Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

fast-selxavg3 error: input to SVD must not contain NaN or Inf
by zhang mingxia 25 Dec '15

25 Dec '15

Dear experts, I run selxavg3-sess for retinotopy analysis and get the error below: Input to SVD must not contain NaN or Inf Error in cond (line 39) s = svd(A) Error in fast_selxavg3(line 254) XCond = cond(XtX) I am also sending the log file and Xtmp.mat. Hope to get the help. Thank you very much in advance. Mingxia Zhang

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Re: [Freesurfer] recon all erro
by Hassan bakhshi 24 Dec '15

24 Dec '15

Hi emad, I think if you change format type of images to nifti it will work as allright. I had a problem like this and it worked for me... On Dec 24, 2015 8:30 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Recon-all error (Emad Ahmadi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Dec 2015 09:50:52 -0500 > From: Emad Ahmadi <emad(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Recon-all error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <B3495F09-E1E9-4057-B839-C407B2182364(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi, > > I ran recon-all on the dicoms of a subject, obtained at Bay 4, and I > received the following error: > > mris_calc -o lh.area.mid lh.area add lh.area.pial > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > Trace/BPT trap > Wed Dec 23 21:59:54 EST 2015 > ERROR: vertexvol > mris_calc -o lh.area.mid lh.area add lh.area.pial > Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri Nov 13 > 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64 > > recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54 EST 2015 > > For more details, see the log file > /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > I have attached the log file. I?d truly appreciate your help. > > Thank you, and with best wishes for a wonderful holiday season for > everyone, > Emad > > > Emad Ahmadi, MD > ----------------------------------------------- > Research Fellow in Radiology > Massachusetts General Hospital > Harvard Medical School > > 25 New Chardon Street, Suite 400 > Boston, MA 02114 > Tel: 617 726 5237 > Email: emad(a)nmr.mgh.harvard.edu > >

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 23 Dec '15

23 Dec '15

Dear colleagues, We are recently using the freesurfer recon-all command recon-all -s XXXX -I XXXX.nii.gz recon-all -s XXXX -all where XXXX stands for the subject ID. I have been trying to execute this command with the different input files: 1) original dicom-files 2) nii-file where the field of view was cut, apart from that the same file as in 3) 3) nii.gz-file, was computed by mri_convert with the files from 1) We guessed results should be the same, but unfortunately, the segmentation looks slightly different in all three cases. Maybe you can help us by trying to find out why the output files are different? Thanks very much in advance! Best regards, Susanne ______________________________________ Susanne Schell, Dipl.-Psych. Sektion Störungen der Persönlichkeitsentwicklung Klinik für Kinder- und Jugendpsychiatrie Universitätsklinikum Heidelberg Tel: (+49) - (0)6221-56 35135 e-mail: susanne.schell(a)med.uni-heidelberg.de<mailto:susanne.schell@med.uni-heidelberg.de>

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recon-all error
by abdulkawi alareefi alareefi 22 Dec '15

22 Dec '15

Hi Freesurfers, I am currently learning how to use freesurfer to process the brain image and I acknowledge your great job. I contacting you regarding that I got an error after using recon-all command. By the way i am sill beginner in both linux and freesurer. Here is the log of the error abdol@abdol-pc:~$ recon-all -s mine -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/abdol/Desktop/freesurfer/subjects Actual FREESURFER_HOME /home/abdol/Desktop/freesurfer -rw-rw-r-- 1 abdol abdol 100038 12月 22 10:59 /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log Linux abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor 2015年 12月 23日星期三 11:01:18 CST ERROR: no run data found in /home/abdol/Desktop/freesurfer/subjects/mine/mri. Make sure to have a volume called 001.mgz in /home/abdol/Desktop/freesurfer/subjects/mine/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mine exited with ERRORS at 2015年 12月 23日星期三 11:01:18 CST For more details, see the log file /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Regards Abdulqawi Alarefi

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Re: [Freesurfer] Recon-all: Pial surface error in cingulate region
by Jaiashre Sridhar 22 Dec '15

22 Dec '15

Dr. Fischl, Since it is a longitudinal study, we have to stick to using 5.1 version. Thanks, Jaiashre.

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Re: [Freesurfer] Recon-all: Pial surface error in cingulate region
by Jaiashre Sridhar 22 Dec '15

22 Dec '15

Dr. Fischl, I am using FS version 5.1.0 Thanks, Jaiashre.

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Re: [Freesurfer] lGI value is aberrantly high
by Marco Bucci 22 Dec '15

22 Dec '15

Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution suggested by Marie Schaer to rereconstruct The images with "randomness" Recon-all -autorecon2-wm -randomness -autorecon3 I tried this fix on two of my subjects With errors. Not all subject resulted Errors in the computation of the gyrification. Can you help me? Marco Bucci Turku Pet Center Sent from my iPhone

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Recon-all: Pial surface error in cingulate region
by Jaiashre Sridhar 22 Dec '15

22 Dec '15

Hello, I am trying to manually edit and fix an error that is occurring in the longitudinal time point of a subject. The error is on the right cingulate region where the pial surface cuts through the white boundary for many slices (in coronal). It is to be noted that the error occurs neither in the cross-sectional time point nor in the base template. I tried using control points and white mater voxel (intensity: 255) to fix this error but it did not work. Is there a specific way to fix this type of error? I have attached an image of this brain with the area of the error highlighted in a blue circle. Thanks, Jaiashre.

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Virtual machine (in virtual box) generating error: Can't locate MNI/Startup.pm in @INC
by Luis Fernado Silva Castro de Araújo 22 Dec '15

22 Dec '15

Hello freesurfers, I installed freesurfer in a linux machine without problems, but when I am trying to install it on a Windows computer within a virtualmachine I keep getting the same error. I’ve tried the instructions in the tutorial and also tried to set an entirely new virtual machine with the same steps I did in my linux set up, to no avail. When I run: recon-all -s SUBJECT -all -i FILE.img I get: INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Dec 22 18:00:14 EST 2015 /tmp/000002_1_4/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s 000002_1_4 exited with ERRORS at Tue Dec 22 18:00:18 EST 2015 For more details, see the log file /tmp/000002_1_4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The log file is too long to put in the body of the e-mail, so here is the pastebin for recon-all.log <http://pastebin.com/3FxHTz3J>. Looking at it, it seems that the problem happens after mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz So I cd’ed into the mri directory and run it, which gave me the error: /media/sf_Desktop/Patients/A.o/000003_1_4/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux Tue Dec 22 17:52:00 EST 2015 Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. tmpdir is ./tmp.mri_nu_correct.mni.2621 /media/sf_Desktop/Patients/A.o/000003_1_4/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2621/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (-1.86265e-09, -1.16415e-10, -1) k_ras = (-7.45233e-09, 1, -5.82338e-11) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2621/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Dec 22 17:52:03 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.2621/nu0.mnc ./tmp.mri_nu_correct.mni.2621/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2621/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. ERROR: file ./tmp.mri_nu_correct.mni.2621/nu1.mnc does not exist! It seems that it fails finding some pearl scripts. I tried installing pearl on the VM, also with any success. Any pointers here would be really appreciated? What you think is happening in this installation? Best, Luis

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Mind Research Network - Postdoctoral Fellow
by Josef Ling 22 Dec '15

22 Dec '15

*Mind Research Network* *Postdoctoral Fellow – Job # 2015.180.M* *Summary* A post-doctoral research position is currently available in Dr. Andrew Mayer’s laboratory at The Mind Research Network, Albuquerque, New Mexico location in the area of cognitive neuroscience. The candidate will work on several NIH-funded projects that use multimodal neuroimaging to study traumatic brain injury and psychosis spectrum disorders. Particular areas of focus include cognitive neuroscience studies of multisensory cognitive control, advanced modeling for diffusion MRI and mechanistic explorations of vascular integrity through multimodal imaging (i.e., task-related BOLD, pCASL, cerebral vascular reactivity and resting state data). *Requirements* A Ph.D. in neuroscience, psychology, computer science or a related field is required. The ideal candidate should possess a strong interest in working in both clinical and pre-clinical research settings, a strong publication record and experience in brain imaging (functional magnetic resonance imaging (fMRI), diffusion MRI, structural MRI, etc). Applicant must also have strong programming skills in Linux and one or more other languages (R, MATLAB, python, etc.). The position is for two years, with a third year extension possible. To apply, visit www.mrn.org and refer to Job # in the “Jobs” section of the website. Or contact Dr. Mayer directly at amayer(a)mrn.org. *The Mind Research Network is an independent non-profit organization dedicated to advancing the diagnosis and treatment of mental illness and brain injury.* *Headquartered in Albuquerque, New Mexico, MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation.* *With an extended community of academicians, researchers, graduate students and technicians, the MRN is uniquely positioned with its national infrastructure to link the brightest minds in neuroscience with some of the most cutting-edge neuroimaging capabilities in the world today* *Equal Opportunity Employer* The Lovelace Respiratory Research Institute Family of Companies is an Equal Opportunity employer–M/F/Veteran/Disability. We are committed to the hiring, advancement and fair treatment of all individuals, and all qualified applicants will receive consideration for employment without regarding to race, color, religion, sex, national origin, sexual orientation, gender identity, age, disability, protected veteran status, or any other protected status as designated by federal, state or local law. For additional information about your rights as an applicant, click here <http://www.eeoc.gov/employers/upload/eeoc_self_print_poster.pdf>. For assistance with our application process, including reasonable accommodations for individuals with disabilities to participate in the application process, please send an email to recruiting(a)lrri.org or call 505-348-9400.

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