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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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 the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
