Dear Freesurfer Experts,
I am a student at the technical university of Delft and currently working on a project to automatically visualize the cortical thickness data of children. To automatically visualize the data I want to use Freeview, to use Freeview as visualization tool I have to write brain specific layout files. To do this automatically I want to know what the layout for the overlay files is, so Freeview can read them automatically. The data for the layout files should be different per brain, I have already acquired the data and I am ready to write it to a layout file, but I can't figure out what the standard way of writing a layout file is, without having to manually do anything. The language in which I want to write the code is Python.
Kind regards,
Eloy Geenjaar
We usually create nifti or mgz files to use as overlays both for the volume or the surface. Is this what you mean?
On 10/28/16 9:17 AM, Eloy Geenjaar wrote:
Dear Freesurfer Experts,
I am a student at the technical university of Delft and currently working on a project to automatically visualize the cortical thickness data of children. To automatically visualize the data I want to use Freeview, to use Freeview as visualization tool I have to write brain specific layout files. To do this automatically I want to know what the layout for the overlay files is, so Freeview can read them automatically. The data for the layout files should be different per brain, I have already acquired the data and I am ready to write it to a layout file, but I can't figure out what the standard way of writing a layout file is, without having to manually do anything. The language in which I want to write the code is Python.
Kind regards,
Eloy Geenjaar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
Thanks for the quick response, I do know that nifti or mgz files are used for the overlay, I was trying to figure out how to write such files though. In what format do I have to write nifti or mgz files for Freeview to be able to load them correctly?
Kind regards,
Eloy Geenjaar
________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Douglas Greve greve@nmr.mgh.harvard.edu Verzonden: vrijdag 28 oktober 2016 17:19 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Creating overlay files automatically
We usually create nifti or mgz files to use as overlays both for the volume or the surface. Is this what you mean?
On 10/28/16 9:17 AM, Eloy Geenjaar wrote:
Dear Freesurfer Experts,
I am a student at the technical university of Delft and currently working on a project to automatically visualize the cortical thickness data of children. To automatically visualize the data I want to use Freeview, to use Freeview as visualization tool I have to write brain specific layout files. To do this automatically I want to know what the layout for the overlay files is, so Freeview can read them automatically. The data for the layout files should be different per brain, I have already acquired the data and I am ready to write it to a layout file, but I can't figure out what the standard way of writing a layout file is, without having to manually do anything. The language in which I want to write the code is Python.
Kind regards,
Eloy Geenjaar
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Look up the specs for nifti files. The spec is publicly available. If you are doing this in matlab, you can use our MRIwrite.m
On 10/31/16 6:01 AM, Eloy Geenjaar wrote:
Dear Douglas,
Thanks for the quick response, I do know that nifti or mgz files are used for the overlay, I was trying to figure out how to write such files though. In what format do I have to write nifti or mgz files for Freeview to be able to load them correctly?
Kind regards,
Eloy Geenjaar
*Van:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Douglas Greve greve@nmr.mgh.harvard.edu *Verzonden:* vrijdag 28 oktober 2016 17:19 *Aan:* freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Creating overlay files automatically
We usually create nifti or mgz files to use as overlays both for the volume or the surface. Is this what you mean?
On 10/28/16 9:17 AM, Eloy Geenjaar wrote:
Dear Freesurfer Experts,
I am a student at the technical university of Delft and currently working on a project to automatically visualize the cortical thickness data of children. To automatically visualize the data I want to use Freeview, to use Freeview as visualization tool I have to write brain specific layout files. To do this automatically I want to know what the layout for the overlay files is, so Freeview can read them automatically. The data for the layout files should be different per brain, I have already acquired the data and I am ready to write it to a layout file, but I can't figure out what the standard way of writing a layout file is, without having to manually do anything. The language in which I want to write the code is Python.
Kind regards,
Eloy Geenjaar
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Eloy Geenjaar