Hi all,
I'm doing some analyses which involve GM volume . It might sound trivial but I
wonder how could GM calculation be done in freesurfer? Is there a way to
compute it based on GM between white and pial surfaces, and will the result of
that approach be different from using what is given by a
Hi, is FS v4.0.5 for Leopard still available? I upgraded from Tiger
and would like to keep the same version for my analyses, but cannot
find the previous version on the ftp site.
Thanks,
Ming Hsu
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Hi Anderson,
at the moment we don't do any GPU programming, but are actively looking
into it and may have something in the not-too-distant future, so I think
you are ok with no graphics card from our perspective. We do use some of
the computational routines in vtk though, so you'll need that e
Anderson,
The freesurfer processing stream (aka, 'recon-all') does not use a
graphics card for processing (yet, we hope to implement some GPU stuff
someday), so your cluster doesnt need any graphics cards, other than
those for actual display usage (tksurfer, tkmedit, etc.).
Nick
On Mon, 2009-01
Dear all,
We are considering to buy a blade system, and FreeSurfer would be one of the applications to run on it. We know that a 3D graphics card, with support for OpenGL and built-in memory+GPU, is recommended. What we are not sure is whether it is mandatory for all the FreeSurfer routines, of if
Hi Martin,
for the MS study we were *very* careful to make sure that the white
matter in the regions of detected effect was normal appearing, so I don't
think it explains the thinning we saw. As for the effect you are seeing,
you'll need to look through your individual subjects to see if this
Hi,
I have been running quite a few clinical subjects (close to 300) through FS
pipeline and comparing cortical thickness from parcellated cortex for each
individual subject to its agematched controls. The subject clinical symptoms
are not specific, ranging from amnesia, reduced ability to gene
It does not do Spearman. It uses a GLM, which is more-or-less a
generalization of Pearson.
doug
Xie, Hong wrote:
According to SPSS, when calculating a correlationship for ordinal
data, select Spearman model; for interval data, use Pearson model. If
qdec deal with pain scale as continuous vari
According to SPSS, when calculating a correlationship for ordinal data, select
Spearman model; for interval data, use Pearson model. If qdec deal with pain
scale as continuous variable, Pearson model should be used. But pain scale is
interval data, Spearman model seemly be correct. Dose qdec hav
why not a continuous model? what model do you want to use?
Xie, Hong wrote:
Thanks a lot. This scrip seemly describes F-test or T-test. In my
study, I want to analyze the correlationship between patient's
cortical thickness and pain scale (from 0 to 6). After I create data
table. Qdec automati
Hi,
For my group analysis I am thinking of reusing a specific set of cortical ROIs
from already published data. I suppose that a target template (fsaverage) and
ROIs itself should be sufficient to have. If I use the same fsaverage for my
cohort, I should be able to get the data out of the ROIs
Thanks a lot. This scrip seemly describes F-test or T-test. In my study, I want
to analyze the correlationship between patient's cortical thickness and pain
scale (from 0 to 6). After I create data table. Qdec automatically put pain
scale into continuous variable category. Actually, pain scale i
Not with QDEC, but you can write your own FSGD, See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Xie, Hong wrote:
Hello,
Thank you for answering me. I searched mailing list and read this
answer email:
/I see that group.levels has four levels. Unfortunately, right now
qdec only supp
Hello,
Thank you for answering me. I searched mailing list and read this answer email:
I see that group.levels has four levels. Unfortunately, right now qdec only
supports two levels for a discrete factor. One the features in the works is to
increase this.
Nick Schmansky
Wed, 27 Feb 2008 11:0
it does not have that option, so you'd have to split
doug
Jeff Phillips wrote:
Hello all,
I am wondering if the FS FAST retinotopy analysis can deal with
within-run alternations of stimulus direction. I have collected data
in which eccentricity and polar angle were manipulated in separate
Hi Lars, I would use the 2nd one. See
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Lars Tjelta Westlye wrote:
Hi,
we have structural data at two time points (t1/t2) for two different
groups (intervention vs control). After processing the data using the long
stream, we want to model
Hi,
we have structural data at two time points (t1/t2) for two different
groups (intervention vs control). After processing the data using the long
stream, we want to model the group X time interactions to detect
intervention specific changes in cortical thickness over time.
Q1) How would you sug
Hi Christine,
yes that is essentially what is measure in ?h.sulc - the integrated signed
dot product of the movement vectors during inflation with the surface
normal (so outward movement in sulci is positive). Certainly you can
specify sulc in mris_anatomical_stats, although I can't remember i
Hello all,
I am wondering if the FS FAST retinotopy analysis can deal with within-run
alternations of stimulus direction. I have collected data in which
eccentricity and polar angle were manipulated in separate runs, but within
each run, a cycle of stimulation in one direction was followed by a c
Perfect fix!
Thanks so much...
Jenifer
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The current stream actually does not run with fixation -- all the fmri
data need to have wedge or ring stimulation. The design matrix is just a
bunch of sines and cosines, nothing fancy.
Jeff Phillips wrote:
Hello all,
I am performing my first retinotopy analysis, and I'd like to get some
mo
Is there any way of measuring sulcal depth with FreeSurfer?
Or is sulcal depth simply measured by the positive values in ?h.sulc - i.e.
negative values are 'gyral heights' and positive values are 'sulcal depths'?
If so is it possible to calculate these values for certain parcellated
regions such a
Hello all,
I am performing my first retinotopy analysis, and I'd like to get some more
information about the model created by paradigm files in the retinotopy
analysis. Specifically, I am unsure whether to include or exclude fixation
periods from the ends of my retinotopy runs. I imagine the ana
Jenifer,
We've seen this on RHEL5 platforms (although there has been no relation
to fsl). A work-around is to add this to the end of
your /etc/X11/xorg.conf file:
Section "Extensions"
Option "Composite" "false"
EndSection
and restart X (Ctrl-Backspace).
You might need to substitute 'Disabl
Hi Kelly,
did you check the aseg.mgz? Did it separate them properly?
cheers,
Bruce
On Mon, 12 Jan
2009, Kelly Silva wrote:
Hello,
I´m sending an image and I want to know how is the best way to separate
cerebelum from the cortex with the preservation of the both structures.
Thanks!
Hi,
Running FSv405 on RHEL5. Recently obtained new error when qdec was
attempted. Have successfully run qdec before on this box using FSv405.
Only update made was to upgrade to FSLv412. Same error persists after
restarting X. Both tkmedit and tksurfer work fine.
Any ideas how to fix?
Many Thanks,
Hi Adrian,
If you run it again can you replicate the crash? If so, can you send us the
subject so we can fix it?
cheers,
Bruce
On Mon, 12 Jan 2009, Adrian
Williams wrote:
Dear all
Came across a segmentation fault while running recon-all, specifically
during mris_make_surfaces... Output
Dear all
Came across a segmentation fault while running recon-all, specifically
during mris_make_surfaces... Output pasted below...
Any ideas/help greatly appreciated!
Adrian.
--
Adrian L. Williams, PhD
Centre for Cognition & Neuroimaging
Brunel University
Uxbridge
Middlesex
UB8 3PH
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