Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30076 discussions

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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manual correction of aparc
by Goldman, Aaron (NIH/NIMH) [C] 27 Apr '07

27 Apr '07

Hi, I had a question regarding midline parcellation defects in some of our subjects (mostly cingulate, entorhinal). I was happy to read on the wiki that the next stable release is expected to improve the accuracy of these labels. However, in the meantime due to SFN submission deadlines, I was wondering if it would be practical to manually correct these parcellation labels in a small number of subjects. If so, is there any documentation on how to do this? Thanks, -Aaron-

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the program for analysis of SI cortex
by Wang, Xin 27 Apr '07

27 Apr '07

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need info for beginner
by napapon＠caltech.edu 26 Apr '07

26 Apr '07

Hi, I am about to install FREE SURFER for my Spectroscopy work. I want to use the software to perform GM/WM segmentation on my single voxel data sets. I am wondering if any one on this mailing list is currently doing this task. I would like to get comments. My study is on a GE 3T scanner. thank you, Pom

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Re: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: [Freesurfer] (no subject)
by rahul＠nmr.mgh.harvard.edu 26 Apr '07

26 Apr '07

Hi Hankee, The eTIV or the ICV is a measure of the head size and with Freesurfer can be found within the aseg.stats file. There are several ways to utlize this for adjusting for head size for individual structures. For one, you can simply take the volume of a region (e.g. parahippocampal gyrus) and divide this by the eTIV/ICV measure and get an 'adjusted volume' and use this for all further statistical comparisons. Another way is to perform a linear regression with the eTIV/ICV measure for all subjects and the volumes of individual regions for all subjects, take the residuals, and utilize these as 'adjusted volume' measures for all further statistical comparisons. Best, rahul > hi,rahul > Sorry,I have not heard about the eTIV or ICV,what does this letter > stand for? and how to use eTIV or ICV to adjust head size? Thank you > very much! > best, > hankee > > hankee£¬duhanjian(a)sohu.com > 2007-04-26 > ----- Original Message ----- > From: rahul > To: duhanjian > Sent: 2007-04-26, 23:18:32 > Subject: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: [Freesurfer] (no subject) > > > Hi Hankee, > > You certainly can use the statistical information regarding the volume, > thickness, and surface area of individual regions, such as the > parahippocampal gyrus (as derived from the ?h.aparc.annot file), to > compare between various groups of subjects. The only recommendation would > be that if you are performing cross-sectional comparisons using the > volumes of individual brain regions, you should use the eTIV or ICV > measure to adjust for head size for individual subjects. > > Best, > > rahul > >> hi,I have question about the ?h.aparc file in stats directory. Can I >> use >> the parahippocample's gray matter volume or other brain structure's >> gray >> matter volume to do statistics analysis? For example,select 15 normal >> people and 15 AD disease patient,using FreeSurfer software to deal with >> them,when It is done, Can I compare the parahippocample's gray matter >> volume which located in /stats/lh.aparc file between patient group and >> normal group? Thank you! >> >> >> hankee£¬duhanjian(a)sohu.com >> 2007-04-26 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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