Freesurfer

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30076 discussions

Unpacking Error
by Avram Holmes 05 Feb '08

05 Feb '08

FreeSurfer Folks, My lab is currently running version 4.0.2 on our server, and since the scanner upgrade we have been unable to unpack our data. When I attempt use the unpacksdcmdir script I get the following error. mri_convert DICOM/08020113/combined//89501876 ./T1_MPRAGE_sag/002 --sdcmlist ./T1_MPRAGE_sag/002/flf -ot cor --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child process exited abnormally We are running with the same flags that we have always run. Is this related to a bug in the script? Thanks for any help you can offer, Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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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nu_correct not found
by Juergen Haenggi 05 Feb '08

05 Feb '08

Dear FS experts I tried to run FS4.0.2 on Linux and the following error occurred: INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 5 07:59:56 CET 2008 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/Turner_Control_01/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ Linux 130.60.235.1 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux Tue Feb 5 07:59:56 CET 2008 nu_correct: Command not found. tmpdir is ./tmp.mri_nu_correct.mni.5963 /usr/local/freesurfer/subjects/Turner_Control_01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5963/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5963/nu0.mnc $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 6.12323e-17, 3.7494e-33) j_ras = (-3.7494e-33, 1.94311e-24, -1) k_ras = (6.12323e-17, 1, 1.94311e-24) writing to ./tmp.mri_nu_correct.mni.5963/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Feb 5 08:00:04 CET 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.5963/nu0.mnc ./tmp.mri_nu_correct.mni.5963/nu1.mnc nu_correct: Command not found. ERROR: nu_correct Linux 130.60.235.1 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Feb 5 08:00:04 CET 2008 [Neuropsycho@130 subjects]$ Any idea what is wrong here? Thanks in advance Best regards Juergen ----------------------------------------------------------- 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

noaseg usage and consequences
by Jerry Yeou-Wei Chen 04 Feb '08

04 Feb '08

Hello, We ran into the following error during autorecon2 with one subject: mri_fill: could not find any points where lh and rh wm are nbrs It has been suggested to another user that the "-noaseg" flag be used. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06560.html) However, we would like to ask how this might affect the subsequent steps and how to take this into account in subsequent group analysis. Also, we would like to clarify if this would prevent the subcortical volumetric calculations. Thanks! - Jerry

3 2

Control points and missing cortex in the surfaces
by Caroline Chapman 04 Feb '08

04 Feb '08

Hello, I have a subject with substantial cortex in the temporal lobe that is labelled in the aseg volumes, but not included in the surfaces. As well there is a bit of cortex that is neither labelled or included in the surfaces. (It is all included in the brainmask.mgz volume, though) I used about 10 ctrl points to try to fix the problem. While it seemed to help in including some of the cortex, some cortex remained not included in the surfaces or aseg labels. Do you have any suggestions for what to try when the ctrl points do not fully include the cortex? The talairach Thanks! Caroline -- Caroline Chapman Research Assistant/Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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recon-all error
by Bill Monaco 04 Feb '08

04 Feb '08

Hi, I've been sourcing the stable3 version of freesurfer and getting an error in the -fix step of recon-all for the lh. I'm running the command line: recon-all -subjid <SUBJID> -fix -hemi lh and I get the following output in scripts/recon-all.log #-------------------------------------------- #@# Fix Topology lh Mon Feb 4 08:44:46 EST 2008 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/biggs_011/users/PRECREST_MEMPRAGE_nrecon/VESS80_nrecon_vb15_MEMPRAGE/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga VESS80_nrecon_vb15_MEMPRAGE lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-24 (nv=134720, nf=269504, ne=404248, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 3903 ambiguous faces found in tessellation segmenting defects... defect 12 : 5 vertices have been added to the surface total of 5 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 12 overlap defect 11 reading input surface /autofs/space/biggs_011/users/PRECREST_MEMPRAGE_nrecon/VESS80_nrecon_vb15_MEMPRAGE/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Linux windu 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Feb 4 08:45:28 EST 2008 Any suggestions as to how to fix this or info as to what the problem may be? Thanks, Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128

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Talairach transformations in tkregister2 and WM editing for aseg.stats
by Teddy Youn 01 Feb '08

01 Feb '08

Hi, Our group is currently trying to use FS on a cohort of DAI/TBI patients and have encountered several problems. We recognize the limitations with using FS on brains that may have severe deformation; however, we wanted to get some feedback: 1) When loading the talairach transformation on tkregister2, the registration of some of our more severe TBI brains has been pretty bad. Some have loaded coronal orientations twice for the corresponding axial and coronal orientations of the T1 images. Others are poorly rotated and even flipped in orientation. For poorly registered images, is it better to use a program like SPM to manipulate the image and then convert to a register.dat format for FS, or is MRItotal sufficient (through FS)? 2) For some of our more severely injured DAI patients, the wm.mgz is missing a lot of voxels in subcortical structures (single voxels all along the white matter areas. Should we be filling in these areas with "white" or "grey" with the volume brush if we do not want to those voxels to be counted in the aseg.stats file? Our assumption is that the DAI in these patients is causing the white matter missing voxels. (We know that this may only apply for the volumes-based Desikan-Killany atlas and not for the Destrieux surface-based atlas.) Any help you can provide would be great, -Teddy Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

2 1

Problems on MAC 10.5
by Martin Kavec 01 Feb '08

01 Feb '08

Hi, I have upgraded my Mac OS X to 10.5 and after that nu_correct says: Can't locate MNI/Startup.pm .... $FREESURFERHOME/mni/bin/nu_correct line 37 Anybody has an idea, what could be wrong? Obviously, the file is there. Thanks, Martin

2 2

Freesurfer qcache error
by William R Mcgarry 01 Feb '08

01 Feb '08

When running qcache (on a recent version of freesurfer) after running recon-all -s 4964-14_recon -all command, I get the following error: ERROR: number of vertices in /usr/local/freesurfer/subjects/4964-14_recon/surf/lh.thickness does not match surface (138139,137319)ERROR: reading curvature file Linux localhost.localdomain 2.6.23.14-107.fc8 #1 SMP Mon Jan 14 22:07:11 EST 2008 x86_64 x86_64 x86_64 GNU/Linux Any ideas? This happens for multiple subjects without any known cause or covariance. --------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.2 RedHat release: Fedora release 8 (Werewolf) Kernel info: Linux 2.6.23.14-107.fc8 x86_64

2 1

mris_wm_volume
by Gallo, Antonio (NIH/NINDS) [F] 01 Feb '08

01 Feb '08

Hello All, We are trying to obtain an accurate measurement of the total WM volume (cerebral WM + WM hypointensities) in a group of patients with multiple sclerosis (MS). As per Bruce's suggestion, we are now using mris_wm_volume that gives more accurate measures than aseg.stats. When looking at our data we have noticed that within the WM surface (yellow line) there are many voxels labeled as Cerebral-Cortex (mainly in places where we put cp to expand the WM surface), and some others labeled as None (mainly in places of iuxtacortical MS lesions). As expected basing on how mris_wm_volume works, we have noticed that WM volume actually change upon manual editing of these mislabeled voxels in the aseg.mgz (i.e. relabeling them as actual WM). Thus, we were wondering if there is any way to capture and correct for all these mislabeled voxels in a more automated manner (i.e. automatically considering Cerebral-Cortex and None voxels included in the WM surface as actual WM in the mris_wm_volume computation). In this way it should be possible to get more accurate measures of WM volumes as well as save a lot of time in manual editing. Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

1 0

thresholding problems/visualizing .curv files
by swallace＠nmr.mgh.harvard.edu 01 Feb '08

01 Feb '08

Warm greetings from the first floor- I am having an issue with my .curv files, similar to what Adam from the archives had a little over a year ago: On Tue, 25 Apr 2006, adam walczak wrote: Hello, I am testing the output of some data I ran through the reconstruction process. While attempting to view the rh.sphere volume with the rh.curv overlay, I only could see the red lines, not the green lines. I noticed that I had to adjust the settings (view--configure--curvature display). I had to change the value of the threshold midpoint to .2 and the threshold slope to 3.5. Only then could I see both. Is this normal, or maybe is something wrong...all of the processes said they finished without error. Thanks. Adam I know Bruce replied and said that there looked to be something wrong, and to include the screen shots of what default thresholding looks like. I am running this on a Centos 4 machine with a frozen version of Freesurfer from Nov 2005. Thanks for the assistance! Stuart

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