Dear FreeSurfer team,
I apologize for posting this again.
I tried to run glm_fit to fit group membership. For this model, I have 3
diagnostic groups namely, HC, MCI, AD, and added lobar (Frontal, Parietal,
Occipital, Temporal) WMH as the covariates.
My contrasts are as follow:
Group membership:
Hi Shady,
Try assembling the design as this:
EV1: Group 1 (coded as 0/1)
EV2: Group 2 (coded as 0/1)
EV3: Group 3 (coded as 0/1)
EV4: Sex (coded as +1/-1)
EV5: Site (coded as +1/-1)
The contrasts to compare the three groups are then:
C1: [1 -1 0 0 0]
C2: [1 0 -1 0 0]
C3: [0 1 -1 0 0]
C4: [-1 1 0
Hi everyone,
I just installed the latest version of Ubuntu (Ubuntu 16.04 LTS) and I
reinstalled FreeSurfer (centos4). When I computed recon-all it exited with
errors (nu_correct crashed). I have attached the .log files. I have already
used FreeSurfer with older versions of Ubuntu and I have nev
actually I had forgotten that we described the basic surface deformation
to avoid dura in Andre's paper, which is what I first wrote it for:
2008 Brain morphometry with multiecho MPRAGE. van der
Kouwe, Andre J W; Benner, Thomas; Salat, David H and Fischl, Bruce
NeuroImage, 2008.
On Tue, 3
glad to hear it
Bruce
On Wed, 31 Aug 2016, Eelco Van Duinkerken wrote:
Thanks for the suggestion Bruce!That totally solved the problem! Good to
know that with the upcoming version this is solved.
Eelco
On 30 Aug 2016, at 12:36, Bruce Fischl
wrote:
Hi Eelco
we've made a bunch o
Hi rujing
that can be tough. If all your group1 are on one scanner and all group2 are
on the other how can you tell the difference between a group effect and a
site effect? At the very least you should scan some people on both
scanners.
cheers
Bruce
On Wed, 31 Aug 2016, charujing123 wrote
Hi Carol
the bigventricles stuff works much better in the upcoming 6.0 and dev
than it did in 5.3. You might try downloading dev and trying it out
cheers
Bruce
On Wed,
31 Aug 2016, Carol Nguyen wrote:
Hello FreeSurfer Developers,
I am attempting to segment a brain with large ventricles. I
Hi FreeSurfer experts,
When running mri_glmfit I am getting the error "matrix is ill-conditioned or
badly scaled, condno=10182.4"
My fsgd file is attached to this email.
My command is:
mri_glmfit --y
/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/144_GDD_Thickness_RBC_Folate/l
Freesurfer Experts,
I am currently using a Monte Carlo Z-Simulation to perform multiple
comparisons on a data set.
I have played around with various cluster forming threshold and cluster
wise thresholds.
I have no idea what would be considered "too liberal" or "too conservative"
of thresholds and
Dear freesurfer community,
we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have
been experiencing some problems with the final analysis steps.
We are using the qdec. Uploading of the data table has been successful. When we
try to use the “Analyze” command (design) in the
Dear Freesurfer developers:
I'm seeking out ways for performing multi-band slice timing correction
with freesurfer 5.3. I've searched the mailing list, and noticed that there
might be a couple of ways for doing this. But, I still have some conerns
for different ways, and please see below for my qu
Hi Ben
are the bright points segmented as wm in the wm.mgz? If so, you might try
erasing them and rerunning
cheers
Bruce
On Wed, 31 Aug 2016, Benjamin Baird wrote:
Dear Freesurfer experts,
We are currently working with some scans that were collected on a GE 3T
scanner. The goal is to analyz
Hi Kristina - I suspect there's some misregistration, or part of the brain
mask (and hence the anatomical segmentation) missing or something like
that. Do you mind uploading the tracula directories of this subject for me
to take a look at?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
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