Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

parcellation questions
by Xing Wang 13 Jul '09

13 Jul '09

Dear freesurfer experts, I have several new templates established based on 1,000 MRI images of Chinese volunteers. I want to use freesurfer to do parcellation on these templates. Could you tell me how to do the processing or if you could give me some advices. Thanks a lot! Cindy Department of Radiology, XuanWu Hospital, Beijing ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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autorecon2-error
by whblqh＠mail.ustc.edu.cn 12 Jul '09

12 Jul '09

Hello,everyone I test freesurfer on my computer and demand "recon-all -s bert -autorecon2",but there were some errors,as follows: ........ #-------------------------------------------- #@# Cortical ribbon mask Mon Jul 13 02:59:19 CST 2009 /home/whb/soft/freesurfer/subjects/bert/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bert mris_volmask.bin: error while loading shared libraries: /home/whb/soft/freesurfer/lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied Linux localhost.localdomain 2.6.21-1.3194.fc7 #1 SMP Wed May 23 22:35:01 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Jul 13 02:59:20 CST 2009 I don't know what's the reason. would you like to help me£¿ Thanks in advance. Hai-bao Wang Jul-12, 2009

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functional ROI
by Krajcsi Attila 11 Jul '09

11 Jul '09

Hi, If I want to run a functional ROI according to this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup#Gro… , is it possible to have the subjects' name in the output file? Is it possible that the volume of an unmasked region (region defined only by anatomical label and not by functional statistics) is larger than the volume of the structure itself (found in aseg.stat)? Did I miss something? Thank you, Attila

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cannot read file as type 3
by Lars M. Rimol 11 Jul '09

11 Jul '09

Hi, What does it mean when mris_surf2surf produces the error message that the input file cannot be read "as type 3" ? The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file. Thank you! yours, LMR

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Fwd: Re: question: qdec vs GLM DODS
by Rosa Steimke 10 Jul '09

10 Jul '09

Hi! i have a question regarding the differences between qdec and glm dods. im trying to find out how to analyze my data. I have 1-2 variables of which I want to see the relation to thickness (Autism (discrete) + Empathy (continuous))and maybe 1-2 (gender+IQ) variables that I would want to controle for. Now i cannot understand whether it would be better for me to use the General Linear Model DODS or qdec. What are the differences/advantages. thanks in advance. Rosa Rosa Steimke Student Master of Neuroscience Vrije Universiteit Amsterdam -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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4D to 3D
by Mayuresh Korgaonkar 10 Jul '09

10 Jul '09

Dear Freesurfer authors, I have been working with the command line group analysis tutorial from the freesurfer wiki website. Unfortunately I did not "qcached" my data with recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the tutorial (see below) at the end of which I get a single 4D file "lh.gender_age.thickness.10B.mgh" concatenated over all subjects Is there a way to split this file into 3D files so that I have a thickness file for each individual subject? Thanks, Mayuresh mris_preproc --fsgd gender_age.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com

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v.4.0.5 cross-sectional & v.4.4.0 longitudinal
by Elizabeth Selgrade 10 Jul '09

10 Jul '09

Hello, Can I use v.4.4.0's longitudinal processing stream on scans that I cross-sectionally segmented with v.4.0.5? If so, do I need to rerun any steps of the cross-sectional processing before using these segmentations as inputs in the longitudinal processing? I know a similar question was already posted on the listserve. I apologize for asking again, but I can't find the response. Many thanks! Liz Selgrade --- Elizabeth S. Selgrade Research Health Science Specialist VISN 6 MIRECC Durham, NC

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image matrix
by Feng-Xian 10 Jul '09

10 Jul '09

Hi, I want to check the image matrix after doing autorecon-all. When I look at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions”. This is said that that image matrix is 256 x 256 x 256. Right? And, I want to know how many voxels do an inflated surface have? Where dir and what text do I to get that? And, do FreeSurfer have a text that including the value of cortical thickness? I want to know the information of cortical thickness’s value at all pixels of whole brain for each subject. If yes, what text has the information of the value of cortical thickness and where do I find that text? If no, how can I get the information? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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Surface based volumetry vs Voxel based morphometry
by Pedro Paulo de Magalhães Oliveira Junior 09 Jul '09

09 Jul '09

It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of subcortical structures. The plain question people ask me is: what`s the advantage of FreeSurfer over SPM in terms of volumetric measures. I have some answers for this. I have wrote something about in the FAQ of FreeSurfer but I was wondering if there's some comparative study or some better idea on this. ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business

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pial surface
by Barnali Basu 09 Jul '09

09 Jul '09

Experts, I have successfully run recon-all (all the 3 processes autorecon1,2 and 3) on a subject. When I see the surfaces on tksurfer, I dont get to see the pial surface. I gather I could construct Pial surface by running autorecon2-pial. Would this affect in any way, since I have already finished autorecon3. Do I have to run autorecon3 again ? Any help would be appreciated Thanks Barnali

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