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 ?
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? 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> 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.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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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