Thanks Christian.
Could you advise what parameters can be changed, and in what file?
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
>>>>
>>>>
>>>
>>>
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