It should be 10^-abs(sig)

On 02/06/2015 12:53 AM, Bronwyn Overs wrote:
> Hi Doug,
>
> Thanks for all of your help. I am investigating the differences 
> between the design matrices now.
>
> I have one more query about the sig.table.dat file put out by the GLM 
> using the parcellated ROIs. When I transform each of the values in 
> this file to p values using 10^"value", some of the resulting p-value 
> are >1. Do you know why this would be happening? Here is an example of 
> one of my sig.table.dat files, where 10^.799 = 6.295:
>
> lh.aparc.thickness                me_gender_ageRem me_group_ageRem
> lh_bankssts_thickness               0.107  -2.752
> lh_caudalanteriorcingulate_thickness  -2.616  -0.190
> lh_caudalmiddlefrontal_thickness   -0.701  -4.258
> lh_cuneus_thickness                 0.799  -1.178
> lh_entorhinal_thickness             1.669  -4.129
> lh_fusiform_thickness              -0.088  -6.808
> lh_inferiorparietal_thickness      -0.665  -1.477
> lh_inferiortemporal_thickness       0.149  -7.985
> lh_isthmuscingulate_thickness      -0.476  -2.393
> lh_lateraloccipital_thickness       0.212  -1.189
> lh_lateralorbitofrontal_thickness   0.288  -7.657
> lh_lingual_thickness                1.148  -1.594
> lh_medialorbitofrontal_thickness    1.405  -4.461
> lh_middletemporal_thickness         0.727  -7.215
> lh_parahippocampal_thickness       -1.059  -2.854
> lh_paracentral_thickness           -0.514  -0.282
> lh_parsopercularis_thickness        0.444  -3.541
> lh_parsorbitalis_thickness         -0.110  -7.075
> lh_parstriangularis_thickness       0.244  -4.769
> lh_pericalcarine_thickness          0.376  -0.218
> lh_postcentral_thickness           -0.485  -0.832
> lh_posteriorcingulate_thickness    -0.135  -1.241
> lh_precentral_thickness             0.196  -2.102
> lh_precuneus_thickness              0.018  -1.361
> lh_rostralanteriorcingulate_thickness  -1.208  -2.073
> lh_rostralmiddlefrontal_thickness   0.437  -4.470
> lh_superiorfrontal_thickness       -0.141  -2.743
> lh_superiorparietal_thickness      -0.288  -0.365
> lh_superiortemporal_thickness       0.227  -4.646
> lh_supramarginal_thickness         -1.185  -1.354
> lh_frontalpole_thickness           -0.325  -0.521
> lh_temporalpole_thickness          -0.067  -4.074
> lh_transversetemporal_thickness    -0.009  -1.618
> lh_insula_thickness                 0.553  -6.063
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au <http://neura.edu.au>
>
> Follow @neuraustralia on twitter 
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>
> On 5/02/2015 10:46 am, Douglas N Greve wrote:
>> How sure are you that you are using the exact same model? Can you output
>> the design matrix from SPSS? Can you input the FS design matrix into
>> SPSS? Are you sure you are using the exact same input data?
>>
>> On 02/04/2015 06:32 PM, Bronwyn Overs wrote:
>>> Ahh right. I have just understood which part of the output I needed to
>>> look at. However, for the ROI GLM there are only 1-2 regions that were
>>> significantly different between groups, while the SPSS ANCOVA showed
>>> significant group differences for the majority of parcellated regions.
>>> I have confirmed that I am using the exact same model for each, so it
>>> is only the analysis method that differs. Do you know why these two
>>> methods would produce such disparate results?
>>>
>>>
>>> Kind regards,
>>>
>>> Bronwyn Overs
>>> Research Assistant
>>>
>>> Neuroscience Research Australia
>>>
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>
>>> neura.edu.au<http://neura.edu.au>
>>>
>>> Follow @neuraustralia on twitter
>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>
>>> On 5/02/2015 3:16 am, Douglas N Greve wrote:
>>>> I'm not sure that I understand what I'm looking at. If it is an ROI
>>>> analysis, then there is no surface, it should be about 40 numbers, one
>>>> for each ROI.
>>>>
>>>> On 02/03/2015 06:26 PM, Bronwyn Overs wrote:
>>>>> Hi Doug,
>>>>>
>>>>> Thanks for your correction.
>>>>>
>>>>> I have now completed the FDR for my case-control comparisons, and it
>>>>> appears that none of the regions survived. This is again quite
>>>>> confusing given the large number of parcellated regions that survived
>>>>> FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the
>>>>> sig.mgh file from ROI analysis looks as you would expect (it looks
>>>>> very strange to me):
>>>>>
>>>>>
>>>>>
>>>>> Kind regards,
>>>>>
>>>>> Bronwyn Overs
>>>>> Research Assistant
>>>>>
>>>>> Neuroscience Research Australia
>>>>>
>>>>> Neuroscience Research Australia
>>>>> Margarete Ainsworth Building
>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>
>>>>> neura.edu.au<http://neura.edu.au>
>>>>>
>>>>> Follow @neuraustralia on twitter
>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>>>
>>>>> On 4/02/2015 9:35 am, Douglas Greve wrote:
>>>>>> Yes, it should be .^
>>>>>>
>>>>>> On 2/3/15 5:33 PM, Bronwyn Overs wrote:
>>>>>>> Hi Doug,
>>>>>>>
>>>>>>> I am having a problem with the line in Matlab 2014b:
>>>>>>> p = 10^-abs(sigmat);
>>>>>>> I keep getting the following error:
>>>>>>> Error using  ^
>>>>>>> Inputs must be a scalar and a square matrix.
>>>>>>> To compute elementwise POWER, use POWER (.^)
>>>>>>> instead.
>>>>>>>
>>>>>>> Do you know why this would be?
>>>>>>>
>>>>>>> Kind regards,
>>>>>>>
>>>>>>> Bronwyn Overs
>>>>>>> Research Assistant
>>>>>>>
>>>>>>> Neuroscience Research Australia
>>>>>>>
>>>>>>> Neuroscience Research Australia
>>>>>>> Margarete Ainsworth Building
>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>>>
>>>>>>> neura.edu.au<http://neura.edu.au>
>>>>>>>
>>>>>>> Follow @neuraustralia on twitter
>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>>>>>> the NeuRA Magazine<http://www.neura.edu.au/help-research/subscribe>
>>>>>>>
>>>>>>> On 4/02/2015 2:22 am, Douglas Greve wrote:
>>>>>>>> There is not a way to do it from the command line. You can do it in
>>>>>>>> matlab, something like
>>>>>>>>
>>>>>>>> sig = MRIread('sig.mgh');
>>>>>>>> sigmat = fast_vol2mat(sig);
>>>>>>>> p = 10^-abs(sigmat);
>>>>>>>> fdr = .05;
>>>>>>>> pthresh = fast_fdrthresh(p,fdr);
>>>>>>>> ind = find(p < pthresh); % This will be a list of ROI indices that
>>>>>>>> survive FDR
>>>>>>>>
>>>>>>>> doug
>>>>>>>>
>>>>>>>> On 2/2/15 10:26 PM, Bronwyn Overs wrote:
>>>>>>>>> Hi Doug,
>>>>>>>>>
>>>>>>>>> That makes perfect sense. Just one more thing then, how do you
>>>>>>>>> conduct an FDR via the command line for an ROI mri_glmfit analysis?
>>>>>>>>>
>>>>>>>>> Kind regards,
>>>>>>>>>
>>>>>>>>> Bronwyn Overs
>>>>>>>>> Research Assistant
>>>>>>>>>
>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>
>>>>>>>>> Neuroscience Research Australia
>>>>>>>>> Margarete Ainsworth Building
>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>>>>>
>>>>>>>>> neura.edu.au<http://neura.edu.au>
>>>>>>>>>
>>>>>>>>> Follow @neuraustralia on twitter
>>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe
>>>>>>>>> to the NeuRA Magazine
>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe>
>>>>>>>>>
>>>>>>>>> On 3/02/2015 2:00 pm, Douglas Greve wrote:
>>>>>>>>>> This is not something you would run the MC sim on because there
>>>>>>>>>> is no clustering, it is just a list of ROIs with their p-values.
>>>>>>>>>> The p-values are uncorrected. You can do bonferoni correction
>>>>>>>>>> across all the ROIs (or just the ones you are interested in). You
>>>>>>>>>> could do FDR too.
>>>>>>>>>>
>>>>>>>>>> doug
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 2/2/15 9:39 PM, Bronwyn Overs wrote:
>>>>>>>>>>> Thanks Doug, that worked well.
>>>>>>>>>>>
>>>>>>>>>>> However, is it possible to run a monte-carlo simulation with
>>>>>>>>>>> this GLM ROI analysis? I attempted to run it using the following
>>>>>>>>>>> command...
>>>>>>>>>>> mri_glmfit-sim --glmdir
>>>>>>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs
>>>>>>>>>>> --cwpvalthresh  0.05 --2spaces
>>>>>>>>>>> and received the following error:
>>>>>>>>>>> ERROR: could not determine file for
>>>>>>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir/mask
>>>>>>>>>>>
>>>>>>>>>>> Kind regards,
>>>>>>>>>>>
>>>>>>>>>>> Bronwyn Overs
>>>>>>>>>>> Research Assistant
>>>>>>>>>>>
>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>>
>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>> Margarete Ainsworth Building
>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>>>>>>>
>>>>>>>>>>> neura.edu.au<http://neura.edu.au>
>>>>>>>>>>>
>>>>>>>>>>> Follow @neuraustralia on twitter
>>>>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
>>>>>>>>>>> the NeuRA Magazine
>>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe>
>>>>>>>>>>>
>>>>>>>>>>> On 3/02/2015 11:03 am, Douglas Greve wrote:
>>>>>>>>>>>> Even easier. Run aparcstats2table, then run mri_glmfit passing
>>>>>>>>>>>> the output of aparcstats2table with --table (instead of --y).
>>>>>>>>>>>> There's something on the wiki about it, also look for the ROI
>>>>>>>>>>>> tutorial.
>>>>>>>>>>>> doug
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/2/15 6:20 PM, Bronwyn Overs wrote:
>>>>>>>>>>>>> Hi Doug,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am not sure how to run an ROI analysis using mri_glmfit. Is
>>>>>>>>>>>>> there a wiki page detailing this method (I was unable to find
>>>>>>>>>>>>> one)? Is the first step to map lh.aparc.label and
>>>>>>>>>>>>> rh.aparc.label from fsaverage to each of my individual
>>>>>>>>>>>>> subjects using mri_label2label? When I do so and then view the
>>>>>>>>>>>>> mapped label for an individual subject in freeview, it appears
>>>>>>>>>>>>> to be a continuous label for all of the parcellated regions
>>>>>>>>>>>>> combined. Is this correct?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Kind regards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Bronwyn Overs
>>>>>>>>>>>>> Research Assistant
>>>>>>>>>>>>>
>>>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>>>>
>>>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>>>> Margarete Ainsworth Building
>>>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>>>>>>>>>
>>>>>>>>>>>>> neura.edu.au<http://neura.edu.au>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Follow @neuraustralia on twitter
>>>>>>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>>>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe
>>>>>>>>>>>>> to the NeuRA Magazine
>>>>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 3/02/2015 3:31 am, Douglas Greve wrote:
>>>>>>>>>>>>>> First, I would run the ROI analysis in mri_glmfit to see if
>>>>>>>>>>>>>> you get the same results as in SPSS. In the handfull of these
>>>>>>>>>>>>>> cases, no one has been able to correctly replicate the FS
>>>>>>>>>>>>>> design matrix in SPSS, so I suspect that is part of the
>>>>>>>>>>>>>> discrepancy. The other thing is that ROI and vertex-wise
>>>>>>>>>>>>>> analyses are simply different. As an extreme example, if some
>>>>>>>>>>>>>> of the vertices are pos and some are neg  then they would
>>>>>>>>>>>>>> cancel out when you average them in an ROI but individually
>>>>>>>>>>>>>> could be significant at the vertex level. If you analyze the
>>>>>>>>>>>>>> average over the cluster then that should come out as
>>>>>>>>>>>>>> significant.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> doug
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 2/1/15 11:36 PM, Bronwyn Overs wrote:
>>>>>>>>>>>>>>> Dear FreeSurfer Mailing List,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I have a sample of schizophrenia and control subjects for
>>>>>>>>>>>>>>> whom I have run a case-control analysis of cortical
>>>>>>>>>>>>>>> thickness using two separate methods (GLM vertex-wise
>>>>>>>>>>>>>>> analysis in freesurfer, repeated measures ANCOVA analysis of
>>>>>>>>>>>>>>> parcellated data in SPSS). However, for each methods of
>>>>>>>>>>>>>>> analysis I am getting extremely different results. For the
>>>>>>>>>>>>>>> GLM in Freesurfer I have only 1 small cluster in the frontal
>>>>>>>>>>>>>>> lobe that differs between cases and controls (controlling
>>>>>>>>>>>>>>> for all other IVs, FWMH = 10mm, cluster-forming threshold=
>>>>>>>>>>>>>>> .05, cluster-wise pval=.05), while for the ANCOVA method all
>>>>>>>>>>>>>>> but 8 of the parcellated regions differ significantly
>>>>>>>>>>>>>>> between groups (p<.05). For both methods I have used the
>>>>>>>>>>>>>>> same model of predictors (independent variables = gender,
>>>>>>>>>>>>>>> group, scanning site; covariate = age) and exactly the same
>>>>>>>>>>>>>>> sample of participants. I have also replicated the GLM
>>>>>>>>>>>>>>> analysis using the QDEC GUI to ensure that I had no made any
>>>>>>>>>>>>>>> mistakes.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Can you provide any insight into why I would be seeing such
>>>>>>>>>>>>>>> different results for each method using the same data set?
>>>>>>>>>>>>>>> My findings using the ANCOVA analysis make much more sense
>>>>>>>>>>>>>>> to me, given previous findings of reduced cortical thickness
>>>>>>>>>>>>>>> in schizophrenia subjects. I was surprised not to find the
>>>>>>>>>>>>>>> same pattern of effects using the GLM analysis.
>>>>>>>>>>>>>>> -- 
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Kind regards,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Bronwyn Overs
>>>>>>>>>>>>>>> Research Assistant
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Neuroscience Research Australia
>>>>>>>>>>>>>>> Margarete Ainsworth Building
>>>>>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>>>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> neura.edu.au<http://neura.edu.au>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Follow @neuraustralia on twitter
>>>>>>>>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
>>>>>>>>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe
>>>>>>>>>>>>>>> to the NeuRA Magazine
>>>>>>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
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MGH-NMR Center
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