Dilation operations are slower the larger they are. I checked our code
and we use 50mm actually.
Matt.
On 12/14/17, 4:18 PM, "FSL - FMRIB's Software Library on behalf of Sam P"
<[log in to unmask] on behalf of [log in to unmask]> wrote:
>Hi Matt,
>
>Thank you again for your rapid response. I apologize for not including
>context before; I am still learning how to use the listserv. It is copied
>below. Yes, I was referring to medial wall dilation, exactly. Is there a
>maximum amount of dilation that you wouldn't surpass?
>
>Thanks again,
>Sam
>
>______________________________________________________________
>
>Since you didn©öt include the preceding e-mails I©öm not sure of the
>context. But if this is medial wall dilation I think you need at least
>20mm.
>
>Peace,
>
>Matt.
>
>On 12/14/17, 3:39 PM, "FSL - FMRIB's Software Library on behalf of Sam P"
><[log in to unmask] on behalf of [log in to unmask]> wrote:
>
>>Hi Matt,
>>
>>Thank you for your quick response. I have been looking into your
>>suggestion, and I think dilation might be helpful. What amount of
>>dilation (in mm) do you think would be appropriate?
>>
>>Thank you so much,
>>Sam
>
>
>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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