Thank you so much! Can I also learn whether running vertex-wise analysis without GLM analysis in Qdec is possible or not? As I said, I will compare a single patient with a group of healthy controls, so GLM would not work. What would you suggest for this? Is it possible to extract lGI values from surface data?
Thank you for your help, Buse — Douglas N Greve <gr...@nmr.mgh.harvard.edu> şunları yazdı (7 Kas 2017 21:12): > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
