Hi Qiongmin

why are you trying to read the patches into matlab?

Also, can you send us your full matlab command that generated the error? Sounds like you passed the incorrect file name

cheers Bruce On Tue, 27 May 2014, Caka wrote:

Thank you Bruce,

I convert the fsaverage flat map into a ascii file, using:   mris_convert  -p  lh.cortex.patch.flat  lh.cortex.patch.flat.asc. Now I need to read these two files.

(1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out, it said ‘ Error using ==> read_patch at 28, could not open file …’. (2) I couldn’t find a read_patch_asc.m script in Freesurfer, as is suggestedin https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35813.h tml (3) I found a read_asc.m instead, but when I used it to read the lh.cortex.patch.flat.asc, an error occurred: ‘Error using ==> fgets,  Invalid file identifier. Use open to generate a valid file identifier’.

Could you please give me some advices?Thank you very much!

Best regards, Qiongmin

————————————————Original email--------------------------------------- Hi Qiongmin

1. I think this is a bug in the open GL code that is outside of our

control. We will try to track it down

2. The flat maps aren't really any different than say the inflated

fsaverage surface. If you can generate group (or individual maps) in  fsaverage space you can display them on the flat maps.

3. The index of each vertex in the flattened space is stored in the patch

files so you can always look up what vertex it was on inflated, sphere,  etc...

cheers Bruce

On Mon, 26 May 2014, Caka  wrote:

  Dear Bruce, Doug and all,
  Thanks for your suggestion, it helped a lot.

  (1) I load the fsaverage surface (lh.inflated) in tksurfer, and
  then load
  the fsaverage patch (lh.cortex.patch.flat). The flat map was
  shown for
  several seconds, and then ?an error occurred and tksurfer was
  shut down. The
  terminal said: ?tksurfer.bin:tnl/t_vertex.c:407:
  update_input_ptrs:
  Assertion ?a[j].inputstride == vptr-> stride? failed. Abort(core
  dumped)?.
  ?Could you give me some advice?
  I use a 'CentOS release 6.2' system. The freesurfer is
  ?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0?.?

  (2) Indeed, I want to flatten all cortical thickness surfaces of
  140
  subjects onto the ?lh.cortex.patch.flat? of fsaverage. I just
  don?t
  understand your idea how to do this. After I load
  ?lh.cortex.patch.flat? of
  fsaverage, the tksurfer only shows this flat map (now it lasted
  for several
  seconds and crashed), so how can I ' load whatever overlay you
  want in the
  same way you would on the inflated surface??
  Does it mean that I load the individual flat map on the
  individual inflated
  surface? But I haven?t got the individual flat map yet.?

  (3) I am wondering if there are some table recording the
  transformation
  relationships between the fsaverage surface vertices and the
  flat map
  vertices? If so, then I think all I need to do is extracting the
  cortical
  thickness value of every vertex in individual inflated surface,
  and then
  putting into the corresponding vertex in the flat map.?

  Thank you very much!?

  Best regards,
  Qiongmin?