Freesurfer

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30080 discussions

is pial surface GM surface?
by George He 06 Feb '08

06 Feb '08

Hi freesurfer experts, It seems to me the pial surface should be the surface of gray matter, but when I overlay functional activations on it, it seems to be surface of white matter. The reason I think so is that when I load the same activation in both tksurfer and tkmedit, if I click on an activated area (or any point) on the pial surface in tksurfer, save it, and load it in tkmedit, the point will land on the yellow/green lines while the tksurfer and tkmedit show the same talairach coordinate for the point. If I click on a point that is on the red line in tkmedit, save it, and load it in tksurfer, they (tkmedit and tksurfer) show different talairach coordinates for the points. Question: what is the truth and what should I expect? Thanks, George

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Insula in Bert
by Yong Zhang 05 Feb '08

05 Feb '08

Hi Freesurfer_owner, I'm using Slicer2.6 to load and view FreeSurfer segmentation (Bert) now. I found Slicer cannot show some areas like, Left and Right Insula. And in aseg.stats, the parameters of these areas are listed as 0.0000. I downloaded the bert archive from the Slicer website. Could you tell me if there are models of these areas in bert and where I can find them? Thanks a lot! Yong

2 1

Assigning Subject Name
by Jared Morton 05 Feb '08

05 Feb '08

When I run the first portion of the recon-all script according to the instructions in RecommendedReconstruction, the command I am instructed to use is: *recon-all -i **invol1** -i **invol2** -autorecon1 -subjid ** your_subject_name* This command allows me to specify the input files and assign them a name. When I try to run the entire recon-all script according to the instructions in FSTutorial/MorphAndRecon, I am instructed to use this command: *recon-all -autorecon-all -s <subjid>* However, unlike the script for the first portion of the recon-all script, there does not appear to be anything in this command that allows me to specify my input files and assign them a name. Because my subject name is not specified, I cannot get the recon-all script to run. How do I assign a subject name without having to run the first portion of the recon-all script? Any help will be greatly appreciated. -- Jared Morton M.S. Rosalind Franklin University of Medicine and Science

3 2

Normalization
by Caroline Chapman 05 Feb '08

05 Feb '08

Hello, I am stuck on trying to fix a normalization output problem with one of my subjects. While the reconstruction ran through completely without error, the output looks strange (See attached .tif image). The wm surfaces outline the pial surfaces, and the pial surfaces outline outline a bit further, even extending to include parts of the skull. The talairach.xfm looks good; however, similar to the tkmedit output, the wm surfaces extend to where the pial surface should be. I tried running "mri_normalize <s/mri/nu.mgz. <s/mri/T1.mgz -gentle", and this did not help. Do you have any suggestions for how to correct the surfaces here? 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

1 0

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

1 0

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

1 0

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

2 1

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

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