Thanks Matt!
Yes, the surface and timeseries files display correctly in the workbench.
Could you tell me what you mean by "mask the medial wall"? I dont know what
I could do here.
It appears to me that FILM does not even read the surface file -- I receive
the same error even when no input2 ("--in2") is specified, while I believe
it should say "file missing".
Best, Blazej
On 21 March 2017 at 18:03, Glasser, Matthew <glass...@wustl.edu> wrote:
> I wouldn’t recommend smoothing with the inflated surface, but rather the
> midthickness surface (which you can create by averaging the white and pial
> surface coordinates). As for your command, it looks correct to me. Do the
> surface and timeseries files display correctly in Connectome Workbench? Is
> the medial wall masked?
>
> Peace,
>
> Matt.
>
> From: Blazej Baczkowski <bm.baczkow...@gmail.com>
> Date: Tuesday, March 21, 2017 at 9:00 AM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org>
> Subject: Re: [HCP-Users] film_gls surface mode error Newmat: incompatible
> dimensions
>
> Hi Matt,
>
> Here are two commands that produce the error:
>
> 1) film_gls --in=test.lh.func.gii --in2=lh.inflated.surf.gii
> --mode=surface --rn=SURF_STATS --con=design.con --pd=design.mat --ar
>
> 2) film_gls --in=test.lh.func.gii --in2=lh.inflated.surf.gii
> --mode=surface --rn=SURF_STATS --con=design.con --pd=design.mat --thr=0.1
> --ms=15 --epith=5 --sa
>
> While this one runs smoothly:
>
> film_gls --in=test.lh.func.gii --in2=lh.inflated.surf.gii --mode=surface
> --rn=SURF_STATS --con=design.con --pd=design.mat --noest
>
> Thanks!!
> Blazej
>
> On 21 March 2017 at 14:50, Glasser, Matthew <glass...@wustl.edu> wrote:
>
>> Please post your film_gls command line.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Blazej
>> Baczkowski <bm.baczkow...@gmail.com>
>> Date: Tuesday, March 21, 2017 at 8:33 AM
>> To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org>
>> Subject: [HCP-Users] film_gls surface mode error Newmat: incompatible
>> dimensions
>>
>> Hello everyone,
>>
>> I encounter a problem with FSL's "film_gls" (v5.0.9) when performing
>> first level GLM analysis in surface mode. Data were projected to fsaverage5
>> space (10242 vertices). It appears that the problem occurs when FILM
>> estimates the autocorrelation, because it works perfectly fine with
>> "--noest" option.
>>
>> Here is the respective error message:
>>
>> *paradigm.getDesignMatrix().Nrows()=413*
>> *paradigm.getDesignMatrix().Ncols()=6*
>> *sizeTS=413*
>> *numTS=10242*
>> *Calculating residuals...*
>> *Completed*
>> *Estimating residual autocorrelation...*
>> *Fitting autoregressive model...*
>>
>>
>> *An exception has been thrown*
>> *Logic error:- detected by Newmat: incompatible dimensions*
>>
>> *Trace: SubMatrix(=); AutoCorrEstimator::fitAutoRegressiveModel.*
>>
>> My data has 413 timepoints and the design matrix consists of 6 columns
>> (enclosed). The volumetric analysis with the same design matrix and
>> autocorrelation estimation does not produce any error. The design matrix
>> was created with FSL FEAT/Glm Setup.
>>
>> Many thanks in advance for any help.
>>
>> Best regards, Blazej
>>
>>
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