Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

calculation of total cortical gray matter volume
by Michael Harms 24 Jul '07

24 Jul '07

Hello FS-list, Could you please confirm the recommended current approach for calculating the total cortical gray matter volume. Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculation (illustrated using tcsh syntax) is: @ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white` My only hesitation is that I noticed the resulting value doesn't quite match the value of "total gray matter volume" that is output by mris_anatomical_stats. Is this because mris_anatomical_stats uses a older approach that is no longer considered quite as accurate? thanks, Mike Harms

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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 27 Jun '07

27 Jun '07

Hi Xin, I will Doug handle this one. And please email the list in your replies. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer beginner. I have another question. I want to compare the cortical thickness between two small groups (2X2). I can not work through the steps in the tutorial on my data. The mri_glmfit commend always returns with "bad design, ill-constructed," and stops. Do you have any detail instructions of two group comparison? > Thank you again, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 4:06 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > Within the *h.aparc.annot files for each subject, there should be > individual label files for *h.precentral.label and *h.postcentral.label. > If you take a look at your *h.aparc.stats, there should be a value for the > thickness and volume. You can, of course, take this *h.aparc.stats file > and upload it into matlab, spss or any other stats package and do > statistics on these values. > > Best, > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Dear Rahul >> The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. >> Thank you, >> >> Xin >> >> ________________________________ >> >> From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] >> Sent: Mon 4/30/2007 3:52 PM >> To: Wang, Xin >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ROI of SI cortex >> >> >> >> Hi Xin, >> >> What exactly do SI and MI cortices refer to? >> >> rahul >> >> On Mon, 30 Apr 2007, Wang, Xin wrote: >> >>> 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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slice thickness
by T. Song 21 Jun '07

21 Jun '07

Hi All: I have a question about the slice thickness. To get a "good" freesurfer reconstruction, especially the "accurate" statistic analysis, what it the maximum slice thickness can I use when acquire the DICOM image? Thanks! Tao

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Difficulties with segmentation follow-up
by Jeffrey Spielberg 11 May '07

11 May '07

Hi, I sent a message to the forum last June regarding a problem with segmentation of the acc we were running into. We kept having areas of the rostral and caudal acc labeled as corpus callosum or "unlabelled subcortical". I got a reply that this was being worked on and I was wondering if this is now fixed in 3.0.4, and if not if there is any timeline for releasing a fix? Thanks, Jeff

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RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 03 May '07

03 May '07

Hi Xin, Within the *h.aparc.annot files for each subject, there should be individual label files for *h.precentral.label and *h.postcentral.label. If you take a look at your *h.aparc.stats, there should be a value for the thickness and volume. You can, of course, take this *h.aparc.stats file and upload it into matlab, spss or any other stats package and do statistics on these values. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Dear Rahul > The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. > Thank you, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 3:52 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > What exactly do SI and MI cortices refer to? > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> 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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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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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

2 1

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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Freesurfer April 2007