Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere
by Adam Mezher 08 Nov '13

08 Nov '13

Absolutely, sorry about that, the group is now cc'd. the ls -l says: -rw-rw-r-- 1 vhasfcwui cind 0 Nov 6 15:57 lh.sphere so it has 0 size to it, and I can't open it in tksurfer -bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere Using Freesurfer version 5.1. subject is PPMI_290_S_3829m12_i395612 hemi is lh surface is sphere surfer: current subjects dir: /cind/00/PPMI/Freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /cind/07/PPMI/Freesurfer/subjects checking for nofix files in 'sphere' Reading image info (/cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612) Reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz surfer: Reading header info from /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz ERROR: reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/surf/lh.sphere Read 0 bytes, expected 1 Perhaps I should first try deleting the file and rerun as you recommended? Thanks, Adam On Fri, Nov 8, 2013 at 2:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Adam > > can you cc the list on your replies so that others can answer? What does > ls -l say about the sphere? Can you open it in tksurfer? Maybe the > partition filled at some point when it was being written but things opened > up later? You might just deleted the lh.sphere file and run > > recon-all -make all -s <subject> > > cheers > > Bruce > > > On Fri, 8 Nov 2013, Adam Mezher wrote: > > Hi Bruce, >> >> Yes I checked and the partition is not full, there should be ample space >> available. >> Do you have any other ideas? I've never come across this error before. >> >> Thanks, >> -Adam >> >> >> Filesystem Size Used Avail Use% Mounted on >> cosf:/cind/07 2.3T 2.0T 167G 93% /cind/07 >> >> On Fri, Nov 8, 2013 at 2:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Adam >> >> can you check to make sure that the partition isn't full? >> >> Bruce >> On Fri, 8 Nov 2013, Adam Mezher wrote: >> >> Hi FreeSurfer experts, >> >> I am repeatedly running into an autorecon3 error (see below). >> Any ideas how to fix >> this? It appears that the software is having an issue reading >> /surf/lh.sphere and >> immediately exits afterward. >> >> Thank you, >> Adam >> >> >> >> Adam Mezher >> >> Staff Research Associate II >> >> Center for Imaging of Neurodegenerative Diseases >> >> San Francisco VA Medical Center >> >> 4150 Clement St. (114M) >> >> San Francisco, CA 94121 >> >> Tel: 415-221-4810 Ext. 4629 >> >> Fax: 415-668-2864 >> >> >> >> >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from ../surf/lh.sphere... >> mris_register: could not read surface file ../surf/lh.sphere >> ERROR: reading ../surf/lh.sphere >> Read 0 bytes, expected 1 >> Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 >> 15:50:53 EDT 2010 x86_64 x86_64 >> x86_64 GNU/Linux >> >> recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at >> Wed Nov 6 15:57:07 PST >> 2013 >> >> >> >> >> 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. >> >> >> >>

4 3

-autorecon 3 error: error reading surf/lh.sphere
by Adam Mezher 08 Nov '13

08 Nov '13

Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... mris_register: could not read surface file ../surf/lh.sphere ERROR: reading ../surf/lh.sphere Read 0 bytes, expected 1 Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at Wed Nov 6 15:57:07 PST 2013

2 1

sulci depth in table
by Tara Ann Miskovich 08 Nov '13

08 Nov '13

Hello, I am extracting sulci depth using the following mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc Do you know how I could put this into aparcstats2table? Thank you, Tara

2 3

glm_fit --prune
by celine＠nmr.mgh.harvard.edu 08 Nov '13

08 Nov '13

Hi, When using glm_fit with an input volume that has many voxels with a 0 value (due to a previous thresholding for quality reasons), and the voxel removes might be distributed randomly across our population, is there a way not to take into account those voxels in the glm_fit model? I saw the --pune flag, but I am not sure if it is the one to use. Thanks Celine

2 1

saving in GIFTI .func.gii format
by SHAHIN NASR 08 Nov '13

08 Nov '13

Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

algorithm developer position open
by Gennan Chen 07 Nov '13

07 Nov '13

Hi! All, We have an algorithm developer position open at Synarc. If you are interested, please send me your resume. Position Description: The algorithm developer engineer works with our scientific groups to come up innovative image processing and data mining/pattern recognition algorithms to maintain scientific lead in all TA areas Responsibilities: Work with Scientists and TA lead on surveying literature /algorithms and existing commercial implementation for specific tasks. Prototype and validating algorithms on large dataset by using in house cluster or Amazon EC2. Prototype related UI elements and addressing integration on Synarc internal proprietary platform. Work with Scientists and TA lead on journal/conference publications and intellectual properties related document. Qualifications: Education: PhD in biomedical engineering, physics, applied math or computer science Experience: Must be expert in ITK and Matlab Familiar with HPC like condor or SGE is a must have Experience with EC2 will be a plus Experience with VTK or QT will be a plus. Experience with Python/Java/SQL will be a plus Skills: Good written and verbal communication skills. Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Gennan Chen Engineering Manager, Synarc ________________________________ This email message 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 intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

1 0

Is there anyway to define multiple processing cores for FreeSurfer to speed up its commands?
by Emad Ahmadi 07 Nov '13

07 Nov '13

Hello, I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle. I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox). Thank you, Emad Emad Ahmadi, MD ------------------------------------------------ Research Fellow Department of 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

2 1

Segmentation question
by Rashmi Singh 07 Nov '13

07 Nov '13

FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi

2 3

Re: [Freesurfer] Segmentation question
by Louis Nicholas Vinke 07 Nov '13

07 Nov '13

Hi Rashmi, Several of the morphometry stats were changed between 5.1 and 5.3. I don't remember the specifics, but Doug or someone else on the list may know. Alternatively, you could use the mri_segstats from 5.3 to calculate the morphometry stats for your 5.1 data. -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: > I am using version V5.1.0 is it different for that or the information is > the same irrespective of the version I use. > Rashmi > > On 11/7/13 1:57 PM, "Louis Nicholas Vinke" <vinke(a)nmr.mgh.harvard.edu> > wrote: > >> Hi Rashmi, >> This page has the definition you are looking for (FS v5.3). >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >> >> -Louis >> >> On Thu, 7 Nov 2013, Rashmi Singh wrote: >> >>> FreeSurfer experts, >>> May you please educate me how the supra tentorial volume (STV) >>> measured by >>> FreeSurfer and which date does it take as input file to calculate this >>> variable. >>> Thanks, >>> Rashmi >>> >>> >> >> >> 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. > > > >

1 0

fMRI-data mri_convert, missing header
by Philipp Heimbeck 07 Nov '13

07 Nov '13

Hello! I'm encountering a problem with converting fMRI-Data from dicom- to NIfTI-files (single file). The problem only occurs with data aquired on Siemens Vision, data from Siemens Trio work just fine. The "Siemens ASCII header" is missing (files have not been anonymized) and every dicom-file has its own series number. This is true for all functional data (10 subjects, one run each). Other programs can't convert these dicom-files either (dcm2nii, NIfTI-1 converter for BVQX). Do you know if there is a possible solution for this problem? In more detail, when running mri_convert, the following happens: ... Getting Series No Scanning Directory INFO: Found 218 files in ../run INFO: Scanning for Series Number 67 INFO: found 1 files in series INFO: loading series header info. INFO: sorting. RunNo = 66 WARNING: file ../MR.9500.260 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (512 512 1), nframes = 1, ismosaic=0 PE Dir COL COL FileName ../MR.9500.260 Identification NumarisVer VB33D ScannerModel MAGNETOM VISION PatientName deleted, shows correctly Date and time StudyDate deleted, shows correctly StudyTime 150948.046000 SeriesTime 153015.877000 AcqTime 153606.293000 Acquisition parameters PulseSeq ep_fid Protocol unknown PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 60 InversionTime -1 RepetitionTime 60 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 66 SeriesNo 67 ImageNo 260 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 96.0000 80.1658 98.1990 VolRes 0.3750 0.3750 3.0000 VolDim 512 512 1 Vc -1.0000 0.0000 -0.0000 Vr -0.0000 -0.9848 -0.1736 Vs -nan -nan -nan VolCenter -nan -nan -nan TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=60.00, TE=60.00, TI=-1.00, flip angle=90.00 i_ras = (-1, 0, -0) j_ras = (-0, -0.984808, -0.173648) k_ras = (-nan, -nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -0.375 -0.000 -nan -nan; 0.000 -0.369 -nan -nan; -0.000 -0.065 -nan -nan; 0.000 0.000 0.000 1.000; If there's any help, I'm glad to hear it. And if the answer is "no, the data is gone forever", this would be a helpful response, too. Philipp

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