Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

tkregister2
by Reschke, Cole 01 May '07

01 May '07

Is it possible to spatially align PET data to an MRI using tkregister2? Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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Talairach transform
by Chuan.Chih.Yang＠rwth-aachen.de 01 May '07

01 May '07

Dear list, After fixing the Talairach transform automatically, (by mri_convert , the final objective funciton value is fine, ca.0.06) So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and it looked pretty fine with tkregister2. Then I runed recon-all -subjid xxxx -autorecon1 -notalairach, and then viewed it with tkmedit and tkreigister2. Under tkregister2 the talairach transform looks pretty good but not the target.(the oreientations of the target are totally mixed up, those of the moveble volume are correct). I checked orig.mgz are also mixed up, coronal becomes sagittal, sagittal becomes horizontal, etc. Any suggestions about this ? Thanks. Jackie

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FOV in freesurfer
by Trina Kok 01 May '07

01 May '07

Hi All, I have a few scans that were done with a field of view of 200. I was wondering how freesurfer extrapolates that to a 256 by 256 by 256 matrix. Thanks, Trina

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Help with FS
by Lusineh Gharapetian 30 Apr '07

30 Apr '07

Hello, I don't know how to edit a problem that I have run into on several slices in both hemispheres of multiple brains. The problem is that the pial surface line crosses into white matter. I have attached a couple of instances of this occurring. It happens on multiple slices in a row or as a single slice problem. I would greatly appreciate any advice on how to deal with this. Let me know if you need any further information. Thanks! Sincerely, Lusineh Gharapetian Staff Research Associate Multi Modal Imaging Lab (MMIL) UC San Diego office. 858. 822.1818 email. lgharapetian(a)gmail.com

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ROI of SI cortex
by Wang, Xin 30 Apr '07

30 Apr '07

Hello, group I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? Thank you in advance. Xin Wang

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mris_anatomical_stats
by deepa preeti 30 Apr '07

30 Apr '07

Hi all, I wanted to have whitematter, gray volume and avg.thickness for each hemisphere. So when I run mris_anatomical_stats -t thickness <subject> <hemi> I get the following data: mris_anatomical_stats -t thickness <subject> lh using thickness file thickness. total white matter volume = 729800 mm^3 total surface area = 90850 mm^2 total gray matter volume = 181205 mm^3 average cortical thickness = 1.971 mm +- 0.739 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.039 folding index = 1574.464 intrinsic curvature index = 204.376 mris_anatomical_stats -t thickness <subject> rh using thickness file thickness. total white matter volume = 729800 mm^3 total surface area = 90411 mm^2 total gray matter volume = 186292 mm^3 average cortical thickness = 2.020 mm +- 0.729 mm average integrated rectified mean curvature = 0.129 average integrated rectified Gaussian curvature = 0.039 folding index = 1537.208 intrinsic curvature index = 209.604 I see the total white matter vol is same for left & right hemisphere, Is my data correct? Thanks, Deepa Ramasamy.

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RE: [Freesurfer] about the Gray matter volume
by Jenni Pacheco 29 Apr '07

29 Apr '07

Hankee, mris_volume will simply return the volume of the surface you request. You will have to do the subtraction, pial minus white, yourself. Jenni _____ From: hankee [mailto:duhanjian@sohu.com] Sent: Sunday, April 29, 2007 12:24 PM To: Jenni Pacheco Subject: Re: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume I can't see the total gray matter volume in the ?h.aparc.stats file.If I run the mris_volume ?h.surface command in the <subjid>/surf directory, It will produce the new file in this directory? which data will include in this file? After that I use the formula:gm volume = pial volume - white volume to create the total gray matter volume? Am I right? Thank you very much! hankee hankee， <mailto:%3c!--AID_FROMADDRESS_BEGIN--%3eduhanjian@sohu.com%3c!--AID_FROMADDRESS_END--%3e> duhanjian(a)sohu.com 2007-04-30 ----- Original Message ----- From: Jenni <mailto:jpacheco@nmr.mgh.harvard.edu> Pacheco To: duhanjian <mailto:duhanjian@sohu.com> Sent: 2007-04-29, 22:39:59 Subject: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume Hi Hankee, You can use mris_volume to find this if you can’t get it from the aparc.stats: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Jenni _____ From: hankee [mailto:duhanjian@sohu.com] Sent: Sunday, April 29, 2007 10:01 AM To: Jenni Pacheco Subject: Re: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume But I only can see the the total white matter volume in the ?h.aparc.stats file,don't have total gray matter volume it the this file. Thank you! hankee hankee，duhanjian(a)sohu.com <mailto:%3c!--AID_FROMADDRESS_BEGIN--%3eduhanjian@sohu.com%3c!--AID_FROMADDRESS_END--%3e> 2007-04-29 ----- Original Message ----- From: Jenni Pacheco <mailto:jpacheco@nmr.mgh.harvard.edu> To: duhanjian,'freesurfer' <mailto:duhanjian@sohu.com,freesurfer@nmr.mgh.harvard.edu> Sent: 2007-04-29, 21:16:25 Subject: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume This is reported in the ?h.aparc.stats file that is generated when the parcellation is run. Jenni _____ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of hankee Sent: Sunday, April 29, 2007 8:43 AM To: freesurfer Subject: [Freesurfer] about the Gray matter volume How to calculate the total gray matter volume of the brain using FreeSurfer software ? hankee，duhanjian(a)sohu.com <mailto:%3c!--AID_FROMADDRESS_BEGIN--%3eduhanjian@sohu.com%3c!--AID_FROMADDRESS_END--%3e> 2007-04-29

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RE: [Freesurfer] about the Gray matter volume
by Jenni Pacheco 29 Apr '07

29 Apr '07

Hi Hankee, You can use mris_volume to find this if you can’t get it from the aparc.stats: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Jenni _____ From: hankee [mailto:duhanjian@sohu.com] Sent: Sunday, April 29, 2007 10:01 AM To: Jenni Pacheco Subject: Re: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume But I only can see the the total white matter volume in the ?h.aparc.stats file,don't have total gray matter volume it the this file. Thank you! hankee hankee， <mailto:%3c!--AID_FROMADDRESS_BEGIN--%3eduhanjian@sohu.com%3c!--AID_FROMADDRESS_END--%3e> duhanjian(a)sohu.com 2007-04-29 ----- Original Message ----- From: Jenni <mailto:jpacheco@nmr.mgh.harvard.edu> Pacheco To: duhanjian,'freesurfer' <mailto:duhanjian@sohu.com,freesurfer@nmr.mgh.harvard.edu> Sent: 2007-04-29, 21:16:25 Subject: (瑞星提示-此邮件可能是垃圾邮件)RE: [Freesurfer] about the Gray matter volume This is reported in the ?h.aparc.stats file that is generated when the parcellation is run. Jenni _____ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of hankee Sent: Sunday, April 29, 2007 8:43 AM To: freesurfer Subject: [Freesurfer] about the Gray matter volume How to calculate the total gray matter volume of the brain using FreeSurfer software ? hankee，duhanjian(a)sohu.com <mailto:%3c!--AID_FROMADDRESS_BEGIN--%3eduhanjian@sohu.com%3c!--AID_FROMADDRESS_END--%3e> 2007-04-29

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about the Gray matter volume
by hankee 29 Apr '07

29 Apr '07

How to calculate the total gray matter volume of the brain using FreeSurfer software ? hankee，duhanjian(a)sohu.com 2007-04-29

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Gray matter mask
by Anil Roy 27 Apr '07

27 Apr '07

Hello all, Is there a method to generate a gray matter mask in Freesurfer that can be fed into AFNI. Could you please point me to any existing documentation on the FS wiki that already does this as I was unable to find anything. Thanks a lot, Anil.

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