Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

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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stage1
by Timothy O'Keefe 18 Jul '05

18 Jul '05

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

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.mat matrix format for cosine info in mri_convert
by Glenn Lawyer 18 Jul '05

18 Jul '05

Hi, We are also seeing the segmentation fault when running mri_convert on our dicom files. As a work-around, I have written a script that uses xmedcon to batch convert dicom to analyze. I'm planning on posting the script to this list, but want to resolve one little issue first. When I run mri_convert on the resulting analyze files, the COR images are in axial orientation. This is probably because the command"$mri_convert 001/001.img ." "Could not find the direction cosine information. Will use the HORIZONTAL orientation. If not suitable, please provide the information in 001/001.mat file". I want to modify my script so that it creates the .mat file, but do not know the format. I can extract the directional cosine information using dicom2 (dicom2 -t1 001/IMAGE_1.dcm | grep Orientation), giving me Image Orientation (Patient) (0020,0037) 6 DS [0.999848\0.00778219\0.0156255\0.0156255\0.00012207\-0.999878] Could you kindly send me the appropriate 001.mat file for this subject/aquisition? +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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Vertex number
by Sarah Rugheimer 15 Jul '05

15 Jul '05

Hello, Does anybody know if there is a file with or a way to obtain a mapping of the vertex number with say the RAS coordinate system. I know when you are in the tksurfer window by using the mouse/cursor you can see each vertex number with the corresponding RAS coordinate, but is there a way to output all the vertex numbers with the cooresponding RAS coordinates to a file or matrix or some such thing. Thank you very much for any help. Sarah Rugheimer

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edit white matter lesion
by Antao Du 15 Jul '05

15 Jul '05

Hi, I am trying to edit the white matter lesion in wm volume. when I open tkmedit subjid wm. There is a white matter lesion that was misclassified. I paint that region with white matter lesion to white color using button 2. Do I need to paint all ventricle? The manual says that the ventricle is autofilled. But I can't see it and can't find a function to do it. Any helps there? Thanks, Antao

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Freesurfer