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 ! > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > 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> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. 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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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
