Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Automaticky: Jan Sanda is out of the office (příchod 09.11.2015)
by Jan.Sanda＠fnmotol.cz 09 Oct '15

09 Oct '15

Jsem mimo kancelář do 09.11.2015. Poznámka: Toto je automatická odpověď na vaši zprávu "[Freesurfer] PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback" odeslanou dne 10.10.2015 0:58:09. Toto je jediné oznámení, které obdržíte v době nepřítomnosti této osoby.

1 0

PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback
by Frank Scharnowski 09 Oct '15

09 Oct '15

PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback Postdoctoral and PhD positions are available at the University of Zürich, Switzerland. The successful candidate will join a team of real-time fMRI enthusiasts who develop new methods for neurofeedback, and apply them to psychiatric populations (addiction, depression, PTSD). The research agenda involves methods development as well as clinical applications, so anyone with a background in neuroscience, biology, psychology, medicine, computer science, physics, engineering, or related areas is welcome to apply. Previous experience with fMRI is essential. The posts are available immediately, for 3-5 years. Starting salary for postdocs is ~95’000 CHF, and that for PhD students is ~50’000 CHF per year (~6’600/~3’700 CHF net per month, respectively). Zürich offers a thriving international environment, with extensive cultural and outdoor activities and a very high quality of life. Interested applicants should send their CV, a brief statement of research interests, and contact information for 2-3 references. Please feel free to contact me with any questions. Best wishes, Frank -- Prof. Dr. Frank Scharnowski Psychiatric University Hospital Zürich, Switzerland www.neurofeedback-research.org Scharnowski.Frank(a)gmail.com

1 0

mris__label__calc intersect error in longitudinal qcache
by Selvaraj, Bhavani 09 Oct '15

09 Oct '15

Hi, when I try running longitudinal analysis for 2 subjects I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? I saw a similar question in the archived mail list so I tried running this command by itself and this was the comment Segmentation fault I didn't know how to fix this error? should I run them again?? Qdec table Fsid fsid-base years MPS-007_1 MPS-007 3 MPS-007_2mod MPS-007 4 MPS-007_3 MPS-007 4 MPS-005_1 MPS-005 5 MPS-005_2 MPS-005 6 MPS-005_3 MPS-005 6 Thanks, Bhavani

1 0

FAST without preprocessing
by stdp82＠virgilio.it 09 Oct '15

09 Oct '15

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -nostc the analysis is stopped by an error on lacking fmcpr.nii. Thanks Best regards, Stefano

1 0

How to transfer data from Windows 7 to Virtual Box?
by Negar Memarian 09 Oct '15

09 Oct '15

Hi, I'm using Freesurfer5.3 using virtual box on Windows 7, and need to be able to access/transfer my DICOM data from my windows hard drive to the freesurfer/subjects folder in the virtual box. There is unfortunately no help documentation on the quick install webpage for accessing shared drives from host on the guest (virtual box). I've tried "Insert Guest Additions CD image" from the "Devices" tab in virtual box, but the executable files in that folder (e.g., VBoxWindowsAdditions.exe) do not run. I'd appreciate any help. -Negar

2 3

White matter Error
by Thục Trinh 09 Oct '15

09 Oct '15

NCP140539_2_recon.rar <https://drive.google.com/file/d/0B1_Gk_rrHt9jZXZEdTRSc3JoSzg/view?usp=drive…> Hi Freesurfer Experts, We are on the process of troubleshooting our subjects's recon and we came across with this error that we can not determine what kind of problem this is: It seems there is no white matter and pial errors on all slices as we check on three different views (sagital,coronal and axial);however, when we load rh.inflated.nofix surface on both freeview and tksurfer, there is a big difference that at the frontal cortex (area near the medial wall), it appears a handle error and also some hole errors on freeview while it does not on tksurfer. Would you explain how it is visualized that makes us so confused to troubleshoot since we can not find anything wrong on white matter volume to be fixed? Here is our data, Have a nice day, Trinh

2 5

A potential problem in qdec
by chenhf_uestc 09 Oct '15

09 Oct '15

Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but there was an error (acctached error.png) that puzzled me for a long time. I and my colleague help me to check all the files but do not find where is the error. However, if I remove the files gender.levels, group.levels and fsid.levels (I means that I just keep the qdec.table.dat), it works. I can design, display and finally obtain the results. Could anyone give me some suggestions? Any help would be greatly appreciate. Best, Feng

1 0

Error Messages for Accessing Bin
by Timothy Quang-Tin Le 09 Oct '15

09 Oct '15

Hi, I tried the chmod command, but it did not work. How I check that I've downloaded the correct version? Thank you very much Timothy On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you try chmod a+x on one of them and see if it can then be executed? > e.g.: > > chmod a+x /home/tle7/freesurfer/bin/mri_convert > /home/tle7/freesurfer/bin/mri_convert > > and see if you get an error. If not, you probably downloaded the wrong > hardware version > cheers > Bruce > > > > On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote: > > >> Hello, >> When I run the command "sFSstart" on version 5.0.0, I am receiving the >> messages below. Would you please explain to me what the problem is? It >> seems like there is trouble accessing the bin. >> Thank you >> >> -------- freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /home/tle7/freesurfer >> FSFAST_HOME /home/tle7/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii >> SUBJECTS_DIR /home/tle7/freesurfer/subjects >> MNI_DIR /home/tle7/freesurfer/mni >> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2 >> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter >> H 0 >> checking sid number 00152-DT2 >> 1 >> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm >> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 >> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 >> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects >> Actual FREESURFER_HOME /home/tle7/freesurfer >> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP >> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux >> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not >> executable. >> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not >> executable. >> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary >> file not executable. >> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file >> not executable. >> /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not >> executable. >> /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not >> executable. >> /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. >> Binary file not executable. >> /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file >> not executable. >> -cw256 option is now persistent (remove with -clean-cw256) >> /home/tle7/freesurfer/subjects/00152-DT2_v5 >> >> >> mri_convert/home/tle7/freesurfer/subjects/practicemotherdaughter/rawdata/00152-DT2/MR. >> 1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm >> /home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz >> >> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file >> not executable. >> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP >> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 00152-DT2_v5 exited with ERRORS at Mon Sep 28 10:43:57 >> PDT 2015 >> >> tle7@sni-vcs-gotlib:~$ >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > >

3 6

Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
by Julio Alberto González Torre 09 Oct '15

09 Oct '15

I had the same problem too, using VBox and running the .vdi version of FreeSurfer with no modifications. When the "recon-all" reach to the talairach phase, the program stops with this error: #-------------------------------------------- > #@# Talairach Thu Oct 8 20:16:43 EDT 2015 > /media/sf_NEURO/freesurfer_em/subject001/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 athlon i386 GNU/Linux > recon-all -s subject001 exited with ERRORS at Thu Oct 8 20:16:51 EDT 2015 > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The problem is not about mri_nu_correct (as some people say in previous answers to this question). For some reason, this error appears when you are trying to run the reconstruction on files stored on virtualbox shared folders (/media/sf_host/). I don't understand why sometimes it works perfectly, and sometimes the error appears. SOLUTION: The only solution is to copy the subjects to a local folder of the virtual enviroment (for example: the desktop, /home/fsuser/desktop), and then run the recon-all. After reconstruction, you can move the files back to the shared folder. 2015-08-04 5:54 GMT+02:00 Li, Zhihao <zhihao.li(a)bme.gatech.edu>: > Hi FS experts, > > I was trying to run "recon-all" within the VirtualBox of NeuroDebian 8.0 > on a WIN8 host. The program stopped immaturely at the step of > "mri_nu_correct.mni". I went into the folder of "mri" and ran > "mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz" with the output pasted below. Could you please > help me to fix this problem? Thank you very much! > > > ----------------------------------- > > brain:mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > --no-rescale --i orig.mgz --o orig_nu.mgz > /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/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 neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 > (2015-04-24) x86_64 GNU/Linux > Mon Aug 3 22:51:33 EDT 2015 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by nicks@minerva > (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 > tmpdir is ./tmp.mri_nu_correct.mni.31236 > /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/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=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > changing data type from uchar to float (noscale = 0)... > writing to ./tmp.mri_nu_correct.mni.31236/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Mon Aug 3 22:51:38 EDT 2015 > nu_correct -clobber ./tmp.mri_nu_correct.mni.31236/nu0.mnc > ./tmp.mri_nu_correct.mni.31236/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.31236/0/ -iterations 1000 -distance 50 > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. > (Maybe you should just omit the defined()?) > [brain@neurodebian:/media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri/] > [2015-08-03 22:51:38] running: > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.31236/0/ > ./tmp.mri_nu_correct.mni.31236/nu0.mnc > ./tmp.mri_nu_correct.mni.31236/nu1.imp > > Assertion failed at line 827 in file templates/CachedArray.cc > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=256) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=256) > ERROR: nu_correct > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > >

1 0

Group Analysis with Qdec-- Couldn't find subject 'con_chenchen' in SUBJECTS_DIR
by haidong wang 08 Oct '15

08 Oct '15

Hi FS Experts, When I use Qdec for Group Analysis,I come with an error.Here it is. -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl setenv TUTORIAL_DATA /media/work/FC_DATA/ckd-T1 setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR Data table /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat loaded. Verifying subject data.sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'con_chenchen' in SUBJECTS_DIR Input table: /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat Subj#, SubjID, Data... 1 con_chenchen con ... I load qdec.table.dat successfully.However,QdecProject couldn't find subject 'con_chenchen' in SUBJECTS_DIR. As a result,when I use FDR for correction,there is nothing showing in the terminal. I did not dowload the tutorial data.what's more,I have not put the subjs in my Freesurfer install path. How can I deal with it? Thanks for your patience and I am looking forward for your prompt reply.

1 0

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