On Mon, May 15, 2017 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I think your command lines are correct. I would not expect that swapping
the y and pvr to give the same results. sig=-log10(p)=30 is not totally
unreasonable. I don't understand #2. Why are you running FDR and cluster
correction?

On 05/11/2017 06:39 PM, Martin Juneja wrote:
> In addition to that: I am always getting positive correlations (when I
> load sig.mgh) every time i.e. even when I correlated thickness and
> gyrification. None of the voxels/areas showing negative correlation
> between any of the structural measures
>
> On Thu, May 11, 2017 at 11:26 AM, Martin Juneja <mj70481@gmail.com

> <mailto:mj70481@gmail.com>> wrote:
>
> Hi Dr. Greve,
>
> I doubt these results because of following:
>
> (1). When I compare sig.mgh files created using following two
> commands i.e. correlation between LGI and CV versus CV and LGI:
> mri_glmfit --y Corr_CV_LGI/lh.LGI.10.mgh --fsgd CV_LGI.fsgd dods
> --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.CV.10.mgh
> and
> mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods
> --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh
>
> (a). I do not get identical maps. Please find attached screen shot.
> (b). Here, colorbar showing a value of around 30, does that
> reflect -log10(p)? I am not sure if thats normal?
>
> (2). Assuming magnitude from colorbar is normal then I performed
> FDR correction- I am assuming its same command as following as
> mentioned in FS manual:
> mri_glmfit-sim --glmdir Corr_CV_LGI/lh.VL.glmdir --cache 1.3 pos
> --cwp 0.01 --2spaces
>
> After running FDR correction, cache.th13.pos.sig.cluster.mgh and
> cache.th13.neg.sig.cluster.mgh, none of these are showing me any
> significant clusters, instead its showing a constant magnitude
> (same color) over whole brain?
>
> Thanks.
>
>
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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