Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 discussions

About the average subject
by jorge luis 13 Feb '08

13 Feb '08

Hello all Hello all We are planning to perform a cross-sectional study involving two population of subjects. I think we have to choice one among two possibilities : 1-Make a single average subject for both populations and resample all the subject to this average for the statistical analysis. 2-Make two average subjects, one for each population. In the last case we are not sure what is the right posterior processing in order to get the most accurate results from the final statistical parametric map. Any help is welcome In advance thank you Jorge Phd Student ______________________________________________ ¿Con Mascota por primera vez? Sé un mejor Amigo. Entra en Yahoo! Respuestas http://es.answers.yahoo.com/info/welcome

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Binary Masks
by Anil Roy 12 Feb '08

12 Feb '08

Hello All, I want to create a binary mask volume for stg and tried the following command # mri_label2vol --label trial_labels/rh.superiortemporal.label --temp /mnt/win/MRI_data/Trial_Runs/Freesurfer/1195/mri/brainmask.mgz --o testmask.mgz The label was created using mri_annotation2label When I opened up this label in tkmedit, I could see that the cortical regions of STG are in white and everything else is in black. My questions is if it is possible to fill in the regions within this label: in other words if I can also have the white matter that the label encompasses included in the mask. Also, is there a different method that is normally used for creating binary masks? Thanks, Anil.

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[Fwd: Re: [Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs]
by lbotelho＠nmr.mgh.harvard.edu 12 Feb '08

12 Feb '08

Subject: Re: [Freesurfer] Cortical and White Matter Parcellation and Segmentation Outputs From: lbotelho(a)nmr.mgh.harvard.edu Date: Tue, February 12, 2008 4:09 pm To: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- Hi, 1. Some samples with the cortex/gray matter gaps in the parcellation results. Is the mri_convert --fill_parcellation utility useful here? 2. My interest and use is focused on aseg+aparc and wmparc too, thanks for pointing this clearly. 3. The sample in attachment is less than optimal (though a 3T MPRAGE, 1mm3) but to illustrate the challenge in this kind of data. Thanks for the suggestion of control points. Can you point me some reference about its usage? Best, Luis > Hi Luis, > > 1. I'll leave this for Doug. > 2. The aseg.mgz is indendent of (and produced before) the mri_segment > step (which produces the wm.mgz). In general we don't use the cortical > part > of the aseg as the surfaces in our experience are more accurate. > 3. Can you give an example of this? I would think control points could > help. Note that we don't use image intensity, but rather local gradient > maximum to position the pial surface, which should be independent of local > bias. > > cheers, > Bruce > > > On Mon, 11 Feb 2008 > lbotelho(a)nmr.mgh.harvard.edu wrote: > >> 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 >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

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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

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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

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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

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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

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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

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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

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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

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Freesurfer February 2008