[Freesurfer] Job: Postdoc in Cognitive Neuroscience at UConn
University of Connecticut College of Liberal Arts and Sciences Postdoctoral Fellow in Cognitive Neuroscience The University of Connecticut’s new Brain Imaging Research Center (BIRC) invites The BIRC is a 3,200 square foot, research-dedicated imaging facility housing a research-dedicated 3T Siemens Prisma scanner and simultaneous high-density EEG/ERP, with a major focus of cognitive neuroscience research. The Postdoctoral Fellow will contribute to multiple funded NIH studies of language processing, reading, word acquisition, and cognition, under PIs Dr. Jay Rueckl and Dr. Peter Molfese. Prior experience in research using MRI/fMRI is required. Responsibilities will include the design and execution of fMRI and behavioral experiments; fMRI data analysis; formulating and participating in writing of scientific papers as part of the research team; participating in grant writing towards the eventual goal of independent funding; and developing independent projects in the areas of speech, reading, and language. Minimum Qualifications: · Ph.D. in Psychology, Cognitive Neuroscience, or Related Field · Experience with fMRI Experimental Design · Experience with MRI/fMRI Data Analysis (e.g. AFNI, FSL, SPM, Freesurfer) Preferred Qualifications: · Strong Analytical Statistical Skills (e.g. SEM, HLM, Data Mining) · Experience with EEG/ERP Data Collection and Analysis · Programming Skills (e.g. C/C++, Python, R, E-PRIME) · Experience with Computational Modeling The anticipated start date is September 1, 2015, but is negotiable. Salary will be commensurate with qualifications and experience. Interested applicants should send a cover letter describing qualifications, a CV, and any supporting materials to UConn Careers (www.jobs.uconn.edu http://www.jobs.uconn.edu/). Select “Apply Now to be redirected to Academic Jobs Online to complete your application. Names of three references should be included in the cover letter; letters will be submitted to Academic Jobs Online. Inquiries can be addressed to Peter Molfese, Chair o Screening of applications will begin immediately and continue until the position is filled. The University of Connecticut is an EEO/AA employer. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Error from mri_glmfit-sim - Input volume voxel dimensions do not match
Hello, We're running into a bit of a hiccup in trying to do an analysis of subcortical volume differences between groups using mri_glmfit instead of the tables generated by asegstats2table. The error occurs at the end of our pipeline when running mri_glmfit-sim: ERROR: Input volume voxel dimensions do not match those in the registration file.” The full processing script is currently doing these steps: 1. mri_vol2vol --mov somesubj/mri/aseg.mgz —targ $FREESURFER_HOME/average/mni305.cor.mgz —xfm somesubj/mri/transforms/talairach.xfm —o somesubj/mri/aseg-in-mni305.mgz 2. mri_concat to concatenate all participants data together and output GroupAnalysis-in-MNI305.mgz 3. mri_glmfit --y GroupAnalysis-in-MNI305.mgz --fsgd Study1.fsgd dods --C group_diff.mtx --C group-x-age.mtx --C g1g2.intercept.mtx --C g1g2.age.mtx --glmdir study1.glmdir 4. Visualization works: tkmedit fsaverage orig.mgz -aseg -overlay study1.glmdir/group_diff/sig.mgh -fminmax 0.1 5 5. Correction (mri_glmfit-sim) breaks. mri_glmfit-sim --glmdir study1.glmdir --grf 1.3 neg --cwpvalthresh .05 Full error below, any help would be appreciated! Freesurfer 5.3 running on Mac OS X 10.9.x Peter J. Molfese, Ph.D. Research Scientist Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 pmolf...@haskins.yale.edu cd /zappa/kstudy /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir study1.glmdir --grf 1.3 neg --cwpvalthresh 0.05 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Dec 17 15:37:22 EST 2014 Darwin cab.haskins.lab 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 pmolfese setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y GroupAnalysis-in-MNI305.mgz --fsgd study1.fsgd --C DATA/group_diff.mtx --C DATA/group-x-age.mtx --C DATA/g1g2.intercept.mtx --C DATA/g1g2.age.mtx --glmdir study1.glmdir DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 2.396839 mri_volcluster --in study1.glmdir/g1g2.age/sig.mgh --mask study1.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig study1.glmdir/g1g2.age/grf.th1.3.neg.sig.cluster.mgh --sum study1.glmdir/g1g2.age/grf.th1.3.neg.sig.cluster.summary --ocn study1.glmdir/g1g2.age/grf.th1.3.neg.sig.ocn.mgh --cwpvalthresh 0.05 --seg fsaverage aparc+aseg.mgz --fwhmdat study1.glmdir/fwhm.dat --sign neg --thmin 1.3 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: study1.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 795592 Found 795592 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file.___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Mac OS X 10.8.5 breaks recon-all
I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted running the process with both my own data that works on Freesurfer 5.3 with 10.8.4 and receive the same error message. I have two identical computers, with only one updated to 10.8.5, which will make further testing straightforward. I attached the log below of the attempt to run the bert data with just one MRI. The error message is the same for other data. bugr output: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 12.5.0 x86_64 - Please include the following additional information in your report: 1) subject name - bert (and any other subject) 2) the entire command-line executed - recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T 3) the error message generated - see below 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting === BEGIN ERROR REPORT === recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz... # #@# MotionCor Tue Sep 17 12:49:59 EDT 2013 Found 1 runs /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Tue Sep 17 12:50:13 EDT 2013 /Volumes/MRIData/srtt/freesurfer/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Tue Sep 17 12:50:20 EDT 2013 For more details, see the log file /Volumes/MRIData/srtt/freesurfer/bert/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all
The DYLD message does not appear on the 10.8.4 system. Both systems have homebrew (http://brew.sh) installed for handling linux dependencies, but that message only appears on the 10.8.5 system. Disabling homebrew does not resolve the error for me. Best, Peter On Sep 17, 2013, at 2:40 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello, Do you know if the following line: dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid from the log file you you've attached, also exists when you run the same case on the machine running 10.8.4? I will update my Mac tonight to the most recent version of OSX and attempt to duplicate the issue. I will keep you updated. -Zeke On 09/17/2013 12:57 PM, Peter J. Molfese wrote: I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted running the process with both my own data that works on Freesurfer 5.3 with 10.8.4 and receive the same error message. I have two identical computers, with only one updated to 10.8.5, which will make further testing straightforward. I attached the log below of the attempt to run the bert data with just one MRI. The error message is the same for other data. bugr output: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 12.5.0 x86_64 - Please include the following additional information in your report: 1) subject name - bert (and any other subject) 2) the entire command-line executed - recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T 3) the error message generated - see below 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting === BEGIN ERROR REPORT === recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz... # #@# MotionCor Tue Sep 17 12:49:59 EDT 2013 Found 1 runs /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Tue Sep 17 12:50:13 EDT 2013 /Volumes/MRIData/srtt/freesurfer/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
Re: [Freesurfer] Mac OS X 10.8.5 breaks recon-all
I have dependencies for AFNI and the fBIRN QC tools. The dependencies get installed to /usr/local and I can disable the path extension to those binaries. -Peter On Sep 17, 2013, at 3:01 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Ok. Thanks for the info. But what dependancies were required to be installed (using homebrew)? Other than installing XQuartz, freesurfer should run on a clean system. -Zeke On 09/17/2013 02:53 PM, Peter J. Molfese wrote: The DYLD message does not appear on the 10.8.4 system. Both systems have homebrew (http://brew.sh) installed for handling linux dependencies, but that message only appears on the 10.8.5 system. Disabling homebrew does not resolve the error for me. Best, Peter On Sep 17, 2013, at 2:40 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello, Do you know if the following line: dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid from the log file you you've attached, also exists when you run the same case on the machine running 10.8.4? I will update my Mac tonight to the most recent version of OSX and attempt to duplicate the issue. I will keep you updated. -Zeke On 09/17/2013 12:57 PM, Peter J. Molfese wrote: I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted running the process with both my own data that works on Freesurfer 5.3 with 10.8.4 and receive the same error message. I have two identical computers, with only one updated to 10.8.5, which will make further testing straightforward. I attached the log below of the attempt to run the bert data with just one MRI. The error message is the same for other data. bugr output: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 12.5.0 x86_64 - Please include the following additional information in your report: 1) subject name - bert (and any other subject) 2) the entire command-line executed - recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T 3) the error message generated - see below 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting === BEGIN ERROR REPORT === recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz... # #@# MotionCor Tue Sep 17 12:49:59 EDT 2013 Found 1 runs /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /Volumes
[Freesurfer] Job: Postdoc in Cognitive Neuroscience at Haskins Laboratories
Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The selected candidate will contribute to multiple funded NIH studies of speech perception, reading, word acquisition, and language processing. Prior experience in research using MRI/fMRI is required. Responsibilities will include assistance with design and execution of fMRI and behavioral experiments; fMRI data analysis; formulating and participating in writing of scientific papers as part of the research team; participating in grant writing towards the eventual goal of independent funding; and developing independent projects in the areas of speech, reading, and language. Position requirements include: - Experience with MRI/fMRI data acquisition and analysis - Strong analytical and statistical skills - Strong computer and data management skills Additional desirable qualifications include: - Experience with MRI/fMRI data analysis using AFNI and/or FreeSurfer - Experience with EEG/ERP analysis - Experience with modeling, broadly construed - Programming skills, e.g., Python, R, Matlab The successful applicant will join Haskins Laboratories (www.haskins.yale.edu), a private, non-profit research institute located in downtown New Haven, CT. Founded in 1935, our primary focus is on speech, language, reading, and their biological bases. Haskins Laboratories has long-standing, formal affiliations with the University of Connecticut and Yale University. We are also actively engaged in research collaborations and partnerships with institutions, groups, and individuals around the world. We house facilities for conducting eye tracking, including 3 Eyelink 1000 eye-trackers, EEG/ERP (both Biosemi and EGI systems), ultrasound and NIRS technology, and a mock fMRI scanner, which replicates the 3T scanner used for fMRI research at Yale University. Interested applicants should direct application materials to Dr. W. Einar Mencl, Director of Neuroimaging Research (ei...@haskins.yale.edu) including cover letter, statement of research interests, CV, and three letters of recommendation. Please reference Job Posting #5001. This position is initially for a one-year duration, with potential of an additional 1-2 years contingent on performance and continued funding. Applications should be submitted by 15 May 2013; the application process will continue until the position is filled. International applicants are welcome. Haskins Laboratories is an Equal Opportunity Employer. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Recent paper on FreeSurfer reliability
We run things on an Xgrid cluster that is now a mixture of Macs running Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from asegstats2table and aparcstats2table are identical after running 100 subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also ran a few subjects on the cluster and on individual computers (not on the cluster so to speak) and the results are identical. Best, Peter Hi, The paper entitled “The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements”, PLoSONE, Vol 7(6), e38234 (2012) may be of interest to all of you. It can be found at: http://dx.plos.org/10.1371/journal.pone.0038234 Cheers, Ed ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] mri_cvs_register error on Mac
All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but no solution. I'm running the most recent version from version 5.1 with the patch on the release notes page ($Id: mri_cvs_register,v 1.15.2.9 2011/05/26 14:03:26 lzollei Exp $). Running the process on a Mac Pro running 10.6.7 with 40GB of RAM (10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64). I've tried the process on several different Macs. Previous emails thought it was because the Mac wasn't running a 64-bit version of freesurfer, but there don't appear to be 64-bit binaries available for Mac yet. Any help would be appreciated. Peter surf2vol(98451) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 29571! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: surf2vol on a darwin9.8 named duke.haskins.lab by pete Mon Dec 5 13:21:35 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: surf2vol on a darwin9.8 named duke.haskins.lab by pete Mon Dec 5 13:21:35 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries
Sorry for the delay in responding, I wanted to try every permutation that I could think of. I updated the tracula binaries for snow leopard (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html) and that gives me some of the same, and some different issues that may help. First, if the bvec file is in the correct format (3 columns), then it copies the file correctly and trac-all continues smoothly. If the file is in the 3 row format (needing to be transposed), then tracula will only copy the first 9 numbers out of it giving the error of not having the correct number of bvecs to bvals. So that seems fixable, I just need to reorient all of our bval and bvec files into the correct format. I'm still a bit unsure why tracula won't create the bvec and bval files during the mri_convert stage. I have been using dcm2nii to create these two files but then continue to give tracula the path to the dicom files. So the orientation of this file could be related to how dcm2nii writes the files. Any suggestions would be very welcome. As it stands, my current workflow is: 1. use dcm2nii to create bvec and bval files 2. reorient bvec and bval files to be 3 column and 1 column format respectively. 3. run trac-all -prep with a config file showing where the dicom images are and hand specifying the bvec and bval files Peter Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yale.edu CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intende d recipient, please contact the sender immediately by reply e-mail and destroy all copies of the original message. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects
A script is definitely the easiest way to process quite a few subjects. You
can save some headache by using a recon-all command with an input for your
image files. For example: recon-all -s sleep_001 -i sleep_001.nii -all will
create a subject folder in the correct location named sleep_001 and begin the
entire freesurfer pipeline taking the NIFTI image sleep_001.nii as the input.
You can modify it to just import the files by dropping the -all.
I've included a bash script below for simplifying this. This script takes the
NIFTI files you want to process as arguments and then automatically sets the
Subject ID and begins processing. Once it completes a single subject, it will
start the next subject. You can track the progress of subjects by seeing which
folders have been created in the SUBJECTS_DIR. If you have a multiprocessor
system, you can run the script with different subjects in multiple terminal
windows.
To execute the script:
1. Save the script as fs_subject.sh
2. chmod +x fs_subject.sh
3. place the script in a folder with all of your NIFTI files (not required but
may make your life easier)
4. execute the script with ./fs_subject.sh sleep_001.nii sleep_002.nii
sleep_003.nii (don't forget to replace sleep_* with your NIFTI file names)
4a. If your subjects meet a standard naming convention you could do something
like: ./fs_subject.sh sleep_*.nii (this would submit all subjects fitting the
pattern of having sleep_ at the beginning of the name.
#!/bin/bash
# ./fs_subject.sh
# takes nifti files as arguments for submitting into freesurfer pipeline
#setup Freesurfer if not currently loaded on path
export FREESURFER_HOME=/usr/local/freesurfer
#source $FREESURFER_HOME/SetUpFreeSurfer.sh
. $FREESURFER_HOME/SetUpFreeSurfer.sh
for FS in $*
do
subjectID=$(/bin/echo $FS | /usr/bin/sed 's/.nii//')
recon-all -s $subjectID -i $FS -all
done
Hope this helps! Ultimately if you have a lot of computers and a lot of
subjects, using Sun Grid Engine (SGE) or Apple's xgrid (if you have Macs) can
really expedite the processing of subjects.
Best,
Peter
Date: Fri, 15 Jul 2011 12:22:38 -0500
From: Freesurfer Local Archive freesur...@jonca.org
Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there
are too many subjects
To: ??? wgh0...@126.com
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Message-ID:
cabphhh-zcmapcqq+0x66d0exqqgdt-vpvojxt30o0p63kzo...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
I suspect that your subject directory/file names will match some
pattern. You can use combination of a loop and shell ls command to
cycle through all the subjects matching provided pattern. For example
if you have data in directories you would do something line this:
#!/bin/tcsh
cd /path/to/native/files
for x in `ls -dA1 name_pattern_*`;
do
mkdir -p $SUBJECTS_DIR/${x}/mri/orig
$FREESURFER_HOME/bin/mri_convert ${x}.nii.gz
$SUBJECTS_DIR/${x}/mri/orig/001.mgz
done
If all files are in the same directory substitute '-dA1' for -A1 and
it should work. Note this assumes that you have nifti files, for DICOM
you will need to modify it further.
Cheers,
Jacek
2011/7/15 ??? wgh0...@126.com:
??Hi Bruce,
?In our research,if there are?100 subjects,how?can I ?process these data
easily.For example?when I want to compare their thickness's difference?at
first?I should do
mri_convert? bert.nii bert.nii.gz,but when there are too many subjects,is
there a way to do all of these 100 subjects at the same time?
?Many thanks,
?Wang
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HelpLine at
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Re: [Freesurfer] error during mri_cvs_register
Is there a reason that the Mac binaries are not available in 64-bit versions? On Jun 21, 2011, at 3:11 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Date: Tue, 21 Jun 2011 21:11:54 +0200 From: Martin Kavec martin.ka...@gmail.com Subject: Re: [Freesurfer] error during mri_cvs_register To: David Brang dbr...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu, rspr...@nmr.mgh.harvard.edu Message-ID: BANLkTi=4zcqwpzuam0olpmzgw6mo5fk...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi David, FreeSurfer's binaries for MAC are still 32-bit and apparently cvs tries to allocate more that is possible. The lines of the error code below suggest that. I had the same problem and had to opt for x86_64 linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and takes ~ 2 days to finish. Regards, Martin surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly On Mon, Jun 20, 2011 at 11:34 PM, David Brang dbr...@gmail.com wrote: Thanks for the advice Priti, I deleted the old cvs files and re-ran but still no luck. I also tried a new subject on a different Mac (still 10.6.7) and received the same error. Thanks David On Mon, Jun 20, 2011 at 12:56 PM, rspr...@nmr.mgh.harvard.edu wrote: Hi David, I usually get PETSC errors when I have files from a previous unsuccessful runs of cvs and mri_cvs_register is trying to overwrite the same set of files. I've always found that deleting all the cvs related files before starting mri_cvs_register from scratch usually solves the issue. You can try doing that to see if it works for you. Thanks, Priti Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David -LOG-- ?step = 12 === elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: ?7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: ?0.000686 Removing unwanted tetrahedra. Hole seconds: ?3.3e-05 Repairing mesh. Repair seconds: ?6.9e-05 Adding Steiner points to enforce quality. Quality seconds: ?4.27942 Smoothing mesh. Smooth seconds: ?0.299788 Writing nodes. Writing elements. Writing faces. Output seconds: ?0.036639 Total running seconds: ?4.61682 Statistics: ? Input points: 8 ? Input facets: 6 ? Input holes: 0 ? Input regions: 0 ? Mesh points: 81870 ? Mesh tetrahedra: 491585 ? Mesh faces: 995562 ? Mesh subfaces: 24784 ? Mesh subsegments: 530 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face ?mesh nodes = 81870 mesh elts = 491585 ?building index src ?done building the list ? ? ?count inserted = 0 elapsed = 0 seconds ?element count = 1 ? ? ?count inserted = 10 elapsed = 0.302 seconds ?element count = 1128168 ? ? ?count inserted = 20 elapsed = 0.496 seconds ?element count = 3256402 ? ? ?count inserted = 30 elapsed = 0.411 seconds ?element count = 5222879 ? ? ?count inserted = 40 elapsed = 0.343 seconds ?element count = 7039018 ?done building octree - total elements = 8705605 ?penalty_weight = 1000 setting bc 205.891 174.948 225.515 - 0 0 0 ? ? ?instead 205.881 174.938 225.505 - norm = 0.0173205 setting bc 205.891 174.948 27.6148 - 0 0 0 ? ? ?instead 205.881 174.938 27.6248 - norm = 0.0173205 setting bc 205.891 35.1985 225.515 - 0 0 0 ? ? ?instead 205.881 35.2085 225.505 - norm = 0.0173205 setting bc 205.891 35.1985 27.6148 - 0 0 0 ? ? ?instead 205.881 35.2085 27.6248 - norm = 0.0173205 setting bc 52.3002 174.948 225.515 - 0 0 0 ? ? ?instead 52.3102 174.938 225.505 - norm = 0.0173205 setting bc 52.3002 174.948 27.6148 - 0 0 0 ? ? ?instead 52.3102 174.938 27.6248 - norm = 0.0173205 setting bc 52.3002 35.1985 225.515 - 0 0 0 ? ? ?instead 52.3102 35.2085 225.505 - norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 - 0 0 0 ? ? ?instead 52.3102 35.2085 27.6248 - norm = 0.0173205 ?computing statistics for the displacement application error ?average norm of error in placement = 0.0173205 ?iterating ?done with candidates ?Active BCs = 92200 ?Total BCs = 548640 ?no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message
Re: [Freesurfer] mri_cvs_register update
Is this significant enough that we should re-run data processed using the standard recon-all stream in version 5.1? Thanks, Peter On Jun 10, 2011, at 3:28 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 2 Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT) From: Lilla Zollei lzol...@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cvs_register update To: freesurfer@nmr.mgh.harvard.edu Message-ID: pine.lnx.4.62.1106101257120.4...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi, We found a bug in the mri_cvs_register script after the release. Please, download the new version of applyMorph and mri_cvs_register from one of the below links for Linux Centos4, Linux Centos4 x86 64 and Mac Leopard respectively: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel --Lilla ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] DTI Paramters
Hello, We're gearing up for a new study and planning to collect DTI data along with both functional and anatomical data. Is there a particular protocol that Freesurfer (and Tracula) will work best with? I found the suggested sequences for anatomical reconstruction, but didn't see any for DTI specifically. Also, any idea when version 5.1 will be out of beta? Thanks, Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yale.edu ___ Freesurfer mailing list Freesurfer@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.
