Freesurfer August 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
82 discussions

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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longitudinal stuff
by Sky Raptentsetsang 11 Aug '08

11 Aug '08

Hi Bruce, From the processing that's been performed we're fairly certain that the issue is only with the -long script. So I just wanted to verify with you if I processed our many baseline subjects with version4 (cross-sectionally), while the -long script is being bug-fixed, I could simply start the subjects longitudinal scans once your fix is in place. So from your investigations thus far, could you tell us if the FSv4 cross-sectional processing will be altered due to any fix that might be put into place in the near future? Many thanks as always! Cheers, Sky

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Fwd: talairach_afd failed
by 李日 11 Aug '08

11 Aug '08

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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talairach_afd failed
by 李日 11 Aug '08

11 Aug '08

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recon error
by Ilana Hairston 10 Aug '08

10 Aug '08

Hi there, I am new to free surfer, and am trying to analyse brains of kids ages 8-11. running recon1 i get the following error message: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Looking at past mailings seems you recommended checking the registry. However, during recon no file called ???.dat was created as far as i can tell, and without specifying --reg i get the error: ___$ tkregister2 --s C2647 --mov C2647_070809cv.img INFO: no target volume specified, assuming FreeSurfer orig volume. ERROR: no registration file specified thanks, ilana -- You must believe in free will; there is no choice.

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Watershed Error
by Vina Goghari 09 Aug '08

09 Aug '08

Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty ! I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process? Thanks, Vina

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Freesurfer August 2008