Hi Giedre, Can you send me just the pial surface of this subject, and the recon-all.log (in the scripts folder) and I'll have a look. Please also let me know which version of freesurfer you are running, and which matlab version.
Best, Marie On Mar 4, 2015, at 3:08 AM, "Stripeikyte, G." <g.stripeik...@umcutrecht.nl<mailto:g.stripeik...@umcutrecht.nl>> wrote: Hi Marie, Thanks for advice. I have attached a screenshot of overlaid lGI. I have at least 4 subjects with extremely high values of total 106. Best, Giedre From: Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday 3 March 2015 21:00 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] lGI ?h.pial-outer-smoothed Hi Giedre, Small intersections like that are fine and won't affect the lGI computation, so you are good with that. Values around 20 are however more preoccupying! Can you send me a screenshot of the lGI overlaid on the surface for this subject using tksurfer or freeview? Best, Marie NB: if you are interested in thickness as well, you might want to correct the segmentation in the parahippocampal gyrus for this subject (the "drop-shaped" WM inclusion in the cortex). On Mar 3, 2015, at 6:58 AM, "Stripeikyte, G." <g.stripeik...@umcutrecht.nl<mailto:g.stripeik...@umcutrecht.nl>> wrote: Dear freesurfers, I am analysing localGI and noticed that sometimes scans with ?h.pial-outer-smoothed surface intersect ?h.pial surface (attached pic.). Is this normal or should I correct parameters and rerun localGI? Also when I extracted ROI lGI values I got some extremely high results. For example in lh_insula and rh_insula, for some participants lGI reach about 20. Scans look normal of these participants. Are such high values possible or something wrong with calculation? Sincerely, Giedre ________________________________ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. <pial-outer-smoothed.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. <lGI_distribution.pdf>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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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