Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

New FreeSurfer Version
by David Soscia 26 Jul '05

26 Jul '05

Hey Guys, Has the new version of FreeSurfer been released yet? I spoke with Dr. Killiany at BU two Fridays ago and he told me it was going to be released very soon. If so, where can I get it because I don't see it anywhere on the FreeSurfer dowload page. Thanks, Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Convexity value
by XJ Kang 25 Jul '05

25 Jul '05

Hi, What are the units of "convexity" values (the last column) in ?h.sulc.asc? Probably in mm? The values are <+- 1. It seems the values are two small for "the signed distance" that a vertex moves during the inflation process. Thanks. XJ

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MNI
by Timothy O'Keefe 25 Jul '05

25 Jul '05

After generating a cortical surface rendering, I would like to overlay my EPI activation maps. I considered rendering a cortical surface for all my participants but, they are all normalized to MNI space. Despite the structural variabilities which remain even after normalization, is it still common for people to use a single FreeSurfer rendering for visualization (given all your EPI data are also normalized to MNI)? -T

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Re: [Freesurfer] Tksurfer: Unable to view .orig file
by Arvind Gururajan 24 Jul '05

24 Jul '05

Hi Bruce, I found out what was wrong. If any of you had the same problem, it could be due to this. Vertices for freesurfer are in millimeters, and I had them in meters. Thanks for your help and good luck with the course. Arvind On 22 Jul 2005, Bruce Fischl wrote: > Hi Arvind, > > it's the middle of the FSL/FreeSurfer course, so we're all really busy. > Hopefully we'll get to it next week. > > Bruce > On Thu, 21 Jul 2005, Arvind Gururajan > wrote: > > > Hi, > > > > Could anyone please tell me what could be wrong? What more information do I > > need to provide? Your help will be really appreciated. > > > > Arvind Gururajan > > > > On 20 Jul 2005, Arvind Gururajan wrote: > >> Hi Bruce, > >> > >> I had a single file with both hemisphere data points. Was able to make a > >> crude separation into two hemisphere. Probably couldn't have messed up > >> here, I used a different software to visualize them, and it was fairly > >> clean separation. > >> > >> I used the following command to convert from .asc to .orig. > >> > >> mris_convert > >> /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc > >> /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig > >> > >> .xdebug_tksurfer for the subject is empty, here it is anyways. > >> > >> Thanks for your help. > >> > >> Arvind > >> > >> > >> On 14 Jul 2005, Bruce Fischl wrote: > >>> Hi Arvind, > >>> > >>> you need to give us more info, and the .xdebug_tksurfer files. > >>> > >>> Bruce > >>> On Thu, 14 > >>> Jul 2005, Arvind Gururajan wrote: > >>> > >>>> Hi, > >>>> > >>>> I have trouble viewing .orig files in Tksurfer. I used mris_convert > > to > >>>> generate .orig files from .ascii( with number of vertices and > > triangles > >> for > >>>> each hemisphere). Any quick thoughts on what could be wrong ? No > > error > >>>> messages. > >>>> > >>>> Help would be appreciated. > >>>> > >>>> Arvind Gururajan > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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problem with recon-all
by Russ Poldrack 24 Jul '05

24 Jul '05

hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all. If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything. here is the output from "recon-all-nmr -all -subjid bert" (same thing happens if I just use recon-all): Fri Jul 22 13:33:27 PDT 2005 /Users/Shared/freesurfer/bin//recon-all-nmr -all -subjid bert /Users/Shared/freesurfer/subjects/bert subjid bert SUBJECTS_DIR /Users/Shared/freesurfer/subjects FREESURFER_HOME /Users/Shared/freesurfer AutoSeg Enable = 1 Darwin ######################################## program versions used $Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 b ert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/ minctracc.c,v 96.11 2004/ 02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19 :02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:4 9 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using COR format here it just stops, which is presumably not the expected behavior with the -all flag. I also tried with a new dataset converted to mgz format and with the -autorecon1 option and the same thing happens. Any ideas what might be going on here? cheers russ --- Russell A. Poldrack, Ph.d. Assistant Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: poldrack(a)ucla.edu web: www.poldracklab.org

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mgz file format?
by Renat Yakupov 22 Jul '05

22 Jul '05

Hi everybody, I noticed the new FreeSurfer tutorial on the website and all 3D volumes are specified as *.mgz files there. What happened to old COR format? Is mgz the format of the new FreeSurfer distribution that is supposed to come out soon? Best, Renat.

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Re: [Freesurfer] Tksurfer: Unable to view .orig file
by Arvind Gururajan 22 Jul '05

22 Jul '05

Hi, Could anyone please tell me what could be wrong? What more information do I need to provide? Your help will be really appreciated. Arvind Gururajan On 20 Jul 2005, Arvind Gururajan wrote: > Hi Bruce, > > I had a single file with both hemisphere data points. Was able to make a > crude separation into two hemisphere. Probably couldn't have messed up > here, I used a different software to visualize them, and it was fairly > clean separation. > > I used the following command to convert from .asc to .orig. > > mris_convert > /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc > /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig > > .xdebug_tksurfer for the subject is empty, here it is anyways. > > Thanks for your help. > > Arvind > > > On 14 Jul 2005, Bruce Fischl wrote: > > Hi Arvind, > > > > you need to give us more info, and the .xdebug_tksurfer files. > > > > Bruce > > On Thu, 14 > > Jul 2005, Arvind Gururajan wrote: > > > > > Hi, > > > > > > I have trouble viewing .orig files in Tksurfer. I used mris_convert to > > > generate .orig files from .ascii( with number of vertices and triangles > for > > > each hemisphere). Any quick thoughts on what could be wrong ? No error > > > messages. > > > > > > Help would be appreciated. > > > > > > Arvind Gururajan > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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Re: [Freesurfer] Tksurfer: Unable to view .orig file
by Arvind Gururajan 20 Jul '05

20 Jul '05

Hi Bruce, I had a single file with both hemisphere data points. Was able to make a crude separation into two hemisphere. Probably couldn't have messed up here, I used a different software to visualize them, and it was fairly clean separation. I used the following command to convert from .asc to .orig. mris_convert /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig .xdebug_tksurfer for the subject is empty, here it is anyways. Thanks for your help. Arvind On 14 Jul 2005, Bruce Fischl wrote: > Hi Arvind, > > you need to give us more info, and the .xdebug_tksurfer files. > > Bruce > On Thu, 14 > Jul 2005, Arvind Gururajan wrote: > > > Hi, > > > > I have trouble viewing .orig files in Tksurfer. I used mris_convert to > > generate .orig files from .ascii( with number of vertices and triangles for > > each hemisphere). Any quick thoughts on what could be wrong ? No error > > messages. > > > > Help would be appreciated. > > > > Arvind Gururajan > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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mri_label2vol
by Dragana Viceic 20 Jul '05

20 Jul '05

Hello, I would like to convert a label file into analyze, but I can't find mri_label2vol in Freesurfer package. Is it a part of another program or package? Thanks in advance, Dragana

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RE: [Freesurfer] stage1
by Fornito, Alexander 19 Jul '05

19 Jul '05

Hi, The new version of recon-all certainly sounds exciting. Any dates for Linux release planned? I'm looking at starting processing on a large set of images and wouldn't want to begin and then re-do some of the processing because a superior method came out. Regards, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 7/19/2005 11:32 AM To: Ray Fix Cc: FreeSurfer Mailing List Subject: Re: [Freesurfer] stage1 Hi Ray, you shouldn't compare across datasets that use the subcortical segmentation (aseg) and those that don't. The aseg fills the entire ventricle, and thus changes the effective folding pattern on the medial wall, requiring a different atlas and parcellation targets. The advantage is that it is quite a bit more robust and fully automated in 90-95% of the cases we've tested (including elderly and AD), plus you get the whole subcortical segmentation for either structural or functional analysis. cheers, Bruce p.s. the subcortical does take a long (>15 hours) time, but reduces person time as most datasets go through without any manual fixing. On Mon, 18 Jul 2005, Ray Fix wrote: > Hello Doug, > > Thanks for the info. I tried out the Tiger install a couple of weeks ago and > was very impressed but when I tried to process bert, it took so long that I > finally gave up. > > What is the advantage of doing this subcortical segmentation step? For > example, will it potentially improve the results of later stages? > > In the README file in freesurfer/subjects it states that the sample should be > processed with > > recon-all-nmr -all -subjid bert > > Do you recommend adding -nosubcortseg to the recon-all-nmr script? > > Previously, I used to use recon-all. It looks like it that is a grepped / > stripped subset of the -nmr version. Is recon-all deprecated? > > When I run recon-all with bert I get an error about DoCANormalize not being > defined. > > Will I be able to correctly compare samples that I have run in previously > releases using recon-all? > > Thank you. Yours confused, > > Ray Fix > > > On Jul 18, 2005, at 10:26 AM, Doug Greve wrote: > >> >> That one now automatically does subcortical segmentation, which will take >> about 24 hours. Add -nosubcortseg to the command-line (AFTER -stage1) to >> disable it. >> >> doug >> >> Timothy O'Keefe wrote: >> >> >>> Also, I am using the OSX Tiger snapshot of FreeSurfer with a new >>> recon-all script courtesy of Doug Greve. >>> >>> On Jul 18, 2005, at 10:03 AM, Timothy O'Keefe wrote: >>> >>> >>>> I ran recon-all stage1 and it took a very long time. Well, at least >>>> longer than people document. I didn't time it, but it must have taken >>>> close to 10 hours. >>>> >>>> Also I received this error during mri_fill(): >>>> ... >>>> using +/- offset search region where offset is 39..... >>>> using +/- offset search region where offset is 42..... >>>> using +/- offset search region where offset is 45..... >>>> using +/- offset search region where offset is 48..... >>>> mri_fill: could not find pons >>>> No such file or directory >>>> INFO: Modifying dst c_(r,a,s), using the transform dst >>>> INFO: Modifying dst c_(r,a,s), using the transform dst >>>> INFO: Modifying dst c_(r,a,s), using the transform dst >>>> talairach cc position changed to (0.90, -7.51, 23.75) >>>> INFO: Modifying dst c_(r,a,s), using the transform dst >>>> INFO: Modifying dst c_(r,a,s), using the transform dst >>>> find_cutting_plane:seed point not in structure! Searching >>>> neighborhood... >>>> find_cutting_plane:seed point not in structure! Searching >>>> neighborhood... >>>> ERROR: mri_fill exited with non-zero status >>>> recon-all exited with errors at Sat Jul 16 01:13:52 EDT 2005 >>>> >>>> Are there any suggestions? I am using a single T1 (1x1x1) image acquired >>>> from a Siemens 1.5T machine. I realize I should use multiple images for >>>> averaging, however I am just trying to get a feel for the software. >>>> >>>> -T >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer