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

On Mon, Sep 18, 2017 at 2:41 PM, Douglas N Greve <greve@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
> <greve@nmr.mgh.harvard.edu <mailto:greve@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
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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