Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

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. > > > >

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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

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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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negative thickness value problem
by eunkyung kim 01 Apr '10

01 Apr '10

Dear all I performed recon-all -s subjectID -qcache and obtained thickness data which was normalized to fsaverage template. I'd like to extract thickness value of the '-rh(or lh).thickness.fwhm0.fsaverage.mgh' file in each subjects, so it was transformed to the ascii file format. However, the thickness data obtained from the ascii file did have some negative values. !!! Interestingly, the thickness value that was not normalized to the fsaverage did not have negative values so I was very confused.. Please let me know how can I treat the negative value. I really THANK YOU for your reply. Sincerely, EK.

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autorecon2 error
by Ahmed, F, Me <fahmed＠sun.ac.za> 01 Apr '10

01 Apr '10

Hello, I have been successfully running the recon-all process on all my subjects and have come to a problem with my last subject. I ran autorecon1 without error but when I ran autorecon2, it exited with errors and I don't know why. I have attached the recon-all log and hope someone could give me some insight into what the problem might be. I haven't changed anything so theoretically this subject should have run smoothly as did the 44 others I did previously. Any help would be greatly appreciated. Thank you, Fatima

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Freesurfer April 2010