Have you checked if the registered segmentation and the FA map align correctly
in freeview?
On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A"
wrote:
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Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer
aparc.a2009s+aseg+2mm parc
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Dear Zhac,
Apologies for the mistake in the wiki. As explained in the error message, the
subjects directory is the second argument. Also, if you are using a T2 scan, I
would replace t1 by t2 in the last argument.
The call should be:
(For a T1 addition
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Hi Freesurfer Team,
I want to add additional scan my thalamic segmentation. but my code is not
working. where is the error in my code?
thanks for help
my code:
segmentThalamicNuclei.sh MS14
/Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz
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Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer
aparc.a2009s+aseg+2mm parcellations.
I did the following:
1. Recon-all to obtain --> aparc.a2009s+aseg+2mm
2. TBSS in FSL to obtain --> all_FA_skeletonised
3
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Thanks!!!
El vie., 23 nov. 2018 17:31, Bruce Fischl
escribió:
> Hi Rosalia
>
> try changing the window/level or min/max in the display of the volume.
> Although the brainmask intensities are irrelevant. Anything <5 will be
> masked out, so as long as
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Hi freesurfer-experts,
I am currently trying to run mris_prepoc. However FreeSurfer keeps telling me
that there are no subjects specified.
Thus, I think that the fsgd-file I created is the problem.
I already checked it several times but still don’t
Hi Mahshid
you need to give us a lot more information. What didn't work? We need the
full command you ran and the full screen output (in text form please, don't
send us a snapshot)
cheers
Bruce
On Fri, 23 Nov 2018, Mahshid Fouladivanda wrote:
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Hi Rosalia
try changing the window/level or min/max in the display of the volume.
Although the brainmask intensities are irrelevant. Anything <5 will be
masked out, so as long as it more-or-less outlines the brain v nonbrain
boundary you should be fine.
cheers
Bruce
On Fri, 23 Nov 2018, R
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Dear Freesurfer Developers,
I have a 2-part question:
1) I was advised to use permutation to control for multiple comparisons
in an LGI analysis, would you mind elaborating how to do this in command
line (in terms of command and parameters)?
2) In run
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Hello Rashid,
I would start with getting a cmake command to succeed to try and do the
build. Try looking over the cmake build page here,
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake
- where there is also makefile (makefile.wiki) you can downl
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Dear Mahshid,
could you provide some more details on what exactly is not working? E.g., Did
the installation complete without errors? What command are you typing, what
result do you expect and what is the actual result / error message?
> On November
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Hi Dear experts,
I downloaded and installed freesurfer on CentOS without any problem and also
worked with it. Recently I've switched on mint 19 (an Debian based operating
system) and I tried to setup freesurfer but, it does not worked. I would
appre
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Dear Free Surfer experts,
I am experiencing a problem with 4 participants. Whrn I open the brainmask
with freeview, it appears white (binarized). I was editing this brainmask
and at sone point I switched something and it changed to white. I deleted
alk
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