Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

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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problem on freesurfer
by Xiaoying Tang 08 Mar '10

08 Mar '10

Hi Nick, Sorry, I am not sure whether I can successfully post my problem on the mailing list. So I send you the email and cc it to the mailing list. I now have a problem on freesurfer. After run auto-recon2, I am supposed to get grey matter and white matter. The white matter is in the form of wm.mgz, but I can't find something like gm.mgz. Can you tell me where is the grey matter? Is it aseg.mgz? Looking forward to your early reply. Sincerely, Xiaoying

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Cluster-wise correction error
by lordowen 08 Mar '10

08 Mar '10

Dear Freesurfer experts: We used QDEC to generate the script for cluster-wise correction. After 2 days running, we get error message : ERROR: opening /usr/local/freesurfer/subjects/qdec/group_thickness_age_rh/csd/mc-z.abs.2.69.j001-rh-Avg-Intercept-thickness.csd We checked /csd and find the .csd file already there. But in /contrast, there is no results files (i.e., sig.cluster.summary) exist. And a /tmp.mri_glmfit-sim-8708 exist in the main folder. We need your advise to point out what's the problem and how to solve it. Thank you very much. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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Cortical thickness measurement
by Janani Dhinakaran 08 Mar '10

08 Mar '10

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.

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Freesurfer March 2010