Dear Matt
You were right. The values on the medial wall are all zeros and the time
series are constant. Do you perhaps have a reliable solution to this?
Many thanks in advance!!
Best, Blazej
On 21 March 2017 at 21:51, Glasser, Matthew <glass...@wustl.edu> wrote:
> Are there any zeros on the medial wall? This issue could occur because of
> timeseries with all zeros, as I recall.
>
> Peace,
>
> Matt.
>
> From: Blazej Baczkowski <bm.baczkow...@gmail.com>
> Date: Tuesday, March 21, 2017 at 1:22 PM
> 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
>
> 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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>>
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> Healthcare Information or other information of a sensitive nature. If you
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