Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

running time v4
by ppj＠netfilter.com.br 10 Sep '07

10 Sep '07

Hi, I would like to ask if there's already a benchmark performance of V4 compared to V3. In my environment V3 run a full recon-all in 21 hours full brain. How long I should expect the running time of V4 if I install it? Thanks, Pedro Paulo Oliveira Jr.

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variability
by Leila BH 10 Sep '07

10 Sep '07

Hello, Is there any paper talking about the variability of the used methods (on reconall )? Especially the parcellation? If I reprocess one subject 10 times with the same Freesurfer version, should I expect the same result for parcellation? The freesurfer version that I use is stable3 I tried to see if the parcellation of the new Freesurfer version is similar (visually) to the stable3, and it was very different, is the parcellation method the same in both version? thanks

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Freesurfer and Gaussian Random field theory
by jorge luis 10 Sep '07

10 Sep '07

Hello all I have computed and smoothed some thickness maps using Freesurfer. Next I would like to make inference using Gaussian Random Field theory (GRFT). How can I do it in Freesurfer? If it is not implemented in freesurfer , is there any thing that I have to take into account when applying any GRFT implementation to the statistical parametric thickness maps resulting from Freesurfer analysis? In advance thank you ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Switch hemispheres
by Inês Souta 09 Sep '07

09 Sep '07

Hi, After processing the hole image I realized that the orientation of the original .mgz file was wrong and I've ended up with switched hemispheres. The right hemisphere is where the left should be, and vice-versa. Otherwise the orientation is right. Since I've already made manual edits, is the anyway of switching hemispheres without having to re-process the hole image again? Thanks, Ines

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RE: [Freesurfer] variability
by rahul＠nmr.mgh.harvard.edu 09 Sep '07

09 Sep '07

Hi Leila, Have you noticed other differences in the same subject using V4 vs V3 (i.e. gray/white bounday differences, thickness thickness difference, etc.) using the same subject? The V4 parcellation should theoretically not be much different from the V3 scheme with the exception of improvement in certain areas such as the anterior cingulate, entorhinal, and the inferior parietal lobule. Where exactly do you find the most amount of difference between the two versions? Best, rahul > Hi Leila, > > do you see this in other subjects? We also have a utility > (mris_divide_parcellation) for automatically dividing each parcellation > unit along it's long axis. > > Bruce > > On Sun, 9 Sep 2007, Leila BH wrote: > >> Hi Bruce, >> Thanks for your answer, >> Actually I reprocessed on subject (I have choose one case who doesn't >> need >> any editing) and the parcellation result is more accurate in midline but >> worst in some other part, is it just by chance? That's why I am asking >> about >> the variability(in version 3 /and between V3 and V4). I attached 2 tif >> files >> for more precision. (one is done with vesion3 and one version4) >> In my work I have to parcellate the cortex on 1000 small ROIs, I use >> freesurfer to do that, based on the 35 parcellation, I subdivide each >> one on >> small rois, so my small ROIs are not really based on gyrus and sulcus, >> and >> to validate my method I want to know the 'error' or variability of the >> original 35-parcellation. Do you suggest me to run one subject N times >> to >> see that? Or do you already know the variability of all the Freesurfer >> pipeline (till the parcellation)? >> thanks >> >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> >> Sent: samedi, 8. septembre 2007 03:24 >> To: Leila BH >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] variability >> >> Hi Leila, >> >> Xiao Han's NeuroImage paper discusses thickness variability, and we've >> looked at parcellation variability in-house, but I don't think we've >> published on it. The V4 parcellation is should be a bit more accurate at >> the midline, but not substantially different. >> >> cheers, >> Bruce >> On Wed, 5 Sep 2007, Leila BH >> wrote: >> >>> Hello, >>> >>> Is there any paper talking about the variability of the used methods >>> (on >>> reconall )? Especially the parcellation? If I reprocess one subject 10 >> times >>> with the same Freesurfer version, should I expect the same result for >>> parcellation? >>> >>> The freesurfer version that I use is stable3 >>> >>> >>> >>> I tried to see if the parcellation of the new Freesurfer version is >> similar >>> (visually) to the stable3, and it was very different, is the >>> parcellation >>> method the same in both version? >>> >>> thanks >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

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Convert values in label
by Inês Souta 09 Sep '07

09 Sep '07

Hi again, Is there any way to have access to the numerical values of cortical thickness in an ROI? Thanks, Ines

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mri_convert - segmentation fault (again)
by Jenn Segawa 09 Sep '07

09 Sep '07

Hi, Sorry if this is redundant, I think I'm having the same segmentation problem as others last week, with the mri_convert command I've previously used (with Unix) with no problem. I've tried setenv trick that was previously suggested, but it didn't make any difference. Has anyone had any luck with it? Thanks, Jenn recon-all -autorecon1 -s PROZ06006 -i /space/multnomah/3/users/gow/PROZ06/MRI_raw/PROZ06006/681000-3-1.dcm -i /space/multnomah/3/users/gow/PROZ06/MRI_raw/PROZ06006/681000- 4-1.dcm -i /space/multnomah/3/users/gow/PROZ06/MRI_raw/PROZ06006/681000-5-1.dcm -i /space/multnomah/3/users/gow/PROZ06/MRI_raw/PROZ06006/681000-6-1.dcm YIELDS: INFO: SUBJECTS_DIR is /autofs/space/multnomah_003/users/gow/PROZ06/MRI Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0/stable4 Linux dgow 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06006 mri_convert /autofs/space/multnomah_003/users/gow/PROZ06/MRI_raw/PROZ06006/6810 00-3-1.dcm/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06006/mri/orig/0 01.mgz mri_convert /autofs/space/multnomah_003/users/gow/PROZ06/MRI_raw/PROZ06006/68100 0-3-1.dcm/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06006/mri/orig/00 1.mgz $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /autofs/space/multnomah_003/users/gow/PROZ06/MRI_raw/PROZ06006/6810 00-3-1.dcm... Getting Series No INFO: Found 2352 files in /autofs/space/multnomah_003/users/gow/PROZ06/MRI_raw/P ROZ06006 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. INFO: (256 256 128), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 0.994 -0.056 -0.090 -8.971 ; 0.036 0.977 -0.211 -13.941; 0.100 0.207 0.973 5.321; 0.000 0.000 0.000 1.000; MGH DTI SeqPack Info 0 *tfl3d1_ns 0.000000 0 1 *tfl3d1_ns 0.000000 0 2 *tfl3d1_ns 0.000000 0 3 *tfl3d1_ns 0.000000 0 4 *tfl3d1_ns 0.000000 0 5 *tfl3d1_ns 0.000000 0 6 *tfl3d1_ns 0.000000 0 7 *tfl3d1_ns 0.000000 0 8 *tfl3d1_ns 0.000000 0 9 *tfl3d1_ns 0.000000 0 10 *tfl3d1_ns 0.000000 0 11 *tfl3d1_ns 0.000000 0 12 *tfl3d1_ns 0.000000 0 13 *tfl3d1_ns 0.000000 0 14 *tfl3d1_ns 0.000000 0 15 *tfl3d1_ns 0.000000 0 16 *tfl3d1_ns 0.000000 0 17 *tfl3d1_ns 0.000000 0 18 *tfl3d1_ns 0.000000 0 19 *tfl3d1_ns 0.000000 0 20 *tfl3d1_ns 0.000000 0 21 *tfl3d1_ns 0.000000 0 22 *tfl3d1_ns 0.000000 0 23 *tfl3d1_ns 0.000000 0 24 *tfl3d1_ns 0.000000 0 25 *tfl3d1_ns 0.000000 0 26 *tfl3d1_ns 0.000000 0 27 *tfl3d1_ns 0.000000 0 28 *tfl3d1_ns 0.000000 0 29 *tfl3d1_ns 0.000000 0 30 *tfl3d1_ns 0.000000 0 31 *tfl3d1_ns 0.000000 0 32 *tfl3d1_ns 0.000000 0 33 *tfl3d1_ns 0.000000 0 34 *tfl3d1_ns 0.000000 0 35 *tfl3d1_ns 0.000000 0 36 *tfl3d1_ns 0.000000 0 37 *tfl3d1_ns 0.000000 0 38 *tfl3d1_ns 0.000000 0 39 *tfl3d1_ns 0.000000 0 40 *tfl3d1_ns 0.000000 0 41 *tfl3d1_ns 0.000000 0 42 *tfl3d1_ns 0.000000 0 43 *tfl3d1_ns 0.000000 0 44 *tfl3d1_ns 0.000000 0 45 *tfl3d1_ns 0.000000 0 46 *tfl3d1_ns 0.000000 0 47 *tfl3d1_ns 0.000000 0 48 *tfl3d1_ns 0.000000 0 49 *tfl3d1_ns 0.000000 0 50 *tfl3d1_ns 0.000000 0 51 *tfl3d1_ns 0.000000 0 52 *tfl3d1_ns 0.000000 0 53 *tfl3d1_ns 0.000000 0 54 *tfl3d1_ns 0.000000 0 55 *tfl3d1_ns 0.000000 0 56 *tfl3d1_ns 0.000000 0 57 *tfl3d1_ns 0.000000 0 58 *tfl3d1_ns 0.000000 0 59 *tfl3d1_ns 0.000000 0 60 *tfl3d1_ns 0.000000 0 61 *tfl3d1_ns 0.000000 0 62 *tfl3d1_ns 0.000000 0 63 *tfl3d1_ns 0.000000 0 64 *tfl3d1_ns 0.000000 0 65 *tfl3d1_ns 0.000000 0 66 *tfl3d1_ns 0.000000 0 67 *tfl3d1_ns 0.000000 0 68 *tfl3d1_ns 0.000000 0 69 *tfl3d1_ns 0.000000 0 70 *tfl3d1_ns 0.000000 0 71 *tfl3d1_ns 0.000000 0 72 *tfl3d1_ns 0.000000 0 73 *tfl3d1_ns 0.000000 0 74 *tfl3d1_ns 0.000000 0 75 *tfl3d1_ns 0.000000 0 76 *tfl3d1_ns 0.000000 0 77 *tfl3d1_ns 0.000000 0 78 *tfl3d1_ns 0.000000 0 79 *tfl3d1_ns 0.000000 0 80 *tfl3d1_ns 0.000000 0 81 *tfl3d1_ns 0.000000 0 82 *tfl3d1_ns 0.000000 0 83 *tfl3d1_ns 0.000000 0 84 *tfl3d1_ns 0.000000 0 85 *tfl3d1_ns 0.000000 0 86 *tfl3d1_ns 0.000000 0 87 *tfl3d1_ns 0.000000 0 88 *tfl3d1_ns 0.000000 0 89 *tfl3d1_ns 0.000000 0 90 *tfl3d1_ns 0.000000 0 91 *tfl3d1_ns 0.000000 0 92 *tfl3d1_ns 0.000000 0 93 *tfl3d1_ns 0.000000 0 94 *tfl3d1_ns 0.000000 0 95 *tfl3d1_ns 0.000000 0 96 *tfl3d1_ns 0.000000 0 97 *tfl3d1_ns 0.000000 0 98 *tfl3d1_ns 0.000000 0 99 *tfl3d1_ns 0.000000 0 100 *tfl3d1_ns 0.000000 0 101 *tfl3d1_ns 0.000000 0 102 *tfl3d1_ns 0.000000 0 103 *tfl3d1_ns 0.000000 0 104 *tfl3d1_ns 0.000000 0 105 *tfl3d1_ns 0.000000 0 106 *tfl3d1_ns 0.000000 0 107 *tfl3d1_ns 0.000000 0 108 *tfl3d1_ns 0.000000 0 109 *tfl3d1_ns 0.000000 0 110 *tfl3d1_ns 0.000000 0 111 *tfl3d1_ns 0.000000 0 112 *tfl3d1_ns 0.000000 0 113 *tfl3d1_ns 0.000000 0 114 *tfl3d1_ns 0.000000 0 115 *tfl3d1_ns 0.000000 0 116 *tfl3d1_ns 0.000000 0 117 *tfl3d1_ns 0.000000 0 118 *tfl3d1_ns 0.000000 0 119 *tfl3d1_ns 0.000000 0 120 *tfl3d1_ns 0.000000 0 121 *tfl3d1_ns 0.000000 0 122 *tfl3d1_ns 0.000000 0 123 *tfl3d1_ns 0.000000 0 124 *tfl3d1_ns 0.000000 0 125 *tfl3d1_ns 0.000000 0 126 *tfl3d1_ns 0.000000 0 127 *tfl3d1_ns 0.000000 0 Segmentation fault Linux dgow 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Sep 7 11:47:14 EDT 2007

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Re: FW: [Freesurfer] searching for a method of declaring spherical ROIsin the volume
by Avram Holmes 08 Sep '07

08 Sep '07

Bruce, Thanks for the quick response to my question. I've gone searching instructions on how to run the mri_morphology command but I can't find anything in the wiki or the mailing list archives. All I have been able to locate is the following blub which I get by then I run the command with no flags. usage: mri_morphology [options] <volume> <operation> <# iter> <out volume> -u where which can be [dilate,erode] Is there some place I can go for advice on how to run this? Once again I would be interested in feeding is a set of XYZ coordinates and then creating a sphere around them which I can then use as if it is a structural label. Thanks again for your help, Avram > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, September 05, 2007 11:57 AM > To: Avram Holmes > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] searching for a method of declaring spherical > ROIsin the volume > > Hi Avram, > > mri_morphology implement general morphological operations on volumes, > including dilation. You'll need to convert the .label to a .mgz if that's > what you're using, then back to a label. > > cheers, > Bruce > > On Tue, 4 Sep 2007, Avram Holmes > wrote: > > >> All, >> >> I'm attempting to create some spherical ROIs around peak activated voxels >> > in > >> the volume. Is there anything similar to the label dilate function for use >> > in > >> the volume? >> Thanks for any help you can offer, >> Avram >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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dev environment
by Robert Levy 08 Sep '07

08 Sep '07

Hi, Since the change to the new version of Freesurfer, I have had some problems with some of our lab's older scripts that make use of the Freesurfer matlab toolbox. I haven't delved deep enough into the specifics to ask a question about that (and I don't think the matlab toolbox is supported or suggested for the end-user anyway, right?), but I just realized that stable2 and stable3 give very different results, and stable4 is incompatible with the code altogther, anyway that has made me aware of these big version differences... In general: since it is advised to perform all analyses within a study using the same version of Freesurfer, then is it not advised to use the development environment for a study that has spanned at least 2 versions of Freesurfer, as it frequently changes? Also: since we have been using the development environment, would it be inconsistent to use stable3 for the remaining analyses in that project? Would it be more consistent to use the newest version, as it would be closer to the most recent stage of the development of the dev env than stable3 would be? Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Volume calculation
by Derin Cobia 08 Sep '07

08 Sep '07

How is the volume of each cortical structure (and hemisphere) calculated? It seems I remember from somewhere that it is the thickness x average surface area of the tesselated triangles? Is this right? What I'm most interested in is how the cortical gray matter volume from mris_anatomical_stats is calculated. Is it the average thickness of the whole hemisphere x surface area, or is by adding up the volumes of all the parcellated structures from the atlas? I remember reading about it earlier, but couldn't find any info in the list archive or on the wiki. Thanks. -Derin

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Freesurfer