Freesurfer December 2004

freesurfer@nmr.mgh.harvard.edu

21 participants
28 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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Freesurfer on Latitude X300?
by Kristine Beate Walhovd 03 Jan '05

03 Jan '05

Hi We've had some trouble with displaying the Freesurfer graphics correctly on some new stationary Dell PCs recently. I now need a new laptop, and I'm considering buying a Dell Latitude X300. I won't use it as an analysis machine, mostly just for travel, but I need to be able to display images and work with Freesurfer on it. Most features on this light-weight model are integrated so that they can't be changed, including the graphics card (855GM integrated graphics shipset - up to 64MB), so I was wondering if any of you have any expericence with running Freesurfer on this model, and if so, does it work OK? I'd be grateful for any comments. Thanks, Kristine

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FSL analyze to bfloat
by Jyrki Ahveninen 30 Dec '04

30 Dec '04

Hi, I tried to convert analyze (FSL) img files to bfloat (for group analysis) using spm2bfloat. It complains about the header size. Is there a fix for this? Same problem occurred with spm_to_bfloat.m Thanks, Jyrki header_key sizeof_hdr = 1543569408 data_type = db_name = extents = 4194304 session_error = 0 regular = r hkey_un0 = image_dimension dim = 1024 16384 16384 5120 256 0 0 0 datatype = 4096 bitpix = 8192 dim_un0 = 0 pixdim = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 compressed = 0.000000 verified = 0.000000 glmax = 167772160 glmin = 0 data_history descrip = Externally created avw->header aux_file = orient = originator = 0 0 0 0 0 0 0 0 0 0 generated = scannum = patient_id = exp_date = exp_time = hist_un0 = views = 0 vols_added = 0 start_field = 0 field_skip = 0 omax = 0 omin = 0 smax = 0 smin = 0 incorrect header size in analyze file -- Jyrki Ahveninen, PhD MGH/MIT/HMS - Athinoula A. Martinos Center for Biomedical Imaging CNY 149-2301, 13th Street Charlestown, MA 02129 email: jyrki(a)nmr.mgh.harvard.edu

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tklib8.3.so
by Kevin DeSimone (kdesimon＠Princeton.EDU) 27 Dec '04

27 Dec '04

hi-- i've recently installed the February 18th 2004 (561M) snapshot on my linux. when trying to run any process requiring graphical display of surfaces/volumes, i get the following error: "/usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory" i was able to run these processes just fine w/ the older version of freesurfer (i believe it was the june 27 2003 snapshot) also, i noticed someone posted to the list w/ this problem in April, and the response gave link to .rpm of this missing library. however, that library is dependent on yet another library (libtcl.so.0)-- which i can't find. what's an easy fix for this, so i don't have install libraries for libraries? kevin desimone

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question
by Wan Park 23 Dec '04

23 Dec '04

I want to calculate the gray matter volume in certain areas (eg. cortical area 39). What should I do? Thanks, Wan

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mni_perllib_0.07 installation error
by Joongnam Yang 23 Dec '04

23 Dec '04

Happy holidays for everyone! When I was installing mni_perllib_0.07, the following error messages keep popping out and at the end installation fails. batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at t/batch-1.t line 36 t/batch-1........NOK 14tail: .out29406: No such file or directory t/batch-1........NOK 16/usr/bin/getopt: invalid option -- J /usr/bin/getopt: invalid option -- Q /usr/bin/getopt: invalid option -- l /usr/bin/getopt: invalid option -- S /usr/bin/getopt: invalid option -- s /usr/bin/getopt: invalid option -- o /usr/bin/getopt: invalid option -- e batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 112 `batch' exited with non-zero status code: 256 at t/batch-1.t line 112 Would someone give me a clue on how to fix it? Nam.

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Re: [Freesurfer] wmfill error
by Joongnam Yang 23 Dec '04

23 Dec '04

Thanks Margaret, Is there a reference on how to specify the corpus collosum and pons in the WMFill under Preferences->Expert Preferences in csurf? Nam. >>> Margaret Duff <mduff(a)nmr.mgh.harvard.edu> 12/22/04 12:10 PM >>> i had this problem recently. try using recon-all -stage one in a terminal window instead of process volume in csurf. or specify the corpus collosum and pons in the WMFill tab under Preferences->Expert Preferences in csurf. it probably cant find where to segment. you might want to check the archives for more detail on this problem. hope this helps, margaret On Wed, 22 Dec 2004, Joongnam Yang wrote: > Hi all, > > During "create surface" on csurf, > right after "fill white matter" is done, as soon as "tesselate RH white > matter" starts, > an error message comes up, which is > > images filled: > somedirectory/mri/filled/COR-001...not found, wmfill first. > > I checked the directory of /mri/filled, which did not have COR-00* files. > There was only one file, COR-.info. > It seems that the first process in "create surface" (fill white matter) is > supposed to create all those COR-00* files in the /mri/filled, but none is > created. > I changed permission on the directory, to no avail. > Would someone suggest something? > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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wmfill error
by Joongnam Yang 22 Dec '04

22 Dec '04

Hi all, During "create surface" on csurf, right after "fill white matter" is done, as soon as "tesselate RH white matter" starts, an error message comes up, which is images filled: somedirectory/mri/filled/COR-001...not found, wmfill first. I checked the directory of /mri/filled, which did not have COR-00* files. There was only one file, COR-.info. It seems that the first process in "create surface" (fill white matter) is supposed to create all those COR-00* files in the /mri/filled, but none is created. I changed permission on the directory, to no avail. Would someone suggest something? Nam.

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watershed values
by Goldman, Aaron (NIH/NIMH) 22 Dec '04

22 Dec '04

Hi, I'm trying to adjust the watershed thresholds on a few images, and have a question about the default watershed value. When I run the skullstrip without specifying a watershed value, the recon-all.log file typically says: preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent I'm guessing this means the program first tried a value of 25%, somehow determined it was too high, and then used a watershed threshold of 15% instead. Is this correct? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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recon-all -stage1 error
by Joongnam Yang 22 Dec '04

22 Dec '04

Hi all, I ran recon-all -stage1 -subjid ID with the following errors. Any comment woud be appreciated. ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.8 2002/08/05 00:53:50 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.11 2002/11/06 13:32:23 jason Exp $ $Header: /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is /diskc/NAM/DATADec04/DPJ --------------------------------------------- MotionCor Wed Dec 22 14:10:28 EST 2004 INFO: no runs were found in /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig/XXX, however, there is a volume in /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig, so I am just going to proceed with that as the input. --------------------------------------------- Talairach Wed Dec 22 14:10:31 EST 2004 /diskc/NAM/DATADec04/DPJ/ANAT/mri talairach2 ANAT INFO: registering ANAT Wed Dec 22 14:10:31 EST 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "eng_US" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. (Maybe you should just omit the defined()?) -------------------------------------------- mri_add_xform_to_header /diskc/NAM/DATADec04/DPJ/ANAT/mri/transforms/talairach.xfm /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig /diskc/NAM/DATADec04/DPJ/ANAT/mri/orig Wed Dec 22 14:12:14 EST 2004 --------------------------------------------- Nu Intensity Correction Wed Dec 22 14:12:14 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "eng_US" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/local/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/mni/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/hda7 54459572 26175492 25517692 51% /diskc ------------------------------------------ recon-all exited with errors at Wed Dec 22 14:12:24 EST 2004

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Freesurfer December 2004