Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

why same structure has two different volume in aseg.stats and wmparc.stats, for example: amygdala.
by liyari5018 06 Apr '10

06 Apr '10

Hi freesurfer experts, why same structure has two different volume in aseg.stats and wmparc.stats , for example: amygdala. thanks for your reply! LJ

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dt_recon failed
by movado 03 Apr '10

03 Apr '10

Hi all, I use dt_recon on DTI scans from Siemens machine. The command I used is > dt_recon --i k1/ep2d/81678191 --s k1 --o k1_DTI The error message is as follows sysname Linux hostname movado-laptop machine x86_64 user movado FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/k1_DTI/dwi-ec.nii logyflag 1 X /usr/local/freesurfer/subjects/k1_DTI/dwi-infodump.dat usedti 1 glmdir /usr/local/freesurfer/subjects/k1_DTI IllCondOK 0 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/k1_DTI Loading y from /usr/local/freesurfer/subjects/k1_DTI/dwi-ec.nii Using DTI ERROR: cannot extract sDiffusion.alBValue[1] from /usr/local/freesurfer/subjects/k1_DTI/dwi-infodump.dat What can I do to solve this problem? Thank you advance for the help. movado

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Retinotopy analysis ERROR: selfreqavg failed
by Yuhong Jiang 02 Apr '10

02 Apr '10

Hi, I want to provide more information about the retinotopy analysis error in case someone has insight about the problem. Using the same exact commands (mkanalysis-sess.new, then sfa-sess), I was able to successfully run the retinotopy commands in my old Linux box (the version of sfa-sess was from 2005, and we used matlab 6.5). However, the program hang using the newest version of freesurfer on Linux (the version of sfa-sess was from 2007, MATLAB 7.8). The program hang almost immediately. On Mac OS 10.6 using MATLAB 7.6, the command sfa-sess also hang with an error message of "ERROR: selfreqavg failed". I tried to replace the new sfa-sess with the old sfa-sess, and the new selfreqavg with the old selfreqavg, but the problems were not fixed. Is there a bug in the binary files that makes them incompatible with higher versions of MATLAB, or Mac OS 10.6, or Linux 2.6.9-89.0.15.ELsmp? Thanks for your insight. --Yuhong -- ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166(a)umn.edu, 612-625-7003 http://jianglab.psych.umn.edu/ ----------------------------------------------------------

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Correcting subcortical segmentation
by John Fredy 01 Apr '10

01 Apr '10

Hello all, I'm trying to obtain a set of statistics of subcortical segmentation from a pacient with Huntington's disease. The tutorial of freesurfer shows six possible case of error in freesurfer: correcting white/gray surfaces, topological errors, skull removing, talairach transformation, among others. But, how I can correct subcortical segmentation error? Thanks in advance

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Recon-all problem (with talairach)
by Janani Dhinakaran 01 Apr '10

01 Apr '10

Hello everyone, I wanted to know what I can do to fix this error- it occurs when I'm running recon-all -all -s Subject Tue Mar 30 11:27:20 BST 2010 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010 /home/s0964091/Desktop/Newdata/JS/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux CRIC-0012 2.6.31-20-generic #58-Ubuntu SMP Fri Mar 12 04:38:19 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Mar 30 11:27:20 BST 2010 Thank you for your help Jan -- I am the Sun, I know no darkness.

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Temporal Poles Not Well Segmented
by Stephanie Biglarian 01 Apr '10

01 Apr '10

We're using Freesurfer version 4.5.0_64bit to delineate and calculate cortical thickness. The images we are working with are poor quality and when we run the Freesurfer program, we have problems with the segmentation of prefrontal and temporal areas. We read through previous posts on the mailing list and found that we should apply control points to normalize the white matter on about 20 subjects and possibly use these to apply bias field correction on the remainder. However, it seems that after multiple times of applying control points (about 25 control points per subject) and running the recon-all command, the problem is not corrected. The segmentation does not extend to the farthest part of the temporal poles. The command we are using is: recon-all -autorecon-all -autorecon2-cp -autorecon3 -subjid (subj) -sd (directory) -no-isrunning Are there any better ways of going about this? I have attached screenshots of one of the subjects in two different views.

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Re: [Freesurfer] Volume masks
by Walimuni, Indika S 01 Apr '10

01 Apr '10

Hi Bruce Sure, Its 170x256x256 axial Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX. ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Thursday, April 01, 2010 1:45 PM To: Walimuni, Indika S Subject: RE: [Freesurfer] Volume masks Hi Indika, can you post these to the list so others can answer? What is the "native" space you are using? Bruce On Thu, 1 Apr 2010, Walimuni, Indika S wrote: > Hi Bruce > Thanks for the reply. I used wmparc.mgz file for all the cortical and sub-cortical WM/GM masks. This was the command, mri_binarize --i wmparc.mgz --match "index from LUT" --o outputfile. This effect becomes even more significant after I register the mask to like DTI/FA. But I don't think it is a FreeSufer issue. I think I may have judged based on that. The masks seems fine in the FreeSurfer space and the masks are OK. But when I convert them to our native space using "mri_convert" I see a broadening around the edges. I just want to test if there is another way and see the difference. Am I using the wrong file? If I am to use aparc+aseg.mgz file can I use it for all cortical, subcortical, WM and GM masks? > Truly, > Indika Walimuni > Research Associate > University of Texas Health Science Center > Houston, TX. > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, April 01, 2010 11:38 AM > To: Walimuni, Indika S > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume masks > > Hi Indika, > > you should be able to do this using the aparc+aseg.mgz volume and > mri_binarize. What command line did you use and can you give us an example > of the "spilling"? > > cheers, > Bruce > > > On Thu, 1 Apr 2010, > Walimuni, Indika S wrote: > >> Hi FreeSurfer List >> Is their any way that I can generate cortical > and sub-cortical volume masks by using the surfaces generated by > FreeSurfer. If I can could anyone give me the proper command. Apparently, > The masks I already generated using mri_binarize command, are little bigger > and spilling into the surrounding. >> Thank you in advance, >> Truly, >> Indika Walimuni >> Research Associate >> University of Texas Health Science Center >> Houston, TX. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

2 3

Recon All Failure during Fix topology lh step
by Dave Brohawn 01 Apr '10

01 Apr '10

Hello, I ran into a recon-all error during fix topology lh step, and I'm not sure what to do. The command I ran is: recon-all -autorecon-all -s 20011 -no-isrunning -notal-check Here is the error message: CORRECTING DEFECT 64 (vertices=70874, convex hull=10348) Excessive topologic defect encountered: could not allocate 273534355 edges for retessellation Cannot allocate memory Linux seymour 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:20:55 EDT 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Apr 1 03:08:47 EDT 2010 Here is my info. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/MTH_Study/ PWD: /space/seymour/1/users/MTH_Study ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/MTH_Study/ cd /space/seymour/1/users/MTH_Study --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Can someone help? Thanks, Dave Brohawn

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ncendef: ncid 3: Invalid argument_ Error outputting volume
by Estep, Meredith 01 Apr '10

01 Apr '10

Greetings, When I run recon-all, it appears that the conversion is OK, but I get this message: ncendef: ncid 3: Invalid argument Error outputting volume: possibly disk full? $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=1900.00, TE=2.27, TI=900.00, flip angle=9.00 i_ras = (-1, -1.30385e-08, -5.96046e-08) j_ras = (-4.47035e-08, 2.79397e-09, -1) k_ras = (2.27243e-07, 1, -1.39698e-09) writing to ./tmp.mri_nu_correct.mni.12976/nu0.mnc... ERROR: mincWrite: output_volume exited with 1 ERROR: failure writing ./tmp.mri_nu_correct.mni.12976/nu0.mnc ERROR: converting to minc The disk I am writing to is not full and has plenty of space for writing. Is this a problem with the version I am using? Best, Meredith

2 1

Volume masks
by Walimuni, Indika S 01 Apr '10

01 Apr '10

Hi FreeSurfer List Is their any way that I can generate cortical and sub-cortical volume masks by using the surfaces generated by FreeSurfer. If I can could anyone give me the proper command. Apparently, The masks I already generated using mri_binarize command, are little bigger and spilling into the surrounding. Thank you in advance, Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX.

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