Hi Scott - The bedpost outputs are expected to in a directory called
dmri.bedpostX under the subject's trac-all output directory. You can put
all your bedpost outputs there and proceed at your own risk!
There's a description of other trac-all outputs from the steps before
bedpost here:
http://
Hi,
does anyone know what to do here please? I can see it in file manager.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz CG
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
reading aseg from
/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/ase
What is aparc+aseg-in-highres.mgz?
On Jun 15, 2011, at 5:16 PM, "Sudhin A. Shah" wrote:
> aparc+aseg-in-highres.mgz
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The informati
Hi Ariel
You can use mri_binarize to extract just the label you want and visualize is
(or mri_extract_label)
Cheers
Bruce
On Jun 15, 2011, at 4:48 PM, Ariel Brown wrote:
> Hi There,
> I'm trying to come up with an image of the amygdala to display on a
> single subject's brainmask.mgz. Can
Hello,
If I already ran bedpostx on my diffusion data, how can I skip this step in
tracula and still get it to run smoothly.
Thank you,
Scott
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
One quick question: how to convert hippocampal subfields back to FS space?
Wayne
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for
Hi Shashwath:
The QDEC model in FS will allow you to do this. The website has all the
details.
best,
Alan
On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda wrote:
> Hello Freesurfers - I just finished up with some group ROI analyses on
> thickness and surface area measures derived from Freesurfe
Hi,
I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the
default aparc
mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this
works
But how do I specify aparc+aseg-in-highres.mgz
I tried --aparc+aseg-in-highres but it was not recognised..
Than
Hello Freesurfers - I just finished up with some group ROI analyses on
thickness and surface area measures derived from Freesurfer. Basically ran
the recon-all command, extracted individual ROI measures from the aparc and
aseg files and did my between-group analyses in SPSS. Now, i'd like to
displa
Hi There,
I'm trying to come up with an image of the amygdala to display on a
single subject's brainmask.mgz. Can I display the aseg labels
individually in tkmedit?
Thanks so much,
Ariel
---
Ariel Brown, PhD
Research Fellow
Department of Psychiatry
Mass General Hospital & Harvard
becca,
it should be fixed now. for some reason the world-readable bits were
cleared on that directory.
you can email me directly (or krish) if you encounter any other read
permission problems with the nmr center installation.
n.
On Wed, 2011-06-15 at 13:33 -0400, Rebecca Dautoff wrote:
> Hi a
You are guaranteed not to have overlap regardless of what you do as
there is only one label at each voxel. For Cortex, what you have is
fine. For subcortical, you can use what is in
$FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
which can be ignored.
doug
Sudhin A.
Hi,
I did a fresh download and install of the FS-5.1.0 for CentOS_x86_64
and I am not finding the cvs_avg35 template in
$FREESURFER_HOME/subjects. Plus the cvs settings text file is not
there either. In contrast Mac distribution has it. Is there any
problem with cvs on CentOS_x86_64 platform?
Tha
Hi all
we are having trouble accessing stable5/subjects/fsaverage and are
wondering whether this is permanent and we should move out symbolic links
to stabel5_1_0
thanks,
becca
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.m
It's under review! In short, this is not a purely data driven approach.
It's data + prior info on the anatomy of the tracts derived from a
manually labeled set of subjects. The prior info is the anatomical
segmentation labels that surround the tract. So the knowledge that the
neuroanatomist w
Hi,
Is there anyway to know all the label #s that are in aparc+aseg-inhighres.mgz.
Thank you,
S
On 06/13/11, "Sudhin A. Shah" wrote:
>
>
> Hi Sorry for bothering you again, but I am not sure I understand.
>
> I was running whole brain correlation analysis (voxel by voxel). BUT for
> comp
Hi Anthony
we are trying to get that piece of it published :) Hopefully soon!
Bruce
On Wed, 15 Jun 2011,
Anthony Dick wrote:
Good points Bruce. I guess I am more worried about the people using it, who
will not be as cautious for large datasets. Also--one thing that was a huge
benefit for th
Good points Bruce. I guess I am more worried about the people using it,
who will not be as cautious for large datasets. Also--one thing that was
a huge benefit for the cortical parcellation was a quantification of the
manual vs. automated parcellation differences, but this does not appear
to be
Hi Anthony
we included the tracts that we found that we could segment reliably, under
the guidance of a trained neuroanatomist. Certainly we can only do as well
as the information contained in the diffusion data, but we have found that
we can automated what someone with neuroanatomical experti
Hello Anastasia,
This just reinforces my point. Tracts #7 and #8 of that paper are the
inferior longitudinal fasciculus and the inferior occipitofrontal
fasciculus, respectively. But you have chosen to leave one out
(incidentally, both appear in the Oishi atlas). Note that in this paper,
the a
Hi Anthony - The labeling was done based on Wakana et al 2007. We did not
include the IFOF exactly b/c of the controversy surrounding it.
a.y
On Wed, 15 Jun 2011, Anthony Dick wrote:
Hello all,
Is there any atlas to which these tracs are referenced? For cortical
anatomical boundaries there
Hello all,
Is there any atlas to which these tracs are referenced? For cortical
anatomical boundaries there is broad consensus and a published
referenced atlas, which makes Freesurfer's automatic parcellation of
cortical regions an excellent tool. But there is not (as is often
assumed) as bro
Hi Anastasia,
Thanks for getting back to me and well done on making a very nice program.
The first tracts I would like to have are the optic radiations, but there
are others that would be nice to include: a three part arcuate fasiculus (a
la Catani et al., 2005) rather than a 2 part one, Fornix, a
Hi Seán - Which tracts do you want to add? Our existing tracts have been
labeled on 33 healthy subjects. It's certainly possible to include new
tracts in the atlas but someone has to do the labeling on the same or a
similar set of subjects.
a.y
On Wed, 15 Jun 2011, Seán Froudist Walsh wrote
Can you send me the label?
doug
Righart, Ruthger Dr. wrote:
> Dear Freesurfers,
>
> I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I
> have some problems in that the target label shows little holes while the
> location of the target label seems to correspond rather well
Hi Phoebe,
The fslroi part extracts all the low-b images from the 4D diffusion data
and creates an average low-b mask.
fslroi
is the number of 3D low-b volumes to be extracted from the 4D
diffusion volume. For some reason tracula is unable to read the no. of
low-b images from your dicom hea
Dear Freesurfers,
I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I have
some problems in that the target label shows little holes while the location of
the target label seems to correspond rather well with the source label.
Checking these holes backward to the source s
Hi FreeSurfing Gurus,
I would like to add some new tracts to the Tracula pipeline using my own
regions of interest. What would be the best way to do this?
All the best and many thanks in advance,
Seán
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harv
28 matches
Mail list logo
