Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

downloadable manual
by Eliezer Kanal 14 Aug '08

14 Aug '08

Hello folks - I recently downloaded freesurfer and am slowly becoming more familiar with it. However, having to search through the myriad of pages on the wiki every time I have a question is very cumbersome, and more often than not, fruitless. Is there a downloadable manual available anywhere? Thanks - Eliezer Kanal Graduate Student, Bioengineering Center for Clinical Neurophysiology University of Pittsburgh

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Compute First Level Analysis
by Balaji Goparaju 14 Aug '08

14 Aug '08

Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -------------------------------------------------------------- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -------------------------------------------------------------- ------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing!

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Processing after edits.
by Matt Clarkson 14 Aug '08

14 Aug '08

Hi there, If you run recon-all, and then do some edits, for example control points, then the tutorial says you do: recon-all -autorecon2-cp -autorecon3 -subjid subject4_before Similarly for white matter: recon-all -autorecon2-wm -autorecon3 -subjid 111_manual_edits_before and similarly for brain mask: recon-all -autorecon2-pial -autorecon3 -subjid subject3_before So, if I have done all 3 types of edits, would it be better to do: recon-all -autorecon2-cp -autorecon3 -subjid subject3_before recon-all -autorecon2-wm -autorecon3 -subjid subject3_before recon-all -autorecon2-pial -autorecon3 -subjid subject3_before or would I do: recon-all -autorecon2-cp -autorecon2-wm -autorecon2-pial -autorecon3 -subjid subject3_before While the second option is more than likely quicker, will it make any difference to the results? Many thanks in advance. -- Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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error while loading shared libraries:libtiff.so.3
by lan lin 13 Aug '08

13 Aug '08

I'm using 64 bit Ubuntu and installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-rh9-stable-pub-v…> Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all and got error message while loading shared libraries:libtiff.so.3. I have tried ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 But still got same error message.

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FDR button
by Juergen Haenggi 13 Aug '08

13 Aug '08

Dear FS experts When using the FDR button in the Configure Overlay Display, there appear the FDR corrected new threshold in the terminal after pressing the Set Threshold Using FDR button. However, when changing the rate from 0.05 to e.g. 0.1, the FDR corrected threshold does not change. Why? Furthermore, this threshold is different when the sig.mgz will be truncated. What does mean the option Only marked? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Re: [Freesurfer] cortical thickness
by Pedro Paulo de Magalhães Oliveira Junior 13 Aug '08

13 Aug '08

Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/q… PPJ 2008/8/13 Al-Radaideh Ali <ppxama(a)nottingham.ac.uk> > Hi Pedro, > > I have seen in one email that using mri_surf2vol can map the thickness > values into the volume but I am not sure what to type in the command line or > what steps should I follow to do this. Sorry I am very new to freesurfer. > > Thanks alot > > Ali > > > ------------------------------ > *From:* Pedro Paulo de Magalhães Oliveira Junior > *Sent:* Wed 13/08/2008 14:23 > *To:* 李日 > *Cc:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] cortical thickness > > Hi 李日, > > 1) Is the cortical thickness of the area where you passed the mouse over. > 2) Is the index of the vertex in the cortical model. > 3) Red line select the threshold limit for red color in the map, green line > select the interface between red/yellow coloring. > > Regards, > > Pedro Paulo Jr. > > > > 2008/8/13 李日 <lirizkd(a)gmail.com> > >> Hello, >> I am new to freesurfer, I used recon-all and it finished, I can get the >> thickness map,and i have some questions about the tksurfer tools. I paste a >> picture of the tksurfer tool window in the accessory,and i have labeled 3 >> areas. >> In area 1, I think is the thickness information, what does the number >> 3.274984 mean? >> In area 3, what is the funtion of the red and green line? >> Best Regards. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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cortical thickness
by 李日 13 Aug '08

13 Aug '08

Hello, I am new to freesurfer, I used recon-all and it finished, I can get the thickness map,and i have some questions about the tksurfer tools. I paste a picture of the tksurfer tool window in the accessory,and i have labeled 3 areas. In area 1, I think is the thickness information, what does the number 3.274984 mean? In area 3, what is the funtion of the red and green line? Best Regards.

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cortical thickness for a ROI
by Deniz KATIRCIOGLU 12 Aug '08

12 Aug '08

Hi, I want to learn if there exists a way of overlaying the "cortical thickness output" of "recon-all -*autorecon3*" stage with a ROI drawing (a 3D image file with non-zero values for ROI and zero for the remaining parts) performed in AFNI, so that we can better restrict the cortical thickness to our specific region to extract the thickness information around there, locally. Thanks in advance... Deniz KATIRCIOGLU METU, Turkey

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Re: [Freesurfer] Fwd: talairach_afd failed
by Bruce Fischl 12 Aug '08

12 Aug '08

mri_convert does, but how will you know left from right? On Tue, 12 Aug 2008, [GB2312] ÀîÈÕ wrote: > I can't get access to the original dicoms, does the mri_convert command have > some options to change the .img data to the right .mgz format data? And why > the .img has this problem. > thanks, and my english is poor,sorry. > > > 2008/8/12, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> >> the problem is using .img (analyze) format. Can you get access to the >> original dicoms? >> >> On Tue, 12 Aug 2008, [GB2312] ÀîÈÕ wrote: >> >> Hi Bruce Fischl, >>> I started with the .img and .hdr data, First I used command >>> 'mri_convert' >>> and convert the data to .mgz format. >>> and then I used tkmedit to display. Can you tell me how to correct it? >>> >>> thanks >>> >>> Tim >>> >>> >>> 2008/8/11, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>> >>>> >>>> Hi Tim, >>>> >>>> can you tell us what form the data that you started with was in? >>>> Something >>>> is wrong with the direction cosines as tkmedit is displaying the brain >>>> upside-down (and it thinks that sagittal is horizontal). >>>> >>>> cheers, >>>> Bruce >>>> >>>> >>>> On Mon, 11 Aug 2008, [GB2312] ÀîÈÕ wrote: >>>> >>>> Hello: >>>> >>>>> I am a new to FreeSurfer, and i run the following command : >>>>> recon-all -autorecon1 -s temp , and it exit with some errors: >>>>> >>>>> >>>>> Mon Aug 11 15:49:56 CST 2008 >>>>> talairach_avi done >>>>> >>>>> cp transforms/talairach.auto.xfm transforms/talairach.xfm >>>>> >>>>> #-------------------------------------------- >>>>> #@# Talairach Failure Detection Mon Aug 11 15:49:57 CST 2008 >>>>> /home/liri/liri/freesurfer/subjects/temp/mri >>>>> >>>>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >>>>> >>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >>>>> Linux liri-desktop 2.6.24-19-generic #1 SMP Fri Jul 11 23:41:49 UTC 2008 >>>>> i686 GNU/Linux >>>>> >>>>> recon-all exited with ERRORS at Mon Aug 11 15:49:57 CST 2008 >>>>> >>>>> >>>>> I have seen that it might be caused by the direction cosines in the >>>>> input file were >>>>> all wrong (coronal, saggital, horizontal wrong). so I checked the >>>>> nu.mgz, and it displays >>>>> >>>>> different from the bert subject, if this is the reason , how can i >>>>> correct it. >>>>> >>>>> thanks >>>>> tim >>>>> >>>>> >>>> >

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cortical thickness at different locations
by Al-Radaideh Ali 11 Aug '08

11 Aug '08

Hi, I managed to measure the cortical thickness for different subjects and to display their maps. Bu t I am not sure if I can measure the cortical thickness at some points in the cortex or at least the cortical thickness for some cortical regions. Best regards Ali Al-Radaideh PhD student SPMMRC, The University of Nottingham,UK This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer