Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-22 Thread Blazej Baczkowski 
Works!!!

Thanks a lot!

Best, Blazej

On 22 March 2017 at 13:11, Glasser, Matthew <glass...@wustl.edu> wrote:

> You can use wb_command -metric-dilate first and then reapply the medial
> wall mask on the outputs.
>
> Peace,
>
> Matt.
>
> From: Blazej Baczkowski <bm.baczkow...@gmail.com>
> Date: Wednesday, March 22, 2017 at 4:01 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
>
> 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.
>>>>

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-22 Thread Glasser, Matthew 
You can use wb_command -metric-dilate first and then reapply the medial wall 
mask on the outputs.

Peace,

Matt.

From: Blazej Baczkowski 
<bm.baczkow...@gmail.com<mailto:bm.baczkow...@gmail.com>>
Date: Wednesday, March 22, 2017 at 4:01 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] film_gls surface mode error Newmat: incompatible 
dimensions

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<mailto: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<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 1:22 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 9:00 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote:
Please post your film_gls command line.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Blazej Baczkowski 
<bm.baczkow...@gmail.com<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 8:33 AM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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 ma

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-22 Thread Blazej Baczkowski 
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
>>>
>>>
>&

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-21 Thread Glasser, Matthew 
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<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 1:22 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 9:00 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote:
Please post your film_gls command line.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Blazej Baczkowski 
<bm.baczkow...@gmail.com<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 8:33 AM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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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http://lists.humanconnectome.org/mailman/listinfo/hcp-users


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Health

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-21 Thread Blazej Baczkowski 
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
>>
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-21 Thread Glasser, Matthew 
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<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 9:00 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote:
Please post your film_gls command line.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Blazej Baczkowski 
<bm.baczkow...@gmail.com<mailto:bm.baczkow...@gmail.com>>
Date: Tuesday, March 21, 2017 at 8:33 AM
To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" 
<HCP-Users@humanconnectome.org<mailto: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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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
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or the taking of any action in reliance on the contents of this information is 
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Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-21 Thread Blazej Baczkowski 
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  wrote:

> Please post your film_gls command line.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Blazej
> Baczkowski 
> Date: Tuesday, March 21, 2017 at 8:33 AM
> To: "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
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

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Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

2017-03-21 Thread Glasser, Matthew 
Please post your film_gls command line.

Peace,

Matt.

From: 
>
 on behalf of Blazej Baczkowski 
>
Date: Tuesday, March 21, 2017 at 8:33 AM
To: "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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HCP-Users@humanconnectome.org
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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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