Mark,
sorry but it's still unsuccessful. First, though, let us make sure I
understand what you mean by "scaled" mask. What I did is I took the
image mask.nii.gz (from the same analysis that yields the residuals I'm
interested in using), added the value 10 to all voxels (so brain voxels
are = 11, non brain voxels are =10), and then added this mask to the
residuals image.
If I run the analysis however it still gives the following error:
Stats
mkdir -p custom_timing_files ; /bin/cp /imaging/mm03/STMemory/FSL2/sub203/Regressors/sub203_TGT.txt custom_timing_files/ev1.txt
mkdir -p custom_timing_files ; /bin/cp /imaging/mm03/STMemory/FSL2/sub203/Regressors/sub203_NN-TGT.txt custom_timing_files/ev2.txt
/imaging/local/linux/bin/fsl-4.0.1/bin/film_gls -rn stats -sa -ms 5 -sp /imaging/local/linux/bin/fsl-4.0.1/bin/susan_smooth filtered_func_data design.mat 1000.0
Log directory is: stats
parad.getDesignMatrix().Nrows()=150
parad.getDesignMatrix().Ncols()=6
sizeTS=150
numTS=0
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
Warning: Number of voxels = 0. Spatial smoothing of autocorrelation estimates is not carried out
Tukey M = 12
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
Completed
Saving results...
An exception has been thrown
Logic error:- detected by Newmat: Maximum or minimum of null matrix
Error: FILM did not complete - it probably ran out of memory
Have I misunderstood your suggestion?
all the best
martin
Mark Jenkinson wrote:
> Dear Martin,
>
> I think it will still have problems generating a proper mask if you
> add a constant
> everywhere.
>
> I suggest you add a scaled mask image and see if that works.
>
> Otherwise it is probably trying to analyse voxels where there is zero
> variance in
> the res4d (because it is outside the mask) and failing because of that.
>
> All the best,
> Mark
>
>
> On 10 Apr 2008, at 17:16, Martin M Monti wrote:
>
>> Mark,
>>
>> thank you, I did add a constant to the whole image, but it still is
>> not completing. The error however is now a little further down, in
>> the stats:
>>
>> An exception has been thrown
>> Logic error: detected by Newmat: Minimum or maximum of null matrix
>>
>> Error: FILM did not complete - it probably ran out of memor
>>
>> I tried running the same script with/without FILM (in fact, this
>> analysis is on residuals which should already have been
>> pre-whitened..), but i get exactly the same error. Is there any other
>> feature of the residuals that may be causing this?
>>
>> thanks
>>
>> martin
>>
>> Mark Jenkinson wrote:
>>> Hi,
>>>
>>> The problem is most likely due to the fact that res4d has a zero mean.
>>> This causes problems for mask generation and intensity normalisation,
>>> which is where this crashes.
>>>
>>> Add on a scaled mask image to your res4d (to give it a non-zero mean)
>>> before running FEAT and you'll probably be fine.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>>
>>>
>>> Martin M Monti wrote:
>>>> Dear All,
>>>>
>>>> I'm running a 2-step regression by taking the residulas of a a
>>>> first-level and using them into another first level.
>>>> However, as I run the "second" first-level I consistently get the
>>>> following error:
>>>>
>>>> Prestats
>>>>
>>>> Total original volumes = 150
>>>>
>>>> /imaging/local/linux/bin/fsl-4.0.1/bin/fslroi
>>>> /imaging/mm03/STMemory/FSL2/sub203/sub203_Flobs_Res example_func 75 1
>>>> /imaging/local/linux/bin/fsl-4.0.1/bin/fslmaths
>>>> /imaging/mm03/STMemory/FSL2/sub203/sub203_Flobs_Res -thrp 10 -Tmin
>>>> -bin mask -odt char
>>>> /imaging/local/linux/bin/fsl-4.0.1/bin/fslmaths
>>>> /imaging/mm03/STMemory/FSL2/sub203/sub203_Flobs_Res -mask mask
>>>> /imaging/mm03/STMemory/FSL2/sub203/sub203_Flobs_Res
>>>> /imaging/local/linux/bin/fsl-4.0.1/bin/fslmaths
>>>> /imaging/mm03/STMemory/FSL2/sub203/sub203_Flobs_Res -ing 10000
>>>> filtered_func_data -odt float
>>>> ERROR:: Empty mask image
>>>> ERROR:: Empty mask image
>>>> ERROR:: Empty mask image
>>>> ERROR:: Empty mask image
>>>>
>>>> etc ..
>>>>
>>>> As I inspected the input data file ("sub203_Flobs_Res.nii.gz" above
>>>> -- which is simply a copy of the res4d.nii.gz file in the stats
>>>> folder of the "first" first-level analysis) I noticed that by when
>>>> the process has finished (and given the error above) it is empty,
>>>> yet I am sure that it was not empty before launching the feat script.
>>>>
>>>> Ideas what I'm doing wrong?
>>>>
>>>> all the best
>>>>
>>>> martin
>>>>
>>
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