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
|