Thank you Bruce. I can load it as patch as you suggested. I can also load the curvatures to color it. Thus I imagine in the data, there would be 2D locations of the vertices, and their indices respect to the full surface. Is it true? How can I read this information (e.g. into matlab) ? Thanks again! Also thanks to anyone who would like to comment!
best Peng
On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Peng
the flat maps are stored in a different format than the surfaces, called a "patch" format (since they are only a piece of the whole surface - not the entire thing). You can load them with file->load patch in tksurfer. Not sure about freeview, perhaps Ruopeng can comment?
cheers Bruce
On Fri, 9 May 2014, peng wrote:
More information, error from tksurfer is as following:
======================== MRISalloc(16711682, 480): could not allocate vertices Cannot allocate memory ============
---------- Forwarded message ----------
From: peng prion.w@gmail.com Date: Fri, May 9, 2014 at 1:01 PM Subject: a question on flat surface To: "Freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change.
Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong.
Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best Peng
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