 |
 |
Hi Jeff, Yes - fsl_regfilt demeans both the design.mat time courses and the data before filtering, and then adds the data mean back to the result. Cheers, Paul On 29 July 2015 at 16:55, Jeff Stevenson <[log in to unmask]> wrote: > Thanks paul, and just to be sure: the mat file with the nuisance > variables input into fsl_regfilt, is it demeaned or not? > jeff > > From: paul mccarthy > Reply-To: FSL - FMRIB's Software Library > Date: Tuesday, July 28, 2015 at 2:36 AM > > To: FSL - FMRIB's Software Library > Subject: Re: [FSL] using fsl_regfilt to regress out confounds > > Hi Jeff, > > Aah, because you're interested in reporting the absolute FA/F2 values > after stats, my previous advice of globally shifting the data doesn't > really make much sense. In this case, a better approach may be not to use > fsl_regfilt, and to just include your confounds in the design matrix that > you pass to randomise. > > Cheers, > > Paul > > > On 28 July 2015 at 01:33, Jeff Stevenson <[log in to unmask]> wrote: > >> Hi paul, thanks for getting back to me. Seems like we are using the –f >> flag for cols correctly then. F2 is the crossing fiber component of FA from >> bedpost. So it can be small and noisy. Default thresh is 0.05. In our case >> values just above the default thresh go negative when filtered, Which is a >> nonsense value. Does randomise demean the in file? I thought not. We do >> demean the design matrix file with the behavior and covariates. >> Some of those results, when covaried the traditional way, are significant >> with positive cluster means. When filtered and then tested the regions with >> low values are still significant but some of the mean values for the >> clusters are negative. Which is a problem to report. Are you suggesting >> that I add back in the lowest negative from fslstats -R to give a range >0? >> For all measures? GM WM F2 etc… >> Cheers jeff >> >> >> From: paul mccarthy >> Reply-To: FSL - FMRIB's Software Library >> Date: Friday, July 24, 2015 at 4:22 AM >> To: FSL - FMRIB's Software Library >> Subject: Re: [FSL] using fsl_regfilt to regress out confounds >> >> Hi Jeff, >> >> >> >> On 13 July 2015 at 17:02, Jeff Stevenson <[log in to unmask]> wrote: >> >>> Hi folks, I am trying to use fsl_regfilt on some tbss and vbm data >>> and have 2 questons: >>> >>> When removing 2 (or more) nuisance variables (gender etc) I demean >>> both into a 2 col design.mat format, then use the flag –f “1,2” to apply >>> both cols ( or –f “1,2,3” for 3 cols etc)? >>> In other words are components “1,2,3” from ICA the same as columns >>> “1,2,3” in a GLM design.mat? >>> >> >> Yes. If you are regressing using a melodic mixing matrix, '-f 1,2,3' >> refers to components 1,2,3. If you are regressing using a GLM design >> matrix, then '-f 1,2,3' refers to columns 1,2,3 of the matrix. >> >> >>> Secondly, even with only 1 variable when applied to F2 some of the >>> voxels go negative. More so with 2. Should those simply be thresholded to 0 >>> after or is there a constraint flag? How does fthresh and fthresh2 fit into >>> this issue if at all? >>> >> >> I'm not sure what 'F2' is referring to, but the regression may result >> in voxel values dipping into the negative - it may or may not happen, >> depending on the regressor values, and on the raw data values. The fthresh >> and fthresh2 options are irrelevant here - they are only applicable when >> regressing against MELODIC components. >> >> You shouldn't threshold the regressed data, but if you want your data >> to be > 0, it should be safe to apply a global shift to move all of the >> voxel values above zero (assuming that the data will be de-meaned during >> stats anyway). >> >> Cheers, >> >> Paul >> >> >> >>> >>> Jeff >>> >>> >>> >>> >>> >> >