Hi Bruce,

Yes I am trying to do some quantitative analysis rather than just displaying the patches. The only way I know for getting the vertex indices and the coordinations is reading it into matlab.

(1) flat = read_patch(‘lh.cortex.patch.flat’); This command worked today! I rebooted my system.

(2) patch = read_asc(‘lh.cortex.patch.flat.asc’); This command still couldn’t work. The error information is:

??? Error using ==> reshape To RESHAPE the number of elements must not change.

Error in ==> read_asc at 39 v = reshape(v, [4 S(2)])’ ;

Thanks very much!

Qiongmin

--------------------- Original email ----------------------- 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?