Intensity Mean will be the mean value of the input (lGI) averaged over the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum andrange=max-min over the ROI On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote: > Dear Freesurfers, > > I have two questions: > > 1) In the last stage of the recon-all -s <subj> -localGI analysis, > local gyrification index values are calculated at each pial vertices. > Is there any way (command?) to extract /vertex-wise local gyrification > index values/ (of individual subjects) /before running GLM analysis in > Qdec/? GLM analysis is not suitable for my study (single-case), so I > need to extract values for each subject and use them for my own > statistical analysis. > > 2) As far as I know we can extract /parcel-wise lGI/ values using the > following command: > > mri_segstats --annot /subjID/ lh aparc \ > > --i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \ > > --sum lh.aparc.pial_lgi.stats > > > Running this command provides "Intensity Mean, Intensity STD, > Intensity Max, Intensity Min, Intensity Range" values for each > parcellated area. Can you explain these values and what they mean? > > > Thanks, > > -Buse > > > > > On 5 November 2017 at 19:54, Buse Merve Ürgen <buseur...@gmail.com > <mailto:buseur...@gmail.com>> wrote: > > Dear Freesurfer developers, > > I would like to run Local Gyrification Index analysis for a group > of healthy controls and a single patient. After running recon-all > -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi > surf files. In the last stage of this analysis, local gyrification > index values are calculated at each pial vertices. > > In the wiki, it is said that the next process should be done in > qdec, but since I have only one patient, GLM analysis would not be > suitable. Thus, I would like to get the LGI values of each subject > as e.g. text files (like stats files for curvature, thickness, gm > volume), and use them for my own analysis (not in qdec). I know > that we can get parcel-wise anaysis values using this command: > mri_segstats --annot CASE lh aparc \ > > --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ > > --sum lh.aparc.pial_lgi.stats > > But I would like to use vertex-wise analysis values for my won > analysis. Is it possible? Can I learn the command I need to use to > get these values for each subject? > > Thank you, > Buse > > -- > > Buse > > Urgen > > > > > -- > > Buse M. Ürgen > > Ph.D. Candidate Neuroscience Graduate Program National Magnetic > Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research > Center Bilkent University Ankara, 06800 Turkey > > > > _______________________________________________ > 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.
