Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

Postdoctoral Fellow Position: Migraine and TMD Neuroimaging, Neuromodulation and Genetics Research
by Alexandre Dasilva 01 Oct '18

01 Oct '18

External Email - Use Caution Postdoctoral Fellow Position: Migraine and TMD Neuroimaging, Neuromodulation and Genetics Research The Headache and Orofacial Pain Effort (H.O.P.E.) Lab at the University of Michigan School of Dentistry requests applications for a postdoctoral position to work on migraine/pain research programs funded by the National Institute of Health. The programs use novel methodologies in neuroimaging, neuromodulation, and genetics to investigate and target central mechanisms of chronic pain in vivo. Extensive knowledge of neuroimaging analysis software systems and programming experience are required. Previous research experience and publications with positron emission tomography (PET) and/or MRI-based neuroimaging methods and analyses are also needed. We are seeking applicants with advanced degrees and strong self-motivation to work in a highly creative, altruistic, and mentoring environment with students and residents from different departments across campus. The applicant will be exposed to several tech-innovations, many developed in-house, for clinical translational pain research (e.g., migraine, TMD, fibromyalgia, dental and cancer pain), such as mobile technology (GeoPain), augmented/virtual reality, artificial intelligence, multimodal neuroimaging (PET, MRI, fNIRS, EEG) and neuromodulation montages (TMS and [HD]-tDCS). Initially, a curriculum vitae, letter of intent, and contact information for three professional references should be emailed to adasilva(a)umich.edu. *The University of Michigan is an equal opportunity affirmative action employer.* Alex F. DaSilva, DDS, DMedSc Diplomate of the American Board of Orofacial Pain Associate Professor, Department of Biologic and Materials Sciences University of Michigan School of Dentistry Director, Headache & Orofacial Pain Effort (H.O.P.E.) *"Brain as the Target for Pain Research, Treatment, and Education"* http://media.dent.umich.edu/labs/hope/ The Molecular & Behavioral Neuroscience Institute (MBNI) 205 Zina Pitcher Pl, room 1021 Ann Arbor, MI 48109-5720 Office: 734 615-3807 Fax: 734 763-3453

1 0

postdoc ad (fwd)
by Bruce Fischl 01 Oct '18

01 Oct '18

please see the notice of a postdoc opportunity below Bruce https://opportunities.ucsf.edu/content/ucsf-dept-radiology-biomedical-imagi… scholar-laboratory-precision

1 0

Re: [Freesurfer] longitudinal TRACULA -prep error
by Yendiki, Anastasia 01 Oct '18

01 Oct '18

Hi Carissa – Don’t set variables to “None” in the config file. Just remove those lines from the config file altogether – that’s the same as not having any inputs for them. Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, September 27, 2018 at 4:28 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] longitudinal TRACULA -prep error External Email - Use Caution Hello, I’m running into an error in the longitudinal TRACULA pipeline that I’m not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I’d ask again. I’ve successfully run the recon-all longitudinal pipeline and am trying to run the trac-all –prep step with a longitudinal configuration file. Here’s the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=10000.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0000 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0012 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0013 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0014 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0015 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0016 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0017 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0018 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0019 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0020 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0021 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0022 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0023 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0024 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0025 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0026 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0027 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0028 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0029 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0030 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0031 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0032 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0033 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0034 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0035 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0036 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0037 mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot xfmrot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.ecclog /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_eddy.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz corRead(): can't open file /COR-.info $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /... crypt_gkey = *CyXds2s6sOqQ Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:04 CDT 2018 #------------------------------------- /sharedapps/LS/psych_imaging/freesurfer/5.3.0_9.19.18/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Thu Sep 27 13:41:05 CDT 2018 cp /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat /bigraid-03/LS/Data/istar/freesurfer/106/dmri/xfms cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat': No such file or directory Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:05 CDT 2018 Here’s the contents of my configuration file: setenv SUBJECTS_DIR /bigraid-03/LS/Data/istar/Freesurfer setsubjlist= ( 106_day2.fs 106_6mo.fs ) set baselist = ( 106 106 ) set runlist = (1 2) set dcmlist = ( /bigraid-03/LS/RawData/iSTAR/106_day2/106_day2/p*/e*/DTI_all/DTI/*.1 /bigraid-03/LS/RawData/iSTAR/106_6mo /106_6mo/p*/e*/DTI_all/DTI/*.1 ) set bvecfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt set bvalfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt set dob0 = 1 set b0mlist = None set b0plist = None set echospacing=None set doeddy =1 set dorotbvecs =1 set thrbet = 0.5 set doregflt =0 set doregbbr =1 set doregmni =1 set mnitemp= $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz set dogregcvs = 0 set cvstemp =cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat =1 set pathlist = (lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.ccg_PP rh.ccg_PP lh.cab_PP rh.cab_PP ) set ncpts = (5 5 7 5 5 5 4 4) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick =2 set nburnin =200 set nsample = 7500 set nkeep = 5 set reinit =0 Thanks so much for your help! Carissa Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>

1 0

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 01 Oct '18

01 Oct '18

External Email - Use Caution If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes. If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others. This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700 Do the raw images look like that too? From: <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>>> on behalf of Matthew Grecsek <m...(a)grecsek.com<mailto:m...@grecsek.com <m...(a)grecsek.com>>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution Yes, a part of the brain appears missing. See attached screenshot. I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks! a.y

2 6

error glm-fit-sim
by Caroline Beelen 01 Oct '18

01 Oct '18

External Email - Use Caution Dear FS, I followed the group analysis page for glm analysis and it worked fine until the final step. I'm using version 5.3. After performing glm-fit-sim it says "glm-fit done" (for all files), but when trying to open these it says: "Reading colortable from annotation file... Colortable with 1 entries read (originally none) Colortable with 1 entries read (originally none) CTABisentryvalid: index -1 was 00B Resource temporarily unavailable CTABisentryvalid: index -1 was 00B Resource temporarily unavailable Resource temporarily unavailable" (etc..) It opens, but nothing is visible and I have the feeling it cannot open color files?? MRI glmfit gives positive clusters for some values. I therefore used the abs sign for glm-fit-sim. What might be wrong? Thanks. Caroline

2 1

freeview problem on Linux RHEL 7-4 libGLU.so.1
by Avner Meoded 01 Oct '18

01 Oct '18

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in /usr/local/fsl/bin/FSLeyes/libGLU.so.1 any idea ho to solve this problem Thanks avner

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2018