Hi Guillaume,
I am following up on this message from 2017. It looks like output of processing done using CAT12 misses the mesh geometry information which gives an error. For example, I did 'Threshold and transform spmT surfaces' using CAT12 and the output only has only cdata. The fields faces, vertices etc. are missing. See error below.
SPM12: spm_render (v7577) 12:51:58 - 14/02/2023
========================================================================
Error using spm_render
Cannot find a surface mesh to be displayed.
Error in spm (line 1004)
evalin('base',CB)
Error while evaluating UIControl Callback.
Thanks,
Raghavan
On Wed, 18 Jan 2017 13:31:48 +0000, Guillaume Flandin <[log in to unmask]> wrote:
>Dear Nick,
>
>It looks like one of the small issues we have to iron out between SPM12
>and CAT12, where the mesh geometry information gets somehow lost.
>
>Can you display the output file with SPM?
>>> spm_mesh_render disp out.gii
>
>What is returned by:
> g1 = gifti('rh.dicom.resampled.D15_27.gii');
> g1.private.metadata
> g2 = gifti('rh.dicom.resampled.D15_27_2.gii');
> g2.private.metadata
> g = gifti('out.gii');
> g.private.metadata
>
>Best regards,
>Guillaume.
>
>
>On 18/01/17 13:22, nick judd wrote:
>> Hey Guillaume,
>>
>> It’s something to do with spam_mesh_calc, it works using the files
>> before the subtraction.
>> Also it doesn’t even let me display the surfaces using the surface tool
>>> displace surface in CAT12.
>> (this works on the files before subtraction)
>>
>> spm_mesh_calc({'rh.dicom.resampled.D15_27_2.gii','rh.dicom.resampled.D15_27.gii'},’out.gii',
>> 's1-s2')
>>
>> Display /data/nicjud/scans_sorted/R_surf_15mm/out.gii
>> Error using cat_surf_render (line 838)
>> Unknown action.
>>
>> Error in cat_surf_display (line 156)
>> h = cat_surf_render(Pmesh);
>>
>> Error in cat12>pushbutton8_Callback (line 221)
>> cat_surf_display;
>>
>> Error in gui_mainfcn (line 95)
>> feval(varargin{:});
>>
>> Error in cat12 (line 76)
>> gui_mainfcn(gui_State, varargin{:});
>>
>> Error in
>> @(hObject,eventdata)cat12('pushbutton8_Callback',hObject,eventdata,guidata(hObject))
>>
>>
>> Error while evaluating uicontrol Callback
>>
>>
>> best,
>> nick
>>
>> On January 18, 2017 at 1:54:07 PM, Guillaume Flandin
>> ([log in to unmask] <mailto:[log in to unmask]>) wrote:
>>
>>> Dear Nick,
>>>
>>> I don't know. Do you have a longer version of the error message
>>> (including function names and line numbers)? Does it only happen with
>>> data created by spm_mesh_calc?
>>>
>>> Best regards,
>>> Guillaume.
>>>
>>>
>>> On 17/01/17 13:40, nick judd wrote:
>>> > Hey Guillaume,
>>> >
>>> > Thanks for your response, I used spm_mesh_calc. Yet when I go to
>>> > ‘estimate surface model’ in CAT12, I get Error using subsref
>>> > *Index exceeds matrix dimensions*. Any idea why?
>>> >
>>> > Thanks,
>>> > Nick
>>> >
>>> > On Wed, Jan 11, 2017 at 3:30 PM, Guillaume Flandin <[log in to unmask] <mailto:[log in to unmask]>
>>> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>>> >
>>> > Dear Nick,
>>> >
>>> > If you want to evaluate an expression from data on surfaces you can
>>> > possibly use spm_mesh_calc.m. For example:
>>> > spm_mesh_calc({'file1.gii','file2.gii'},'diff.gii','s1-s2')
>>> >
>>> > Best regards,
>>> > Guillaume.
>>> >
>>> >
>>> > On 11/01/17 13:30, Nicholas Judd wrote:
>>> > > I used CAT12 on longitudinal pediatric data (pre & post) to get
>>> > WM, GM and surface data. The WM & GM segmentation were in .nii so I
>>> > could just use FSL maths to subtract post-pre before using a
>>> > multiple regression analysis on the delta images. I also used FSL to
>>> > threshold.
>>> > >
>>> > > I tried to use the surface calculator (subject-wise) in CAT12. I
>>> > renamed my files so they would conform (eg.
>>> > lh.text.resampled.D14_001.gii & lh.text.resampled.D14_001_2.gii);
>>> > separated each subject and entered the expression s2-s1. When I run
>>> > the batch it just simply says 'output.... failed'. Does anyone know
>>> > what I am doing wrong? Or know of an alternative way to derive delta
>>> > images from .gii files? (and threshold)
>>> > >
>>> > > Thanks,
>>> > > Nick
>>> > >
>>> >
>>> > --
>>> > Guillaume Flandin, PhD
>>> > Wellcome Trust Centre for Neuroimaging
>>> > University College London
>>> > 12 Queen Square
>>> > London WC1N 3BG
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > *
>>> > Nicholas Judd* | MSc
>>> > Klingberg Laboratory
>>> > Department of Neuroscience | Karolinska Institutet
>>> > Retzius väg 8 | 171 77 Stockholm
>>> > [log in to unmask] <mailto:[log in to unmask]>
>>> > <mailto:[log in to unmask] <mailto:[log in to unmask]>> |
>>> klingberglab.se <http://klingberglab.se>
>>> > <http://klingberglab.se/>
>>> >
>>>
>>> --
>>> Guillaume Flandin, PhD
>>> Wellcome Trust Centre for Neuroimaging
>>> University College London
>>> 12 Queen Square
>>> London WC1N 3BG
>
>--
>Guillaume Flandin, PhD
>Wellcome Trust Centre for Neuroimaging
>University College London
>12 Queen Square
>London WC1N 3BG
|