Hi Peng
we provide matlab code (read_patch.m) for reading patches and for reading patches converted to ascii format (read_patch_asc.m). You can use mri_convert to generate the ascii format
cheers
Bruce
On Sat, 10 May 2014, peng wrote:
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.edu> wrote:
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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