Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

a question about FS longitudinal stream
by Guang Zeng 10 Mar '10

10 Mar '10

Hi, there, I have a question about FS longitudinal stream, I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine. When I ran the longitudinal stream, one of them stopped at the first step, it failed to do the skull stripping. I changed the watershed threshold, it works now. The question is, for this time point data, I want to use the following command line to finish the rest longitudinal analysis, recon-all -long tp_dat1 base_id -autorecon2 -autorecon3 Is it correct? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Longitudinal Stream...
by Gonzalo Rojas Costa 10 Mar '10

10 Mar '10

Hi: I processed a Longitudinal Stream between two MRIs of same patient taken in different dates... I used the following commands: i) recon-all -all -s <tp1id>, recon-all -all -s <tp2id> ii) recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all iii) recon-all -long <tp1id> <templateid> -all Which information was stored in the <tp1id>.long.<templateid> folder ?... Sincerely, Gonzalo Rojas Costa

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freesurfer atlas and template
by Guang Zeng 10 Mar '10

10 Mar '10

Hello, there, I have two questions about FreeSurfer default atlas and template, Will Freesurfer team build an atlas or template using 3T scans in future? Will Freesurfer team build an atlas or template using patients with disease in future? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/

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realiability of cortical thickness...
by Gonzalo Rojas Costa 10 Mar '10

10 Mar '10

Hi: Freesurfer Developer team: did you published any paper related to the reliability of cortical thickness ?... How you measure that reliability ?.. And, the reliability of the volumetry of different segmented brain structures (such as the hippocampus) ?... And, in the case of the cortical thickness less than 1 mm?... How you can measure it ?... Sincerely, Gonzalo Rojas Costa

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mris_register error
by Gregory Dierksen 09 Mar '10

09 Mar '10

Hello, So I'm attempting to use the V1_predict script to generate a primary visual cortex label and had been receiving an error message. I was able to track down the error to the mris_register command: mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 \ /surf/lh.sphere \ /label/lh.v1.invivo.tif \ /surf/lh.v1.invivo.reg returns this error message: reading surface from /autofs/space/eesmith_001/users/dierksen/Petichial/2988_01192010/surf/lh.sphere... reading template parameterization from /autofs/space/eesmith_001/users/dierksen/Petichial/V1_average/label/lh.v1.invivo.tif... mrisReadTriangleFile(/autofs/space/eesmith_001/users/dierksen/Petichial/2988_01192010/surf/lh.smoothwm): surface doesn't match /autofs/space/eesmith_001/users/dierksen/Petichial/2988_01192010/surf/lh.sphere No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Since it said it could not read the smoothwm file I tried to re-generate this surface using: recon-all -subj_id subject -smooth2 Which returned a "recon-all finished without error" message. I re-ran the above command but got the same error message. Is there another way I can fix the smoothwm surface? Is there a work around? Thanks, Greg

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wm edits and control points
by Dana W. Moore 09 Mar '10

09 Mar '10

Hello everyone, There is an image that needs white matter edits (editing voxels) as well as control points. I know the two commands I need to re-run are autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and somehow combine the -cp and -wm commands, or do I need to do the control points first, re-run, and then do further white matter edits? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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mris_volsmooth without registration
by Chris Filo Gorgolewski 09 Mar '10

09 Mar '10

Hi, my functional runs are already coregistered and resliced to mri/orig.mgz (I use ROI from aseg+aparc and I want to avoid downsampling) so in theory I do not need to use bbregister to prepare registration file for mris_volsmooth. However, --reg argument in mris_volsmooth is mandatory. So far I was running bbregister on already coregistered files. Is there a clever way to skip this unnecessary step? Best regards, Chris

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Re: [Freesurfer] Cortical thickness measurement
by Janani Dhinakaran 09 Mar '10

09 Mar '10

Looking to isolate and measure the thickness of certain brain cortex areas eg- broca's or sensory cortex On 8 March 2010 19:58, Allison Stevens <astevens(a)nmr.mgh.harvard.edu> wrote: > which labels are you looking for information on? > > -- > > On Mon, 8 Mar 2010, Janani Dhinakaran wrote: > > That command gives several options as suggestions and a format for typing >> in >> the command. Following that format I write- >> >> mris_anatomical_stats -a jan lh.pial >> mris_anatomical_stats -a jan lh >> tkmedit mris_anatomical_stats -a jan lh >> tkmedit mris_anatomical_stats -a jan lh pial >> tkmedit mris_anatomical_stats -a jan lh.mgz >> tkmedit mris_anatomical_stats -a jan >> tkmedit mris_anatomical_stats -a jan rawavg.mgz >> mris_anatomical_stats -a jan left >> mris_anatomical_stats -a jan left cortex.mgz >> mris_anatomical_stats -a jan left wm.mgz >> >> None of the above give an annotation each label >> What should I have written? >> >> >> On 8 March 2010 14:31, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> >> Use mris_anatomical_stats >>> >>> Janani Dhinakaran wrote: >>> >>> >>>> Hello all, >>>> >>>> Can anyone tell me the commands I'll need to use to extract and measure >>>> the cortical thickness and volume of certain regions of the brain? >>>> >>>> thanks >>>> -- >>>> I am the Sun, I know no darkness. >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >> >> >> > > 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. > > -- I am the Sun, I know no darkness.

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Re: [Freesurfer] How to verify cerebellum segmentation
by Gergely Orsi 09 Mar '10

09 Mar '10

Hi Bruce and Sita, Do you have any suggestions after seeing the modified and original data? Thanks a lot, Gergo

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intersection of triangles from the reconstructed pial surface
by yasheng_chen＠med.unc.edu 08 Mar '10

08 Mar '10

Hi all, I am using tetgen to construct a tetrahedral mesh with the extracted pial surface in subject 004 from the tutorial datasets. But I got an error message from tetgen to say that some triangles are intersecting each other. I am not sure whether anyone has found this before. The file I tested was 004/lh.pial. I first transferred it to asc format with mris_convert, and then make a straightforward transfer to .off (used by tetgen and geomview). I loaded the .off file with geomview and it looks right. Then I run tetgen with the .off file and got an error message like below, which means that there are intersections among the facets. Error: Invalid PLC. Two subfaces (219028, 5283, 5282) and (219054, 5300, 5283) are found intersecting each other. Hint: Use -d switch to find all intersecting facets. This is a little strange to me since the topology issue has been handled in the reconstructed surface, does any one have any clue? Thank you very much! Yasheng

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