Hi Gaurang
it depends on what you are trying to fix. Is it cortical gray matter? If
so, it is usually either the case that the underlying white matter is
incorrect, in which case you fix it and the gray will be accurate, or the
auto-detected class intensities are inaccurate. Can you send us an
I just realized there wasn't a question in my email below.
Is there a way to get a group z-map that is thresholded at some
statistically meaningful threshold (ie. cluster size p value) without
using mri_glmsim
and mri_glmfit? If not, how might I specify a timeseries in the design
matrix?
Thank yo
To whom it may concern:
I had question about Freesurfer, I am trying to correct the gray matter volume.
So I made changes by adding pixels to the contour, and ran recon-all.
Subsequently, when I opened up the file after performing recon-all I saw were
the pixels (which are white) that I added wh
Yes, those are the right commands. That will give you the ces (the
regression coefficient). Typically, people use the pearson correlation
coefficient (pcc), but I have not seen many differences between the two.
On 05/06/2016 05:13 PM, Martin Juneja wrote:
> Thanks a lot Dr. Greve.
>
> So as per
Thanks a lot Dr. Greve.
So as per your suggestion: I ran the command isxconcat-sess -sf sessidlist
-analysis workmem.sm05.rh -contrast encode-v-base -o my-group -all-contrasts
i.e.- without specifying -map argument. So this generates ces.nii.gz and
vesvar.nii.gz in output folder my-group.
To get t
It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by
computing the pearson correation coefficient of the residual error
between adjacent vertices. This is then averaged over all vertices to
compute a mean cor coef. A transform is then applied to compute the
FWHM. This is consi
On 05/06/2016 04:53 AM, maaike rive wrote:
>
> Hi Doug,
>
> Thanks for the reply.
>
> I'm still struggling with this issue though.
>
> 1. For instance, if one corrects surface area for ICV in the GLM,
> shouldn't the fact that this relationship is non-linear be taken into
> account? Since volum
You should not use the sig as that is the first level significance. If
you pass that to the higher level, then the results will be hard to
interpret. I think you'll want to use pcc or ces. Otherwise looks ok.
doug
On 05/06/2016 12:03 PM, Martin Juneja wrote:
> Dear FS experts,
>
> I just finishe
something is going wrong because the FWHM is not-a-number (nan). Can you
send the actual terminal output and not just the log file?
On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
> Thanks for the reply Doug. This is content of my mri_glmfit.log:
>
> -
Hi Qi,
you should process both time points together via the freesurfer
longitudinal stream. Independent processing is less sensitive. Selecting
one of the time points as a template is also bad, as it induces
processing bias, see:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessi
Hi Doug,
I wanted to figure out what is the minimum cluster extent for a given
monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the
following tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
wanted to know if freesurfer estimates the smoothness
Dear FS experts,
I just finished calculating functional connectivity maps using FreeSurfer.
I just want to confirm if the following steps I used are correct:
(1). I defined configured seed regions parameters using fcseed-config
command, say R01.config and R02.config and created seeds using fcseed
Thanks for the reply Doug. This is content of my mri_glmfit.log:
---
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/adits123/Desktop/projectoutputdata
cmdline mri_glmfit --glmdi
The problem is with the estimate of the FWHM for that run. Can you
re-run mri_glmfit and send me the command line and terminal output?
On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
> Dear FS experts,
>
> I ran into an error with one of my mri_glmfit-sim execution
> and was
If you have a label, then you can use mris_anatomical_stats with the -l
option
doug
On 05/06/2016 10:01 AM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I am trying to find the cortical thickness of my ROI which is the
> perisylvian region of the left hemisphere. What I did was to define a
Hi,
There are certainly papers in which thickness is corrected using global mean thickness, and surface area is corrected using total surface area. It is a valid approach, and one that I think is preferable to correcting by using a somewhat arbitrary adjustment
to a non-like measure
Dear FS experts,
I ran into an error with one of my mri_glmfit-sim execution and was not
sure what was going on. The same simulation is currently running for the left
hemisphere without any hiccups but I get this following error for the right
hemisphere:
Dear FreeSurfer,
I am trying to find the cortical thickness of my ROI which is the
perisylvian region of the left hemisphere. What I did was to define a label
based on the anatomical area of this region and tried to define a ROI based
on this label and the command -mri_label2volume. Howevere, I am
Dear FreeSurfer,
I am trying to find the cortical thickness of my ROI which is the
perisylvian region of the left hemisphere. What I did was to define a label
based on the anatomical area of this region and tried to define a ROI based
on this label and the command -mri_label2volume. Howevere, I am
Hi pfannmoe
what version are you using? Could you download dev and try it out and see
if it fixes your problem? I suspect it does
cheers
Bruce
On Fri, 6 May 2016,
pfannmo...@uni-greifswald.de wrote:
> Dear Experts,
>
> in most of my subjects the cortical parcellation with the Desikan-Killiany
Hi,
I am running dti data with trac-all. I followed the command:
trac-all -prep -c /Studies/*/DTI/dmrirc_subject
but it exited with error "*Note: indexing (in both time and space)
starts with 0 not 1! Inputting -1 for a size will set it to the full
image extent for that dimension." *
Before. th
Hi Doug, Thanks for the reply.I'm still struggling with this issue though. 1.
For instance, if one corrects surface area for ICV in the GLM, shouldn't the
fact that this relationship is non-linear be taken into account? Since volume
increases with r^3 and surface with r^2... Same goes for lGI,
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