Hi,
Reviewing the results of recon-all I noticed that
the segmentation of wm and gm was OK but that
the computed pial surface chopped away an
unacceptable amount of gm voxels, too many to
manually edit. Is there a way to cure this problem
by choosing some options?
I used version 4.5.0 on a Mac
Hi,
how does freesurfer perform on brains with tumor? Are the any specyfic
options that could improve the results (like masking for example)?
Cheers,
Chris
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I think the results may be quite unpredictable. It depends on the size of
the tumor, the infiltration, the necrosis, etc.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.4
Dear Optseq Developpers,
Few years ago we used to design our paradigm with optseq. We would
like to use it again but we can't install it.
We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/
we download the linux version 2
we upload it to the our old linux server with matlab
Liang,
We have a very good tutorial which takes you through what you would like
to do. It's located here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual
There is also some information on registration here:
Xiaoying,
There are directions for how to do this located here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions
Allison
--
On Fri, 12 Mar 2010, Xiaoying Tang wrote:
Hi all,
When we do recon-all, we usually do autorecon1, autorecon2,
Ed,
Usually a problem with the pial surface indicates a problem with the white
surface and fixing the wm.mgz will fix the pial. But you said the wm
segmentation is okay in the areas where the pial is a problem?
What area of the brain are you finding this problem?
Allison
--
On Fri, 12 Mar
Hi Ed,
we can't possibly diagnose this without seeing some images.
cheers
Bruce
On Fri, 12 Mar
2010, Ed Gronenschild wrote:
Hi,
Reviewing the results of recon-all I noticed that
the segmentation of wm and gm was OK but that
the computed pial surface chopped away an
unacceptable amount of
Hi Chris,
it depends on where the tumor is and how big it is. It it's within the wm
you could certainly just fill it as a wm edit and things should work.
cheers
Bruce
On
Fri, 12 Mar 2010, Chris Filo Gorgolewski wrote:
Hi,
how does freesurfer perform on brains with tumor? Are the any
Hi Allison,
You are so helpful. Thanks a lot.
Best,
Xiaoying
- Original Message -
From: Allison Stevens astev...@nmr.mgh.harvard.edu
Date: Friday, March 12, 2010 7:43 am
Subject: Re: [Freesurfer] problem on recon-all
To: Xiaoying Tang xta...@jhu.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or
Inf') that has been posted before on the mailing list but I couldn't find a
solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3.
The output of the log file is:
selxavg-sess
Hi all,
After autorecon3, there are two files named wm.mgz and wmparc.mgz. What's the
difference between this two? If I just want the white matter, should I use
wm.mgz or wmparc.mgz? The corresponding grey matter is aparc+aseg.mgz.
Looking forward to your early reply.
Best,
Xiaoying
Did you make it executable? They are run from the shell, not matlab.
doug
Florence POMARES wrote:
Dear Optseq Developpers,
Few years ago we used to design our paradigm with optseq. We would
like to use it again but we can't install it.
We went on the web site :
hmmm, something is going wrong with the whitening. Can you try it
without whitening? Also, look in the 4d volume for some artifact (eg, a
spike). This might account for it.
doug
Leila Reddy wrote:
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain
NaN or Inf') that
Hi Xiaoying,
the wm.mgz is our preliminary estimate of the white matter (a binary
segmentation). The wmparc.mgz is the labeling of the interior of the
white matter by proximity to cortical folds (and it occurs much later in
the analysis)
cheers
Bruce
On Fri, 12 Mar 2010, Xiaoying Tang wrote:
I want to compare 2 different experimental conditions that were
scanned within different runs. For example assume that, in ten runs I have had
conditions 1 and 2 and in another ten runs I have had condition 3 and 4. Now I
want to compare condition 1 and 3. Is it possible?
Regards Shahin
Hello everyone,
I have a colleague (cc'd) who is interested in using FreeSurfer's
segmentation with DTI results he obtained with TBSS. I am not sure
how he should go about this. Any advice is appreciated.
Thanks,
Dana
Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology
Hi Dana,
I guess the easiest thing to do would be to pool FA values by wmparc
region. I'm not sure that using tbss is needed for that though. Did you
have something else in mind?
cheers,
Bruce
On Fri, 12 Mar 2010, Dana W. Moore wrote:
Hello everyone,
I have a colleague (cc'd) who is
Hi,
I'd like to convert a label from fsaverage/MNI-space to the space of a
subject's unpacked, unreconstructed, dicom-format scan. Will this be
possible?
Thank you,
Jesse
--
Jesse Friedman
Martinos Center for Biomedical Imaging, Manoach Lab
Massachusetts General Hospital
149 13th Street #
Hi Allison,
Thanks for the website you provide me. Through reading, I understand how to
averaged extract contrast effect size in each ROI generated by FreeSurfer
(e.g. aparc.a2009s+aseg.mgz). You know, the contrast image is a 3D file for
each subject. However, BOLD data usually is a 4D image
Hi FS experts,
I find that FS does make a great skullstrip and extract a perfect brain (ie.
brain.mgz). I am thinking to register this brain to MNI152 standard space
using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to
subject-specific native space (224*256*176, 1mm). Thanks in
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