Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

qdec error
by Woo-Suk, Tae 10 Feb '08

10 Feb '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } I've processed my data with FreeSurfer 3.04, and ran the group data with qdec of FreeSurfer 4.02.But, qdec reported a error message. I attached.What's the problem?Woo-Suk, Tae

2 1

func2roi average
by Corey Keller 10 Feb '08

10 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. Could someone point me in the right direction? 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

2 1

Fwd: Re: [Freesurfer] qdec error
by William R Mcgarry 08 Feb '08

08 Feb '08

I downloaded some packages for tcl and tk, but they didn't have any effect. I also get this error, which I forgot to include: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0x881c1f0): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0" The output of the command is shown below: $ ldd $FREESURFER_HOME/bin/qdec.bin linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000) Thanks. -Ryan McGarry

2 4

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 ---------------------------------------------------------------------

2 1

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

1 0

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

3 9

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

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer