Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of
voxel-wise cortical thickness difference between left and right hemisphere
of each subject? I need to see the difference map of left and right (lh-rh)
overlaid on both hemispheres!
On Thu, Jul 11, 2013 at 6:01 PM, Douglas
Dear Bruce,
Would you please explain how and where to acquire FLAIR or T2 images to
solve the problem?
BR/Amir
On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote:
Dear Bruce and Doug,
Thank you very much!
PS: I searched through my data folder and didn't find T2 images.
That helps! Great, thanks!
On Thu, Jul 11, 2013 at 11:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
I've attached a matlab script which should do it.
doug
On 07/11/2013 04:28 PM, Martijn Steenwijk wrote:
Dear all,
Is there a way in freesurfer to compute surface wise
Hi all,
Is there a way to ajust the camera lighting / add lights in Freeview?
Currently the lighthing is such that the surface with normal pointing
upwards are illuminated well, but the surface with normal pointing
downwards not that good.
Thanks for replies in advance,
Martijn
Hi Amir
I'm not sure I understand the question. You need to acquire them on each
subject them same way you acquire your MPRAGE/T1-weighted image. Andre van
der Kouwe (ccd) has some sequences you can use on his website if you want
guidance on parameters and such.
cheers
Bruce
On Fri, 12
Dear list,
We are buying a computer dedicated mostly to Freesurfer. Initially we
thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good
choice. However, I noticed that Freesurfer seem better tuned to use CUDA.
Many of the messages I read are from 2010 so I am not sure whether this
Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Amir
I'm not sure I understand the question. You need to acquire them on each
subject them same way you acquire your MPRAGE/T1-weighted image. Andre van
der Kouwe (ccd) has some sequences you
Laura, what is the coefficient of variation? Ie, the stddev/mean
doug
On 07/11/2013 08:54 AM, L. Koenders wrote:
Dear FreeSurfer experts,
We have a question regarding the aparc output from the stats files, and
hopefulle you can help us.
We have 4 independent groups, of about 30 subjects
Dear Freesurfers,
My inflated surface looks smooth in tksurfer, but white matter surface has
holes in it. Is this an indication of topological defects?
Thank you very much!
Sincerely,
Ye
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Hi Ye
almost certainly not. Try running mris_euler_number - it will tell you
the topology of the surface (which is the same for inflated/white/pial/...)
cheers
Bruce
On Fri, 12 Jul 2013, ye tian wrote:
Dear Freesurfers,
My inflated surface looks smooth in tksurfer, but white matter surface
Thanks a lot!
On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
It is the difference but it is on the tesselation of the left hemisphere.
If you want it on the right hemisphere, then you need to perform the
analysis on the right hemisphere.
doug
On
I have the Yeo resting-state fMRI atlases which I downloaded from
http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
They consist of 3 versions, fsaverage being of interest here. The
fsaverage folder provided includes the typical FS folders corresponding a
recon-all for the average
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am running this
ROI follow-up with 5.2.0, could that be a problem? From the release notes, it
didn't look like it would be an issue)
Anyway, I've run the following set of commands:
funcroi-config -roi
Dear freesurfers,
I'm working on a function to import automatically the segmentation
folder into a Brainstorm database. I have a few questions:
- Is there a way to read/get the position of the anterior and
posterior commissures (AC/PC)?
- What file should I read to get the labels
Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am
running this ROI follow-up with 5.2.0, could that be a problem? From
the release notes, it didn't look like it would be an issue)
No, that is
On 07/12/2013 07:18 PM, François Tadel wrote:
Dear freesurfers,
I'm working on a function to import automatically the segmentation
folder into a Brainstorm database. I have a few questions:
- Is there a way to read/get the position of the anterior and
posterior commissures (AC/PC)?
What
Is it possible to combine the lh and rh annotation files into a single
annotation file? How?
-Jeff
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The information in this e-mail
Hi Jeff, do you just want to map the annotations from fsaverage to your
individual subject? If so, you can use mri_surf2surf, something like
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh \
--sval-annot $SUBJECTS_DIR/fsaverage/label/lh.aparc.annot \
--tval
Hi Sarah, I can image several ways to do this. If you can go onto the
surface and find an index that you want to be the center, then you can
create a label file with a single point. It would look something like
this (see fsaverage/label/lh.cortex.label for example):
I followed the tutorial:
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 12, 2013,
In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g.,
cache.th20.pos.sig.ocn.annot), the names of the clusters take the form:
cluster0
cluster-001
cluster-002
…
but the last one is of the form
cluster6
which is to say, no dash and no zero-padding.
I assume they are meant to have a
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