Dear Yann,
On 11 Feb 2019, at 23:29, Yann Quidé wrote:
> Thanks Christian.
>
> Could you advise what parameters can be changed, and in what file?
The cat_defaults.m file has a flag for the atlases. You have to change
the last column, where only the neuromorphometrics atlas is set to
„1“:
% Expert options - ROIs
%=======================================================================
% ROI maps from different sources mapped to Dartel CAT-space of
IXI-template
% { filename , GUIlevel , tissue , use }
% filename = '' - path to the
ROI-file
% GUIlevel = [ 0 | 1 | 2 ] - avaible in GUI
level
% tissue = {['csf','gm','wm','brain','none']} - tissue classes
for volume estimation
% use = [ 0 | 1 ] - default setting
to use this atlas
cat.extopts.atlas = { ...
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','neuromorphometrics.nii')
0 {'csf','gm'} 1; ... % atlas based on 35 subjects
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','lpba40.nii')
0 {'gm'} 0; ... % atlas based on 40
subjects
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','cobra.nii')
0 {'gm','wm'} 0; ... %
hippocampus-amygdala-cerebellum, 5 subjects, 0.6 mm voxel size
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','hammers.nii')
0 {'csf','gm','wm'} 0; ... % atlas based on 20
subjects
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','ibsr.nii')
1 {'csf','gm'} 0; ... % less regions, 18
subjects, low T1 image quality
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','aal.nii')
1 {'gm'} 0; ... % many regions, but
only labeled on one subject
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','mori.nii')
1 {'gm','wm'} 0; ... % only one subject, but
with WM regions
fullfile(spm('dir'),'toolbox','cat12','templates_1.50mm','anatomy.nii')
1 {'gm','wm'} 0; ... % ROIs requires further
work >> use Anatomy toolbox
};
Best,
Christian
>
> Thanks,
>
> Yann
>
>
>
>> On 8 Feb 2019, at 6:31 pm, Christian Gaser
>> <[log in to unmask]> wrote:
>>
>> Dear Yann,
>>
>>
>> On 8 Feb 2019, at 8:27, Yann Quidé wrote:
>>
>>> Dear Christian,
>>>
>>> Thanks for your reply. I selected all atlases for preprocessing; so
>>> I should be able to select any atlas. I was able to use this atlas
>>> for another set of analysis, but not this one.
>>>
>>> Any idea why? Or maybe I should change something in the default
>>> parameters?
>> If you select the atlases in the GUI this should be sufficient.
>> However, if this not worked for you the change in the defaults is the
>> safest way. I will check that the GUI selection will be really used.
>>
>> Best,
>>
>> Christian
>>
>>>
>>> Thanks for your time,
>>>
>>> Yann
>>>
>>>
>>>> On 8 Feb 2019, at 6:16 pm, Christian Gaser
>>>> <[log in to unmask]> wrote:
>>>>
>>>> Dear Yann,
>>>>
>>>> On Thu, 7 Feb 2019 16:43:28 +1100, Yann Quidé
>>>> <[log in to unmask]> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> 1) Thanks Guillaume.
>>>>> Just for reference, when entering manually the contrast in the
>>>>> contrast manager (after building and estimating the model), it
>>>>> crashes (as you mentioned), but not when I enter [ones(1,2)/2
>>>>> -ones(1,2)/2 0 ones(1,15)/15 -ones(1,10)/10].
>>>>> In addition, when looking at the results for this contrast, there
>>>>> is a significant main effect of group all over the place; which is
>>>>> definitely not possible in my population.
>>>>> Anyway I will try your option.
>>>>>
>>>>>
>>>>> 2) I have another question.
>>>>> When using the CAT12 option for ROI analyses, and comparing Time 1
>>>>> vs Time 2 from my longitudinal design, I do not have the choice of
>>>>> the atlas; CAT12 automatically selects the neuromorphometrics
>>>>> atlas (for volumetric measures). Is there any reason for that? How
>>>>> can I use another atlas for this analysis (eg Cobra)?
>>>> You need to select the used atlases before preprocessing. It's not
>>>> possible to do that retrospectively.
>>>>
>>>> Best,
>>>>
>>>> Christian
>>>>>
>>>>> Thanks for your time!
>>>>>
>>>>> Yann
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 18 Jan 2019, at 10:33 PM, Flandin, Guillaume
>>>>>> <[log in to unmask]> wrote:
>>>>>>
>>>>>> Dear Yann,
>>>>>>
>>>>>> Could it be that you entered the contrast as:
>>>>>> [0.5 0.5 -0.5 -0.5 0 0.0667 ... ]
>>>>>> instead of:
>>>>>> [[1 1 -1 -1]/2 0 ones(1,15)/15 -ones(1,10)/10]
>>>>>> so that the contrast vector does not sum to zero (at machine
>>>>>> precision)?
>>>>>>
>>>>>> Again, for the main effect of group, I would use a two sample
>>>>>> t-test
>>>>>> after having averaged the two images per subject.
>>>>>>
>>>>>> Best regards,
>>>>>> Guillaume.
>>>>>>
>>>>>>
>>>>>> On 17/01/2019 22:48, Yann Quidé wrote:
>>>>>>> Thanks Guillaume and Christian,
>>>>>>>
>>>>>>> Christian, I tried without TIV as covariate, but got the same
>>>>>>> error.
>>>>>>>
>>>>>>> I have attached the related SPM.mat, the Error.mat saved
>>>>>>> following the
>>>>>>> crash, and the details from the Matlab command window.
>>>>>>>
>>>>>>> Please let me know if you need anything else.
>>>>>>>
>>>>>>> Thanks again for your time and advice on this.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Yann
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Running job #1
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Running 'Factorial design specification'
>>>>>>> Mapping files :
>>>>>>> ...done
>>>>>>> Design configuration :
>>>>>>> ...done
>>>>>>> Saving SPM configuration :
>>>>>>> ...SPM.mat saved
>>>>>>> Design reporting :
>>>>>>> ...done
>>>>>>> Completed : 09:43:00 -
>>>>>>> 18/01/2019
>>>>>>> Done 'Factorial design specification'
>>>>>>> Running 'Model estimation'
>>>>>>>
>>>>>>> SPM12: spm_spm (v7120) 09:43:00 -
>>>>>>> 18/01/2019
>>>>>>> ========================================================================
>>>>>>>
>>>>>>> SPM12: spm_est_non_sphericity (v6913) 09:43:00 -
>>>>>>> 18/01/2019
>>>>>>> ========================================================================
>>>>>>> Chunk 2/2 :
>>>>>>> ...done
>>>>>>> Temporal non-sphericity (70376 voxels) : ...ReML
>>>>>>> estimation
>>>>>>> ReML Iteration 1 : ...2.662013e-01
>>>>>>> [+4.25]
>>>>>>> ReML Iteration 2 : ...2.289632e-04
>>>>>>> [+4.50]
>>>>>>>
>>>>>>> SPM12: spm_spm (v7120) 09:43:05 -
>>>>>>> 18/01/2019
>>>>>>> ========================================================================
>>>>>>> Chunk 2/2 :
>>>>>>> ...done
>>>>>>> Spatial non-sphericity (over scans) :
>>>>>>> ...done
>>>>>>> Saving SPM.mat :
>>>>>>> ...done
>>>>>>> Completed : 09:43:30 -
>>>>>>> 18/01/2019
>>>>>>> Done
>>>>>>> Done 'Model estimation'
>>>>>>> Running 'Contrast Manager'
>>>>>>>
>>>>>>> SPM12: spm_contrasts.m 09:43:30 -
>>>>>>> 18/01/2019
>>>>>>> ========================================================================
>>>>>>> Contrasts folder :
>>>>>>> ..tudinal_Time_by_Group_no_age
>>>>>>> 0.5 0.5 -0.5 -0.5 0 0.066667
>>>>>>> 0.066667 0.066667 0.066667 0.066667 0.066667
>>>>>>> 0.066667
>>>>>>> 0.066667 0.066667 0.066667 0.066667 0.066667
>>>>>>> 0.066667
>>>>>>> 0.066667 0.066667 -0.1 -0.1 -0.1
>>>>>>> -0.1
>>>>>>> -0.1 -0.1 -0.1 -0.1 -0.1
>>>>>>> -0.1
>>>>>>> <- !invalid contrast
>>>>>>> Failed 'Contrast Manager'
>>>>>>> Error using spm_run_con (line 251)
>>>>>>> Error in contrast specification
>>>>>>> In file
>>>>>>> "/mridata/workingdata/RUSE/spm12_coptsd_cat12.5/config/spm_run_con.m"
>>>>>>> (v7093), function "spm_run_con" at line 251.
>>>>>>>
>>>>>>> The following modules did not run:
>>>>>>> Failed: Contrast Manager
>>>>>>>
>>>>>>>> On 15 Jan 2019, at 8:38 AM, Christian Gaser
>>>>>>>> <[log in to unmask]
>>>>>>>> <mailto:[log in to unmask]>
>>>>>>>> <mailto:[log in to unmask]
>>>>>>>> <mailto:[log in to unmask]>>> wrote:
>>>>>>>>
>>>>>>>> Dear Yann,
>>>>>>>>
>>>>>>>> On Fri, 11 Jan 2019 18:17:57 +1100, Yann Quidé
>>>>>>>> <[log in to unmask] <mailto:[log in to unmask]>
>>>>>>>> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> Any thought on this?
>>>>>>>>
>>>>>>>> To be honest, not. The designs are fine and the contrast for
>>>>>>>> the 2nd
>>>>>>>> model with the group differences is also correct. The only idea
>>>>>>>> I have
>>>>>>>> is to skip the TIV covariate.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> Christian
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Yann
>>>>>>>>>
>>>>>>>>>> On 9 Jan 2019, at 9:08 pm, Yann Quidé <[log in to unmask]
>>>>>>>>>> <mailto:[log in to unmask]>
>>>>>>>>>> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Dear all,
>>>>>>>>>>
>>>>>>>>>> I am analysing longitudinal VBM data (group1, n=10; group2,
>>>>>>>>>> n=15; 2
>>>>>>>>>> time points) using CAT12.5 (r1363).
>>>>>>>>>>
>>>>>>>>>> 1) Looking within group for the effect of time my design
>>>>>>>>>> matrix
>>>>>>>>>> looks like attachment1… all boxes (but the one associated
>>>>>>>>>> with TIV)
>>>>>>>>>> below the matrix are grey, indicating that these data are not
>>>>>>>>>> uniquely specified. As I am comparing the “same brains”
>>>>>>>>>> over time, I
>>>>>>>>>> believe this is ok; is that right?
>>>>>>>>>>
>>>>>>>>>> 2) I also wanted to look at the main effects of time, group,
>>>>>>>>>> and
>>>>>>>>>> their interaction using a 2x2 ANCOVA design (design in
>>>>>>>>>> attachment2).
>>>>>>>>>> I followed the CAT12 manual, and used
>>>>>>>>>> ones(1,n)/n -ones(1,n)/n 0 ones(1,n1)/n1 -ones(1,n2)/n2
>>>>>>>>>> to model the main effect of group (n=2; n1=15; n2=10).
>>>>>>>>>>
>>>>>>>>>> However, the creation of the contrast image crashes when
>>>>>>>>>> using the
>>>>>>>>>> batch mode, with the following error message:
>>>>>>>>>>
>>>>>>>>>> ========================================================================
>>>>>>>>>> Contrasts folder :
>>>>>>>>>> ..tudinal_Time_by_Group
>>>>>>>>>> 0.5 0.5 -0.5 -0.5 0
>>>>>>>>>> 0.066667
>>>>>>>>>> 0.066667 0.066667 0.066667 0.066667 0.066667
>>>>>>>>>> 0.066667 0.066667 0.066667 0.066667 0.066667
>>>>>>>>>> 0.066667 0.066667 0.066667 0.066667 -0.1
>>>>>>>>>> -0.1 -0.1 -0.1 -0.1 -0.1
>>>>>>>>>> -0.1 -0.1 -0.1 -0.1 <- !invalid
>>>>>>>>>> contrast
>>>>>>>>>> Failed 'Contrast Manager'
>>>>>>>>>> Error using spm_run_con (line 251)
>>>>>>>>>> Error in contrast specification
>>>>>>>>>> In file "/Users/y.quide/spm12/config/spm_run_con.m" (v7093),
>>>>>>>>>> function "spm_run_con" at line 251.
>>>>>>>>>>
>>>>>>>>>> The following modules did not run:
>>>>>>>>>> Failed: Contrast Manager
>>>>>>>>>> ========================================================================
>>>>>>>>>>
>>>>>>>>>> When creating the contrast image using contrast manager after
>>>>>>>>>> selecting RESULTS, it works, BUT the result is surprising:
>>>>>>>>>> the main
>>>>>>>>>> effect of group is over the whole brain!
>>>>>>>>>>
>>>>>>>>>> Any idea what goes wrong?
>>>>>>>>>>
>>>>>>>>>> Thanks for your time.
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>>
>>>>>>>>>> Yann
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> <Attachment1.png><Attachment2.png>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Guillaume Flandin, PhD
>>>>>> Wellcome Centre for Human Neuroimaging
>>>>>> UCL Queen Square Institute of Neurology
>>>>>> London WC1N 3BG
>>>>>
>>>>>
>>>>
>>>>
Christian Gaser, Ph.D.
Professor of Computational Neuroscience/Neuroimaging
Biomagnetic Center
Structural Brain Mapping Group
Department of Neurology
Jena University Hospital
Am Klinikum 1, D-07747 Jena, Germany
Tel: ++49-3641-9325778 Fax: ++49-3641-9325772
e-mail: [log in to unmask]
http://www.neuro.uni-jena.de
|