On 04/27/2016 10:24 AM, Martin Juneja wrote: > Dear FreeSurfer experts, > > I am using FsFast functional connectivity walkthrough steps to analyze > fMRI data from: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough > > I am able to run all these steps successfully and can view the > voxel-wise distribution maps. > > I was wondering if it's possible to: > (1). overlay externally defined ROIs (e.g. R1.nii) on these maps e.g. > on pcc (partial correlation coefficient) to find the correlation > coefficient between R1.nii and seed region, may be averaged over > voxels or voxel-wise? Are you trying to just overlay R1 onto the results or do you want to use R1 as a seed? If as a seed, then you need to create a binary mask in the anatomical space, eg, $SUBJECTS_DIR/subject/mri/R1.mgz, then specify -seg R1.mgz -segid 1 when running fcseed-config. > (2). display labels (name of the areas) as well on the distribution maps? It this is in the volume, then you can create a lookup table (similar to $FREESURFER_HOME//FreeSurferColorLUT.txt with the name of your label, then load both as a segmentation. If this is on the surface, then you need to map R1 to the surface (probably mri_vol2surf), then convert to a label (mri_cor2label with --surf option), then convert the label to an annotation (mris_label2annot)
> > Any help would be really appreciated. > > Regards, > MJ > > > _______________________________________________ > 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.
