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11 participants
30080 discussions

Cortical and White Matter Parcellation and Segmentation Outputs
by lbotelho＠nmr.mgh.harvard.edu 11 Feb '08

11 Feb '08

Dear FS experts, 1. There are some frequent mismatches between the white matter and cortex parcellations (aparc+aseg.mgz and wmparc.mgz) with zeroed voxels between them. Would suppressing the option --ribbon when running aparc2aseg either during cortex or white matter parcellation (or both) result in a more close match between aparc+aseg.mgz and wmparc.mgz? Other suggestions? 2. Cortex segmentation output in aseg.mgz is not uncommonly thinner than it should be in my data. Tweaking around the default mri_segment settings for white matter lo/hi and gray matter hi may improve it. I am still looking for optimal settings and the pial surface is not under control. Any specific suggestions? 3. These days acquiring with multichannel headcoils has become almost the norm. Even normalized data seems to suffer somehow. Particularly, superficial and brighter cortex is prone to produce thinner cortex thickness results than cortex in basal regions with less signal. Any workarounds? Many thanks, Luis

2 1

SPGR format
by a.m.fjell＠psykologi.uio.no 11 Feb '08

11 Feb '08

Hi, we have problems converting scans obtained from a GE scanner with a T1-weighted 3-D spoiled gradient recalled (SPGR) sequence to anything freesurfer can read. Any tips? Thanks! - Anders

2 6

freesurfer version difference
by Mithra 11 Feb '08

11 Feb '08

Hello, We used Freesurfer version 4.0.0 for a many of our subjects and version 4.0.1 for the other subjects. Will there be a difference between both the versions. We are comparing individual subjects brain (aseg stats) at 2 different instances. It so happens we are comparing the same subject's brain done with version 4.0.0 with his later structural scan analyzed with version 4.0.1. We are looking at the Hippocampus and Amygdala volumes. Thanks. -- Regards, Mithra Imaging Research Center University of Texas, Austin 3925-B W Braker Lane Austin. TX - 78759 Tel: (512) 232-5725 Fax: (512) 232-4202 www.irc.utexas.edu

3 2

recon-all with DICOM vs. mgz inputs - volume differences
by Jennifer C. Britton 11 Feb '08

11 Feb '08

On the freesurfer wiki, it says that recon-all can be done with DICOM inputs in addition to mgz inputs. In doing recon-all using DICOM or mgz (created via unpacksdcmdir), the volumetric values obtained using mris_volume and mris_wm_volume are different. For example in one subject, with DICOM inputs: pial 505865 and white matter volume 166713. with mgz inputs: pial 510322 and white matter volume 167030. The white matter seems to be fairly close but the pial volume is off by nearly 4000. Can someone explain why there is this difference and which value we should believe? Thanks, Jennifer

2 1

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

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