Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 discussions

qdec error
by William R Mcgarry 08 Feb '08

08 Feb '08

When trying to analyze some data in qdec, after I completed recon-all -all and -qcache for the subjects in my qdec table, I get to the Display tab and pick an option under Scalar. It doesn't matter which option, as they all give me the same two errors repeatedly (forcing me to quit qdec). These are: (1) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x87548598): TclTK error: invalid command name "vtkTemp349" invalid command name "vtkTemp349" while executing "vtkTemp349 FocusInCallback" (command bound to event) and (2) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x8748598): TclTK error: invalid command name "vtkTemp347" invalid command name "vtkTemp347" while executing "vtkTemp347 FinishEditing" (command bound to event) Any help is greatly appreciated. Thanks. -Ryan McGarry --------------------------------------------------------------------- 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 ---------------------------------------------------------------------

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clarification on computation of stats for "unknown" label in aparc
by Michael Harms 08 Feb '08

08 Feb '08

Hello, The "unknown" parcellation in /h.aparc.annot includes vertices of the white/pial surface that correspond to the insula, medial temporal cortex (including hippocampus and amygdala), and the midline. How are the vertices that "cut" through the hippocampus, amygdala, and midline treated during the computation of the volume and thickness measures in ?h.aparc.stats? Do those vertices contribute to the values computed for the "unknown" region, or are they excluded? (That is, are the values for "unknown" in ?h.aparc.stats derived solely from vertices that are considered to correspond to cortical gray matter, based on the aseg.mgz?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

1 0

func2roi average
by Keller, Corey J. 08 Feb '08

08 Feb '08

Hi freesurfers, It says on the func2roi-sess page in the wiki that "At this point, there are four things you can do next: (1) pool the data into a text file, (2) view the hemodynamic response in the ROI for each session, (3) view the final mask, or (4) inter-subject average." However, it doesn't seem to go on to say how to compute the inter-subject average. How can I do this? Thanks again. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital VBK 830, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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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

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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

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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

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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

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Freesurfer February 2008