hi,
I am looking at functional group surface data analyzed with mri_glmfit in
tksurfer (using Freesurfer 4.1). I would like to threshold
using FDR - but only within a specified label - and then see the resulting
functional data map.
Once I have the functional dta loaded as an overlay, I have be
Hi,
I am trying to run a Monte Carlo simulation on functional data constrained to a
label using Freesurfer 4.0.1. I did not use Qdec for data analysis.
Looking at a previous post -
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html
- I see that I should: 1) constr
Hi Doug,
I am trying to run a Monte Carlo simulation on functional data constrained to a
label. Looking at a previous post -
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html
- I see that your advice is to 1) constrain when running mri_glmfit, then 2)
use mri_glm
cope2.nii --seg yourlabel.func.nii --mask zstat1.nii
--maskthresh 2 --masksign abs --o sum.dat
The cope and the zstat are now volumes.
doug
On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote:
Hi Doug,
Thanks for the quick answer. Sorry to be dense, but does this need
somewhere to include re
Hi,
I am hoping do a surface-based functional ROI analysis on subject-specific ROIs
that are both defined structurally and are masked by an all/nothing functional
contrast. func2roi-sess seems perfect for this except that my data are not in
an FS-FAST data/analysis structure, but are instead pr
Hi,
I'm resending this e-mail, as it didn't seem to go through correctly yesterday:
I’m a Freesurfer novice, and I’m confused about how to run a 3rd level
cross-subject analysis on the surface using as input cross-run .gfeats from 10
subjects generated from a 2nd level analysis in FSL.
Followi
Hi,I’m a Freesurfer novice, and am confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTu
Hi Freesurfer experts,
We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm)
data on a Philips 3T scanner using an 8-channel head coil. We are
reconstructing each subject’s surface and mapping functional data processed in
FSL’s FEAT to the surface. For some subjects, w
