Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

more thinner parcelation borders
by Gonzalo Rojas Costa 26 Jul '10

26 Jul '10

Hi: How can I get more thinner parcelation borders ?... Or could I specify a transparency factor ?... Sincerely, Gonzalo Rojas Costa

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Error in Recon-all -all
by York, Philip 26 Jul '10

26 Jul '10

Dear Freesurfer experts, one of my recent recon-all processes exited with errors as seen here mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.92 x + 0.0 Left_Pallidum too bright - rescaling by 0.984 (from 1.000) to 110.2 (was 112.0) Right_Pallidum too bright - rescaling by 0.993 (from 1.000) to 110.2 (was 111.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux ucbirl-ubuntu 2.6.32-22-server #36-Ubuntu SMP Thu Jun 3 20:38:33 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jul 24 23:26:21 MDT 2010 I'm not sure if this is enough of the script to determine where the problem might be, but any advice on how to correct the error would be greatly appreciated. Thank you, Philip

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XYZ Coordinates for Cortical Parcellation
by Ajilore, Olusola 26 Jul '10

26 Jul '10

Hello, I was wondering if there was a list xyz coordinates for all 70 regions generated in the cortical parcellation atlas. Thanks for your help, Olu Ajilore, MD, PhD Assistant Professor Department of Psychiatry University of Illinois-Chicago oajilore(a)psych.uic.edu

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Freesurfer version 4.5
by Toh Hock Wong 26 Jul '10

26 Jul '10

Hi Freesurfer experts, Thanks for Jesse's recent posting which raises my question. I am in the process of compiling a series of control patients with freesurfer version 4.5. Is it possible to save the output after autorecon1( with version 4.5), and use it to continue autorecon2 when version 5 is released? I understand it is not possible to predict wether the upgrade will involve changes to those stages in autorecon1. At least this will help in terms of saving time to manually strip the skull with the next version release. Any suggestions from the experts? Toh Wong Sydney, Australia

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Version 4.5.0 update question
by Jesse Bledsoe 26 Jul '10

26 Jul '10

Hi everyone, We are currently running version 4.2 and will be updating to version 4.5. I have about 60 brains that went through reconstruction with 4.2 and was wondering if the reconstructions/data will be affected at all by updating to 4.5? Will I need to re-run part of recon-all in order to use the updated Destrieux atlas? Thank you for your time, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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spmregister-sess error
by Adam Nitenson 26 Jul '10

26 Jul '10

Hello Freesurfers, I am in the process of unpacking scan data, but am having problems with the spmregister-sess command. I ran recon-all and preproc-sess to completion without error. However, when I run "spmregister-sess -s FB0011090BB", I receive the following error: ">> >> >> ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg" I have unpacked several other subjects before using these same commands without issues. Why might I be receiving this error now? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Segmentation fault at mri_ca_register
by MacDonald, Christine 26 Jul '10

26 Jul '10

Greetings from St. Louis. I recently installed Freesurfer version 4.5 on my Windows XP OS PC after attending your training course held at our institution, Washington University. The install went fine, and I was able to make it through all the checks in your setup and installation series on your wiki page. I attempted to then run a data set of my own and ran into the following error during autorecon2 which I have included the lines of output right before it as well: setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=766 0495: dt=0.028000, rms=0.464 (0.163%), neg=0, invalid=766 0496: dt=0.028000, rms=0.463 (0.154%), neg=0, invalid=766 0497: dt=0.024000, rms=0.463 (0.124%), neg=0, invalid=766 0498: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766 0499: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766 0500: dt=0.000219, rms=0.463 (0.001%), neg=0, invalid=766 0501: dt=0.000014, rms=0.463 (0.000%), neg=0, invalid=766 0502: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=766 0503: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766 Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Jul 23 18:12:09 EDT 2010 /data/TB3241W/TB3241W/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 23 18:12:10 EDT 2010 I am running with 4G of RAM and a quad-core processor. At first I thought it was because of the 2GB max space limit in VMware so I even built and mounted a 100GB drive internal to VMware and ran all the data from there. Additionally when I check the disk space after this error it shows it only used ~1% of the 100GB mounted disk in VMware so I know I have room. Output from typing 'bugr' per your request on wiki is the following: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Debian version: 5.0 Kernel info: Linux 2.6.28-11-generic i686 Any thoughts or guidance as to what may be going wrong? I fully admit to my novice status with Freesufer and kindly look forward to any and all advice. I found one reference to a similar problem searching through your Freesurfer support Old Archive but the response from your organization was just a further inquiry for additional information so I was unsure as to how to proceed. Thank you in advance for the help! Best Regards, Christine Mac Donald Washington University Saint Louis, MO

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Siemens Trio 3T imaging parameters
by Tricia Merkley 25 Jul '10

25 Jul '10

Hi Freesurfers, Does anyone have a suggestion for an optimal scanner protocol for structural scans using Siemens Trio 3T? Thanks, Tricia Merkley

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problems visualizing in tksurfer
by Michael Scheel 25 Jul '10

25 Jul '10

Hi fs-experts, I want to visualize thickness files and am succesful as long I use the Heat LUT. When I use the RedGreen Overlay for some reason the Overlay is visualized purple. Any ideas why that is? I'm running FS 4.5 on a Mabook Pro. Is there a Rainbow-Color LUT to download somewhere? Thanks, Michael s

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error in mri_label2vol
by Mario Ortega 23 Jul '10

23 Jul '10

Hi freesurfer programmers, I have a specific question reagrding the output of mri_label2vol. The image is correctly converted, however the analyze header file has an orientation value set to -1. This is invalid as analyze orient fields can only be 0-5, and my next scripts rely on the orient string to perform transformations. See - http://eeg.sourceforge.net/mri_orientation_notes.html Should I manually edit the orient field in the header? or does -1 field = analyze 4? Thanks, Mario Ortega Here is my specific command line output. running the command: *mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg. img --regheader aparc+aseg.mgz* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.25.2.4 2009/07/08 16:28:40 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 88.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Computing registration based on header RegMat: -------- 0.019 0.998 -0.052 0.000; -0.999 0.021 0.035 0.000; 0.036 0.052 0.998 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.019 -0.998 0.052 128.000; -0.036 -0.052 -0.998 128.000; -0.999 0.021 0.035 88.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 342870 (46013 filled) ASeg2Vol: done Analyze Output Matrix -0.019 -0.036 -0.999 98.696; -0.998 -0.052 0.021 164.924; 0.052 -0.998 0.035 115.862; 0.000 0.000 0.000 1.000; -------------------- *INFO: set hdr.hist.orient to -1* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0

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Freesurfer July 2010