Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

global and hemispherical average GI
by Ambrosino di Bruttopilo-2, S. 22 Oct '12

22 Oct '12

Dear FreeSurfer experts, I am using FS 5.1 to measure local Gyrification index (lGI). I would need to know if and how is possible to calculate the average GI for each hemisphere and for the total cortex...given the local values, is there any formula to compute the hemisperical and global GI? Thanks for any help Sara ------------------------------------------------------------------------------ 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.

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relationship between cortical volume, cortical area and cortical thickness
by L. Koenders 22 Oct '12

22 Oct '12

Dear Freesurfer people, We have a question regarding the relationship between cortical volume, cortical area and cortical thickness measurements derived from the parcellation stat-file. We were under the impression that the volume is equal to the area*thickness. However, this is not the case. Can you tell us how these three measurements relate to each other? Kind regards, Marise Machielsen & Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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Re: [Freesurfer] local GI calculation Error
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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error finding data on bourget
by qtnguyen＠nmr.mgh.harvard.edu 19 Oct '12

19 Oct '12

Dear Freesurfer experts, I'm trying to run structural reconstruction for two subjects DODASD016 and DODASD017. DODASD016 was scanned last Wed Oct 10 and last week I was able to findsession DODASD016, run dcmdir-info-mgh, and run recon-all using pbsubmit. However, after this was done I was unable to unpack the Bold & DTI Data from Bourget. We believe that the recon-all didn't work and when we tried to re-run: (for DODASD016) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 (and for DODASD017) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 ...I got the error message "ERROR: finding data" Can you help me resolve this issue? Or can you direct me to someone who can help? Thank you! Trang

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local GI calculation Error
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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withe matter of cortical Lables
by Gabriel Gonzalez Escamilla 19 Oct '12

19 Oct '12

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error while compiling utils
by Kim, Daniel 19 Oct '12

19 Oct '12

Hi Freesurfer users, I'm trying to compile utils on my Ubuntu 10.04 64 bit machine and I am getting a considerable amount of error while compiling afni.c - I am using gcc-4.4.3, g++-4.4.3 for compilers - I have successfully installed VXL and MNI as per the developer's guide (I am not building any GUI apps) - Had to add "-I/usr/src/linux-headers-2.6.32-43/include" under CFLAGS in utils/Makefile since without it, it would spit out error message saying it cannot find <linux/compiler.h> - under the utils folder, "make" gives an error along the lines of "expected specifier-qualifier-list before ‘size_t’" (attaching error log file) - tried using older compiler gcc-3.3, g++3.3 but problems seems worse I'm a bit stuck here and hoping that someone has had experience similar to this who can lend me some help? Thanks very much! cheers Danny Kim Children's Brain Mapping Centre BC Children's Hospital

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Cortical thickness percent difference surface maps script in matlab feedback wanted.
by Knut J Bjuland 18 Oct '12

18 Oct '12

Dear Freesurfer expert I have produce a script to make percent difference in cortical thickens using information from the mailing list. Could you please take look if this script is correct, or if there is a better way to do it? function [ out ] = diff_map( difference, average ) %percent difference Summary of this function goes here % This function takes two gamma.mgh from group differences 1 -1 and divide % with gamma.mgh from 0.5 0.5 to produce a new mgh with percent % difference between two groups. % Copyright Knut Jørgen Bjuland <knutjbj(a)hotmail.com> % Freesurfer license mat=fast_vol2mat(difference.vol); n=size(mat); for i=1:n(2), mat(i)=difference.vol(i)*100/average.vol(i); end out=difference; out.vol=fast_mat2vol(mat,out.volsize); end

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downsampling surface in native space
by Franz Liem 18 Oct '12

18 Oct '12

Dear FS experts, I would like to downsample a subject's white surface to arrive with a smaller number of vertices in order to feed the surface into FSL's surface tracking. I tried to map the fsaverage6 onto the single subject: mri_surf2surf --hemi lh --srcsubject fsaverage6 --sval-xyz white --trgsubject s01 --trgsurfval white.ico6 --tval-xyz --trgicoorder 6 If I load it into tksurfer, the surface now looks (as expected) much coarser. However, the number of vertices is still ~ 130k. Furthermore, it would be great if vertex x would spatially correspond in all subjects. Any advice is much appreciated, Cheers, Franz

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Cortical thickness percent difference surface maps howto
by Knut J Bjuland 18 Oct '12

18 Oct '12

Hi Is it possible to generate surface maps for the percent difference in cortical thickness between 2 groups within with Freesurfer 5.1? Could you please give link to how to use Matlab to compute the differences as described in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html? Cheers Knut J

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