Thanks Bruce,
When you say the atlas itself is included in the Freesurfer distribution,
do you mean there is a 3D version of it available in the download?
Also, I am not looking for the individual subjects' images, I just want a
copy of the final atlas as a 3D image in analyze/nifti format. (i.e.
Hi Eric,
the talairach.xfm will not be overwritten. When run recon-all the first
time, it creates two files: talairach.auto.xfm and talairach.xfm, which
have the same contents. When you edit the registration, it changes the
talairach.xfm. When recon-all is run again, it sees that the
talairac
Hi,
I have a few very basic clarification questions regarding the recon-all
processing pipeline.
I am currently following the instructions here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Near the end of the page, it instructs me to rerun the whole process using
my new talairach
hi john,
thanks. that's the idea, but what i want is that sub-division is done
within regions that are either determined automatically through the
freesurfer classifier or through manual parcellations. not a fixed template
of parcels that's transferred via the spherical registration.
cheers,
sat
Liz,
a 64bit build is in the works. in the meantime, you can get a version
of mri_robust_register built for lion (64b) here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-lion/
Nick
On Tue, 2012-10-02 at 12:12 -0400, Martin Reuter wrote:
> Hi Liz,
>
> I have no idea about
Would the Lausanne2008 template from the connectome mapping toolkit not do
the trick?
http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html
On 3 October 2012 23:18, Satrajit Ghosh wrote:
> hi bruce,
>
> is there a way to divide consistently (same number of regions
hi bruce,
is there a way to divide consistently (same number of regions and one to
one correspondence - obviously not the exact same areas) across subjects
within aparc regions?
cheers,
satra
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h
You are right, no need to
Bruce
On Oct 3, 2012, at 5:46 PM, Gregory Kirk wrote:
>
> if there is extra skull left after skull stripping but the pial surface is
> fine ( i.e. the left skull did not get
> included in the pial surface ) is it nessesary to adjust watershed parameters
> or manuall
if there is extra skull left after skull stripping but the pial surface is fine
( i.e. the left skull did not get
included in the pial surface ) is it nessesary to adjust watershed parameters
or manually
remove it and reprocess the data set ? I am thinking it is not needed if it is
not causing
Dear all,
I need to measure the distance between 2 points on the same hemisphere for
subject A, in the common surface space as I have to compare it with the
distance between other 2 points for subjects B, C...
I used
mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1
sulc
Not sure.
Maybe try the updated scripts
From
http://martinos.org/~mreuter/long/
Best Martin
Alexandru Hanganu wrote:
>Dear Freesurfer Experts,
>
>While performing the long_mris_slopes cmd, we receive an error:
>
>---
>SUBJECT pls_pd_base00 Running Withi
Hi, FreeSurfer experts
Currently, I am planning to run tractography using wm surfaces as seed masks
and pial surfaces as stop masks implemented in FSL. In order to make fibers go
through one hemisphere to another, I need to remove the medial wall from both
seed surfaces and the pial surfaces. H
Actually, the white matter is affected too within the resection bed.
Just to make sure, using mri_label2label with surface option to pass a
label from subject 1 to subject 2 is equivalent to registering that label
to fsaverage via sphere.reg for that subject, then transferring the label
from fs av
I am running the freesufer on ubuntu and working fine without any other
configuration. I followed the configuration and it is simple
http://mirko.windhoff.net/how_to/install_freesurfer_on_ubuntu
azeez
> From: dkim...@cw.bc.ca
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Wed, 3 Oct 2012 13:03:49
Hello freesurfer users!
I've got a brand new PC with Ubuntu 12.04 64-bit running and following the
freesurfer developer's guide to set up a developer environment, I'm getting
numerous "undeclared function / undefined type" errors during make.
Seeing that the undeclared functions or variable type
Dear Freesurfer Experts,
While performing the long_mris_slopes cmd, we receive an error:
---
SUBJECT pls_pd_base00 Running Within-Subject GLM
Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ...
mri_glmfit --y
/Applications/freesurfer/subjects
Yes, you're right. But in that case, these changes would be quite similar
for right-hippocampus too.
Based on my analysis and literature, Freesurfer has more accurate measures
than FSL. The doctors are quite conservative about boundaries so that
measures are the smallest between Freesurfer and FSL
Hi Ana
the point is that even if you aren't segmenting individual structures, if
some are not in your manual protocol but are in ours, then lateralization
in them will cause lateralization differences in the degree of overlap
between the two
cheers
Bruce
On Wed, 3
Oct 2012, Ana Arruda wrot
I haven't gone so far. I've just done the simplest way. I've search the
proper commands just to do the hippocampus segmentation, but not its
subfields. All my analysis was made with the left and right-hippocampus
volumes from the *aseg.stats *file.
___
Fr
kind of. There are natural lateralizations in the brain that are taken into
account. Not sure what is known about lateralizations of hippocampal
subfield and white matter components though
Bruce
On Wed, 3 Oct 2012, Ana Arruda wrote:
> Thank you very much!
>
> About the previous question, do
Thank you very much!
About the previous question, do the softwares use the same criteria for
each hippocampus?
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The information in th
Hi Daniel,
1. Do you mean the atlas or the parcellation of your subjects? We cannot
distribute the individual subjects in the atlas as the data was collected
under an IRB long ago that didn't include this. The atlas itself (summary
statistics derived from those subjects) is included in the Fre
Dear experts,
I have a couple of questions regarding the cortical parcellation atlas that
is used in Freesurfer:
1) I would like to know if it is possible to obtain the Desikan-Killiany
atlas in 3D analyze/nifti format. With each region of the brain assigned a
discrete integer number (for example
Hi Ana
yes, our Neuron (2002) and NeuroImage (2004) papers describe the
techniques.
cheers
Bruce
On Wed, 3 Oct 2012, Ana Arruda wrote:
I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer,
don't
I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer,
don't have a different away to operate in either hippocampus. Do you agree?
That way of operating confuses me on how to interpret the differences fo
Hi Rashmi,
I assume you've read the skullstrip wiki page, but I've included it below
just in case.
Have you tried different watershed thresholds? Also, you do not need to
include the -clean-bm flag every time. You can run the skullstrip step
once with the -clean-bm to start from scratch, and
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