to follow up - you could use your manual labelings to create a new atlas
using mri_ca_train (assuming you mean subcortical regions). There is some
intelligence in it that you can only take advantage of if you use our
numbering/lut (i.e. left hippocampus is 17, etc...)
cheers
Bruce
On Mon, 7 May 2018, Douglas N. Greve wrote:
Not that I know of. For our atlases, the prob information is
incorporated during trying
On 05/03/2018 05:38 AM, Mageshwar Selvakumar wrote:
Dear Doug,
Thank you for your help. On the query on atlas, We have a atlas that
was built at our institute comprising of 183 regions and these 183
regions are available each as a nifti file with the probability
information of finding the structure at that location. I would like to
build that atlas in freesurfer and use it for our analyses. On reading
your documentation, I found that we have to load in each subject, draw
its labels and build the atlas. I would like to know if we have a way
where we can use these probability information directly and create the
atlas.
Thank you,
Kind regards
Mageshwar Selvakumar, M.Sc
Department of Pharmakologische Bildgebung und Bildanalyse
Friedrich Alexander Universität Erlangen Nürnberg
Office:Fahrstr. 17, 91054 Erlangen
Phone:+ 49-9131-8522898
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Wednesday, May 2, 2018 11:56 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Fw: Query regarding creation of atlas
directly from probabilistic information
For vol2surf, you should make sure that the registration is correct by
running
tkregisterfv --mov ID076_LL_PHGa_l_HvOx_prob.mgz --reg
$FREESURFER_HOME/average/mni152.register.dat --surfs
You ROI should be in the right spot and the surface should cut through
it (or near enough given your projection).
If those are probabilities, then you will need to binarize it
(mri_binarize) before running mri_cor2label
Not sure about your other question. Do you want to get the probabilities
for the DK atlas?
On 05/02/2018 10:26 AM, Mageshwar Selvakumar wrote:
Dear Everyone,
A kind reminder. I'm unable to look beyond this step and am really
looking for some help. I would like to know if we can use the
probabilistic information directly on mri_train
Thank you,
Kind regards
Mageshwar Selvakumar, M.Sc
Department of Pharmakologische Bildgebung und Bildanalyse
Friedrich Alexander Universität Erlangen Nürnberg
Office:Fahrstr. 17, 91054 Erlangen
Phone:+ 49-9131-8522898
------------------------------------------------------------------------
*From:* Mageshwar Selvakumar <mageshwar.selvaku...@outlook.com>
*Sent:* Monday, April 23, 2018 10:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl
*Subject:* Query regarding creation of atlas directly from
probabilistic information
Dear All and Bruce,
This mail is on top of the query I had a couple of weeks back where I
misinterpreted that I had binary mask of each structure
as individual nifti volume files but on closer look, the nifti files
had the probability that the structure is present at that certain
location. On looking into the freesurfer website, I came across this
documentation of creation of Atlas,
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas
SurfaceLabelAtlas - Free Surfer Wiki
<https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas>
Overview. This document provides an overview of two related topics:
How the FreeSurfer pipeline automatically labels a subject's regions
(producing an annotation file) by comparing the subject's curvature
data to an "atlas" ("gcs") file.
surfer.nmr.mgh.harvard.edu
In this documentation the process is done by looping through N
subjects to get the probability information, and these subjects are
registered to the registration template derived from average of
reference templates. I would like to know if I could use these
probability information directly and since the atlas information is
already in the MNI152 space, can I use the registration template which
is already available with freesurfer, and if yes, can someone guide me
on which registration files I must use.
Secondly, I tried using mri_vol2surf and tried to convert the volume
data to a surface data before creating labels, but on doing so I had
errors when creating labels from the surface files.
To convert into volume I ran the below code:
*mri_vol2surf --mov ID076_LL_PHGa_l_HvOx_prob.mgz --ref
ID076_LL_PHGa_l_HvOx_prob.mgz --out
ID076_LL_PHGa_l_HvOx_prob_surf.mgz --hemi lh --mni152reg
--projdist-max -2 0 .1 --reshape --interp nearest*
Then I to convert this surface file into label I ran
*mri_cor2label --i ID080_CPuP_l_HvOx_prob_surf.mgz --l area1.label
--id 076*
And I got the error
*Found 0 label voxels
ERROR: found no voxels matching id 76*
But the process runs fine if I run the mri_cor2label on the volume
file. It would be nice if someone can help me out on where I'm going
wrong here.
Thank you,
Kind regards
Mageshwar Selvakumar, M.Sc
Department of Pharmakologische Bildgebung und Bildanalyse
Friedrich Alexander Universität Erlangen Nürnberg
Office:Fahrstr. 17, 91054 Erlangen
Phone:+ 49-9131-8522898
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