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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

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

3 3

Doubt in thickness computation
by jorge luis 07 Sep '07

07 Sep '07

Hello all In Neuroimage Han. et all ( 2006) it is said about Freesurfer automatic thickness computation : For each point on the gray/white surface, the shortest distance to the pial surface is first computed. Next, for each point on the pial surface, the shortest distance to the gray/white surface is found, and the cortical thickness at that location is set to the average of these two values. What the authors mean by "that location"? It is relative to the gray/white surface or to the pial surface? I would like to get a slightly more insight about In advance thank you Jorge ____________________________________________________________________________________ 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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about inflate the surface
by Ning Liu 07 Sep '07

07 Sep '07

Hi all, When I inflate surface, I find the results I get are different from someone's. The one that I get inflates like a filled balloon, but someone's seemed inflated not enough (especially in the TE). The parameters for mris_inflate command are same. I enclosed these two kinds of inflated surface. Would you please tell me why? Does it caused by the smoothwm file? Thanks a lot. Ning -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time is now.

2 1

wrong values for volume
by Rafael Huber 07 Sep '07

07 Sep '07

Dear Freesurfer Users I did the whole group analysis process, but unfortunately the measure for volume didn't work correctly. I think the problem is, that i couldn't create the "source-files" (the ?h.volume files in the /subject/surf folders) like for the other measures. I did that with a command in matlab, which Bruce Fischl recommended me. When i try to look at the results with the tksurfer the whole hemisphere is yellow and the values for the sig.mgh overlay are all 10000000000. Has somebody an idea how to create the volume measure otherwise, or what went wrong? Thanks for every help in advance. Best regards, Rafael Huber -- Rafael Huber Student Division of Neuropsychology Institute of Psychology University of Zurich

1 0

Directed contrast in FS group analysis
by Juergen Haenggi 07 Sep '07

07 Sep '07

Dear Freesurfer users In order to be absolutely sure about the direction of a contrast I have the following question: gamma = 1*beta1 + -1*beta2 + 0*beta3 + .... Does beta1 always correspond to the class that is entered most superior in the fsgd file and beta2 to the class that is entered as the second class in the fsgd file? Do the other betas correspond to the variables listed from left to right in the fsgd file? Thanks for your confirmation. Best regards Juergen Haenggi ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

version 4
by Don Hagler 06 Sep '07

06 Sep '07

I processed some brains using version 4 and it seems that it took substantially longer than typical for version 3. It took about 3 days for one subject with version 4, compared to 1.5 days for the same subject with version 3.0.5. Is this on par with what others have experienced? At least for this one subject, the inflated surface looks a bit strange for version 4 compared to version 3 (see attached). I haven't yet done a side-by-side comparison for multiple subjects, so I don't know how reproducible this will be. _________________________________________________________________ Gear up for Halo® 3 with free downloads and an exclusive offer. http://gethalo3gear.com?ocid=SeptemberWLHalo3_MSNHMTxt_1

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