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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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