If the medial wall zeros are not dilated away I think film_gls may have
problems. Perhaps the film_cifti script does not do this?
Peace,
Matt.
On 11/27/17, 12:49 PM, "FSL - FMRIB's Software Library on behalf of Sam P"
<[log in to unmask] on behalf of [log in to unmask]> wrote:
>Hello,
>
>I am encountering an error in FSL 5.0.10 that I can't seem to resolve.
>When I try to run film_cifti, I get an error during film_gls as it tries
>to compute parameter estimates for the surfaces. The volume runs through
>just fine, but the surface gifti gives a "process fails to converge"
>error.
>
>I have only seen one post related to this issue in the past, but there
>was not enough information posted to help me resolve the issue on my own.
>The post and its update were from March 21-22, 2017, entitled "film_gls
>surface mode error "Newmat: incompatible dimensions."" The hint to
>solving the issue is that "the command line works fine when the values in
>the medial wall are non-zero and the time series are not constant."
>
>I found that the values in my cifti are non-zero, but when film_cifti
>separates the cifti into giftis (surfaces and volume), each surface gifti
>suddenly has "zero" values. I do not know why this is happening or
>whether it is the main cause of my "process fails to converge" error.
>
>
>Here is an example of my film_cifti command:
>
>film_cifti -i REST1_Atlas.dtseries.nii -o BOLD_299-07_124-1 -l
>30299.L.midthickness.32k_fs_LR.surf.gii -r
>30299.R.midthickness.32k_fs_LR.surf.gii --filmOptions
>"--con=BOLD_299-07_124-1.con --pd=BOLD_299-07_124-1.mat"
>
>I also tried calling film_gls independently:
>
>/mnt/max/software/fsl-5.0.10/bin/film_gls --mode=surface
>--in=outLeft.func.gii --rn=statsLeft --epith=0 --ms=4
>--con=BOLD_299-07_124-1.con --pd=BOLD_299-07_124-1.mat
>--in2=30299.L.midthickness.32k_fs_LR.surf.gii
>
>
>In both cases, I get the following error:
>
>film_cifti error:
>paradigm.getDesignMatrix().Nrows()=226\nparadigm.getDesignMatrix().Ncols()
>=2\nsizeTS=226\nnumTS=32492\nCalculating
>residuals...\nCompleted\nEstimating residual
>autocorrelation...\nCalculating raw AutoCorrs... Completed\nTukey M =
>15\nTukey estimates... Completed\nCompleted\nPrewhitening and Computing
>PEs...\nPercentage done:\n\n\n
>An exception has been thrown\nRuntime error:- detected by Newmat: process
>fails to converge\n\n
>MatrixType = Rect # Rows = 2; # Cols = 2\nTrace: SVD; pinv.\n\n'
>
>film_gls error:
>Prewhitening and Computing PEs...
>Percentage done:
>An exception has been thrown
>Runtime error:- detected by Newmat: process fails to converge
>MatrixType = Rect # Rows = 2; # Cols = 2
>Trace: SVD; pinv.
>
>
>The design matrix has 226 rows (time points) and 2 columns (predictors).
>It was created using the "GLM Setup" function from the drop-down menu of
>the main FSL GUI.
>
>Please let me know if you have any ideas as to why this program is
>throwing an error. I can provide files if necessary.
>
>Thank you,
>Sam
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