Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

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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variable TR
by shahin＠nmr.mgh.harvard.edu 22 Dec '15

22 Dec '15

Hi Surfers We are wondering if we can use freesurfer to analyze ECG-gated fmri. As far as I see, mkanalysis-sess expects a fix TR. Since we are in the design stage, any hint or suggestion to facilitate future data analysis will be highly appreciated. Regards

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Re: [Freesurfer] Help importing files from a previous SPM analysis
by Luis Fernado Silva Castro de Araújo 21 Dec '15

21 Dec '15

Dear Douglas, It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command. If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right? Does the command recon-all also gives me volumes for specific Brodmann's areas? Or do I have to run a labeling to that? Thank you, luis

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Error in QDEC -"Generate Stats Data Tables"
by nellie 21 Dec '15

21 Dec '15

Hi Freesurfer experts,When I tried to use "Generate Stats Data Tables" in QDEC, some errors came out. The related screenshot is attached in this letter, and I found there wasn't any folder named "pubsw" in the "usr". I wonder how to fix these errors? Thanks a lot. Best, Amolie

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qdec
by levi solomyak 21 Dec '15

21 Dec '15

Dear experts, I've been attempting to generate a stats data table in qdec, but each time I get a "Index Error: list index is out of range" error. This is occurring when it is trying to parse the .stats file. I've made sure that the files all line up exactly with the qdec table and that SUBJECTS_DIR is properly sourced so I'm not sure how to fix this problem. Any help would be greatly appreciated! Here are the details of the errors: 1) machine being used: Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 2) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP 3) Current working directory: /projects/IndivRITL/data/leviDiff/Subjects 4) which qdec : /usr/local/freesurfer/bin/qdec 5) After loading the gui, I attempted to generate a qdec stats table. This is the error that was returned: ----------------------------------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 SUBJECTS_DIR : /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 538, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/home/usr/local/freesurfer/bin/fsutils.py", line 115, in parse self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name IndexError: list index out of range ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x278d8060): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 while executing "vtkTemp2 GenerateStatsDataTables" ------------------------------------------------------------------------------------------------------- Thanks, LS -- Levi Solomyak Cole Neuroscience Laboratory (*colelab.org <http://colelab.org/>*) Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers-Newark University

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segmentation fault (core dumped)
by Fengji Geng 21 Dec '15

21 Dec '15

Hi Bruce, I have uploaded all the data to the server. The command that I run is 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. It would be great if you could keep us updated on how the fixing is going. Thanks! --------------------------------------------------------------------------------------------------------------------------------------- Message: 1 Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: segmentation fault (core dumped) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1512211037340.22599(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Fengji hmmm, I don't remember ever seeing a core dump in mri-segstats before. If you upload the entire subject dir (tarred and gzipped) to our ftp site we will fix it. cheers Bruce ----- Fengji

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Qdec visualization
by John Anderson 21 Dec '15

21 Dec '15

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Freesurfer December 2015