Hello.
We recently installed Centos 7 with cuda 8 and tried to build the
FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so.
Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing
to share the binaries with us or share their steps with us? We will greatl
Hi, all.
Is there a 3D MNeI space version of Desikan-Killiany Atlas? (e.g. a sample
3D parcellation using MNI152 brain)
Please let me know where I can find it or how I can get it in using
Freesurfer.
Thank you very much!
Sincerely,
Kwangyeol Baek
___
Dear experts,
I am using freesurfer V5.3. I am trying to fix some error in freesurfer outputs.
The issue is that grey matter misclassified as white matter in temporal lobe
(lh). I tried to edit Wm.mgz and re-run with -autorecon2-wm, but it did not
work.
Looking at the brainmask.mgz, white matter
nsform to the T1. It
> takes longer, but it works.
>
> Gabriel
>
> [image: Inline image 1]
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Dear FreeSurfers,
I received FreeSurfer structural MRI brain data to analyze, but there are some
questions about specific FreeSurfer variables that I could not find answered on
your wiki or in the mail archive:
1.- "Non-White Matter hypointensities":
1.a - Are these the same thing as "gray matt
Hi Karteek
the aseg isn't surface based, sorry, but the watershed that we use to do
the skull stripping is and does use smoothness constraints. If it is
leaving dura around try using mri_gcut.
cheers
Bruce
On Thu, 18 May 2017, Karteek Popuri
wrote:
> Hi,
> My goal is to use the best possible
You can use the aseg.mgz (in v6) or aparc+aseg.mgz in any version.
On 05/18/2017 10:42 AM, Karteek Popuri wrote:
> Hi,
> My goal is to use the best possible skull-stripped version of the input MRI.
> Is brainmask.mgz the one? or I was wondering if anyone has tried improving
> the brainmask.mgz
Hi,
My goal is to use the best possible skull-stripped version of the input MRI. Is
brainmask.mgz the one? or I was wondering if anyone has tried improving the
brainmask.mgz further by masking it out using the aseg.mgz. Will that help with
regards to getting rid of the dura in the brainmask.mgz.
I don't know of a tool that would do it. I could imagine measuring the
spatial autocorrelation function, then running the MC simulation using
that instead of a gaussian (AFNI added this, but it only runs in the
volume). Getting a particular ACF on the surface would be hard.
On 05/16/2017 08:00
how were you examining the registration? When I run the command, the
rh.white.mgz aligns perfectly with the T1.mgz
On 05/16/2017 05:38 PM, Gamaliz wrote:
> Douglas,
>
> The previous message had an images attached that seemed to be too big.
> it was "bounced" automatically. I guess too many imag
1. No, we usually do wm edits/control points first as this can fix the
pial problems.
2. You can put control points in any voxel that is clearly WM with no other
tissue class partial-volumed into it. The intensity threshold depends on
the MR sequence, where you are in the brain and possibl
You will want the "Mean" column. The value is
100*(W-G)
GWC = -
0.5*(W+G)
The area is the surface area of the label. The "SNR" is the spatial mean
gwc divided by the spatial stddev gwc, probably not very useful
On 05/17/2017 01:43 PM, Yaakub, Siti Nurbay
Hi Martin,
Thanks a lot.
So it is uncorrected. Can one use the following cmd to do multiple
comparison correction?
mri_glmfit-sim \
--glmdir lh.testretest.thickness-pc1.fwhm15 \
--cache 4 neg \
--cwp 0.05\
--2spaces
I tried to run above cmd, it shows
ERROR: thresh = 4,0, must be 1.3,
Dear FS team,
I have two questions regarding manuel editing. We were looking at inter-rater
reliability, but noticed it was not too high... However, during editing we used
different criteria. Therefore I would like to ask:
1. Does the order of pial correction, topological deficit, wm cor
Dear All,
At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre
of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo
University Hospital and Diakonhjemmet Hospital, Norway, there is a position
available as a postdoctoral student with employment at Diak
Hi Martin,
Thank you this helps !
Please find last question below inline.
Best,
Matthieu
Le 18 mai 2017 10:33 AM, "Martin Reuter" a
écrit :
Hi Matthieu,
1) you would put a column of score and a column of score X time. The first
allows you to test if the intercept changes based on scores (e
Hi Matthieu,
1) you would put a column of score and a column of score X time. The
first allows you to test if the intercept changes based on scores (e.g.
if hippocampal volume is affected by the score, controlling for whatever
else you included, e.g. age and gender etc) and the second interac
Hi Jahanvi,
there should be a way to display the bar, but I don’t know how (others will
know)!
sig is not FDR corrected.
Best, Martin
> On 18 May 2017, at 08:56, jahanvi patel wrote:
>
> Hi Martin,
>
> Thanks a lot for the reply. Is there a way to display the bar in effect size?
> And is
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