Thank you so much Douglas. That's really helpful.

On Mon, Sep 18, 2017 at 2:41 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

>
>
> On 09/18/2017 05:35 PM, Martin Juneja wrote:
> > Dear Douglas,
> >
> > Thanks a lot for your reply.
> > Could you please clarify why I have to add 0.3 because I am using a
> > positive sign? How did
> > Do you mean if I want to use threshold of 3, then adding 0.3 to this
> > so threshold of 3.3 should be used ?
> The sig map is unsigned. If it were signed, then the p-values would be
> half, and the sig values would be 0.3 greater (sig=-log10(p)). When you
> run glmfit-sim with a signed value (pos, neg), then effectively adjusts
> the p-values to be signed. However, when you view the sig maps, no such
> adjustment takes place.
> >
> > If I use --sim-sign abs, do you think then there is no need to add a
> > number to threshold? Whats the best approach to run this command?
> Correct, if you use abs, you do not need to adjust because abs is
> two-tailed. The answer to your second question is totally up to you.
> Usually, people use a signed  test if they had an a priori hypothesis
> about the direction of the effect.
> >
> > I am really confused here and would really appreciate any
> > clarification on this.
> >
> > Thanks a lot.
> >
> > On Mon, Sep 18, 2017 at 2:20 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> >
> >     On 09/15/2017 02:13 PM, Martin Juneja wrote:
> >     > Hi experts,
> >     >
> >     > I have three questions. I would really appreciate any help.
> >     >
> >     > (1). I ran following commands to estimate relationships between LGI
> >     > and Behav data:
> >     >
> >     >  mris_preproc --fsgd Behav.fsgd --target fsaverage --hemi lh --meas
> >     > pial_lgi --out lh.Behav_LGI.mgh
> >     >
> >     > mri_surf2surf --hemi lh --s fsaverage --sval lh.Behav_LGI.mgh
> --fwhm
> >     > 10 --cortex --tval lh.Behav_LGI.10.mgh
> >     >
> >     > mri_glmfit --y lh.Behav_LGI.10.mgh --fsgd Behav.fsgd dods --C
> >     > Corr-Behav-cor1.mtx --surf fsaverage lh --cortex --glmdir
> >     > lh.Behav_LGI_P.glmdir --eres-save
> >     >
> >     > mri_glmfit-sim_nonortho --glmdir lh.Behav_LGI_P.glmdir --sim
> >     perm 2000
> >     > 1.3 permcsd --sim-sign pos --cwpvalthresh .05 --perm-resid
> >     --overwrite
> >     >
> >     > Finally, cluster summary gives me one clusters with peak at the
> >     > fusiform gyrus as following:
> >     > ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY  MNIZ    CWP
> >     >  CWPLow    CWPHi   NVtxs    WghtVtx   Annot
> >     >    1       -4.045   10153  32101.81    -36.5 -39.5  -15.1  0.00050
> >     >  0.00000  0.00100  64731  -106698.82  fusiform
> >     >
> >     > As you can see number of voxels is 64731, so I when I viewed the
> >     > results in FreeView, its showing me a big cluster, almost all
> >     over the
> >     > brain (please see attached screen shot).
> >     >
> >     > Could you please tell me why I am getting these sort of results,
> and
> >     > how can I fix this? If I change cluster forming threshold from
> >     1.3 to
> >     > 3, would that work? I wanted to make sure before I re-run the
> >     analysis
> >     > because mri_glmfit-sim_nonortho command takes about a day to
> finish.
> >     I don't know whether it would work, but it would make it better.
> >     You can
> >     also just load the sig.mgh file and change the voxel-wise thresholds
> >     until you get reasonably sized clusters, then run using that
> >     threshold.
> >     If you do this, set the glmfti-sim threshold to the value your
> >     selected
> >     during viewing but add 0.3 (needed because you are using a
> >     positive sign).
> >     >
> >     > (2). How can I save output cluster e.g. fusiform gyrus in above
> >     > example in NIFTI MNI volume space so that I can use this cluster
> for
> >     > functional connectivity analysis?
> >     You're probably better of doing your fmri analysis in surface space
> >     because mapping back and forth is a little tricky. But if you want
> >     to do
> >     it, you can do
> >     something like
> >     mri_label2vol --annot /path/to/annot/in/glmfit/dir --temp
> >     $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg
> >     $FREESURFER_HOME/average/mni152.register.dat --fill-ribbon --subject
> >     fsaverage --hemi lh --o output.segmentation.in
> >     <http://output.segmentation.in>.mni152space.nii.gz
> >
> >     The output segmenation will have all the clusters from the annot
> file.
> >     Remember, this mapping is an approximation
> >
> >     >
> >     > (3). If I want to use fusiform gyrus from standard FreeSurfer
> >     > parcellation rather than from my results, how can I save that in
> >     > standard MNI volume space?
> >     same as above
> >     >
> >     > Thank you so much !
> >     >
> >     >
> >     > _______________________________________________
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> >
> >     --
> >     Douglas N. Greve, Ph.D.
> >     MGH-NMR Center
> >     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> >     Phone Number: 617-724-2358 <tel:617-724-2358>
> >     Fax: 617-726-7422 <tel:617-726-7422>
> >
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> >     <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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