Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

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

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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

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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

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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. > >

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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. > >

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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.

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mri_convert error
by Park, Jung Mi 08 Oct '15

08 Oct '15

Hello When I tried to run mri_convert brain.mgz to get brain.nii to get betted brain. nii, I received an error message following next: mri_convert -it mgz -i brain.mgz -ot nii -o brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from brain.mgz... TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00 i_ras = (-1, 7.45058e-08, -7.72998e-08) j_ras = (7.35745e-08, 4.30737e-09, -1) k_ras = (1.49012e-08, 1, 1.80444e-09) writing to brain.nii.gz... niiWrite(): error opening file brain.nii.gz ERROR: failure writing brain.nii.gz as volume type 24 What is the problem to convert brain.mgz into brain.nii? How can I fix the error? Thank you. Jung Mi

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Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
by Aarthi Padmanabhan 08 Oct '15

08 Oct '15

Hi Eugenio the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/ Should I reinstall freesurfer? thanks! ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.iglesias(a)bcbl.eu> Sent: Tuesday, September 29, 2015 10:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation This is really weird. Can you please confirm that the file /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib exists? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- Sent: Tuesday, September 29, 2015 11:39:00 AM Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi Eugenio, Thanks for the response. I just tried that and it still didn't work (same error message). Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 Current Stamp: freesurfer-Darwin-OSX-dev-20150826 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lab wheel 638418 Sep 29 08:37 /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 90075 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 90112 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Thanks, Aarthi ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.iglesias(a)bcbl.eu> Sent: Monday, September 21, 2015 1:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi Aarthi, first of all, sorry for the late reply; you caught me on vacation. Would you mind trying the following: please unset your DYLD_LIBRARY_PATH environment variable, and the run the hippocampal subfield module. You can do that as follows: In bash: unset DYLD_LIBRARY_PATH In (t)csh: unsetenv DYLD_LIBRARY_PATH Let us know if this helps Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Aarthi Padmanabhan" <aarthi(a)stanford.edu> To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Saturday, September 19, 2015 9:32:55 AM Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation Hi, I had posted this earlier and am still having issues. Thank you, I tried running the Hippocampal Segmentation using the Dev version, I get the following error (running on a mac os x Yosemite): I just downloaded the dev version a couple of days ago. Recon-all -all runs fine, but it's unable to run the hippocampals segmentation component. recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1 Subject Stamp: freesurfer-Darwin-OSX-dev-20150826 Current Stamp: freesurfer-Darwin-OSX-dev-20150826 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56 /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Fri Sep 11 11:57:14 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 6182 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Fri Sep 11 11:57:15 PDT 2015 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right \n See log file: /Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib dyld: Library not loaded: @rpath/libmwi18n.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 6219 Trace/BPT trap: 5 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #------------------------------------------ Started at Fri Sep 11 11:57:12 PDT 2015 Ended at Fri Sep 11 11:57:15 PDT 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s 15-03-07.1_3T2 finished without error at Fri Sep 11 11:57:15 PDT 2015 done Thank you, Aarthi _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?
by Matthieu Vanhoutte 08 Oct '15

08 Oct '15

Hello Martin, Could you please find any time to answer me ? Many thanks ! Best regards, Matthieu Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" <matthieuvanhoutte(a)gmail.com> a écrit : > Hi Martin, > > Thank you for helping ! > > 1) What should I use for the parameter estimation: "mass univariate" or Novel > mass-univariate tools (spatiotemporal models)" ? > > 2) I have one group of subjects with different timepoints (non equally > spaced and different numbers of timepoints), and would like to see the > significant change of FA according to time. Will LME study allow me to get > this change and how to define contrast to assess it ? Are the results of > this longitudinal study directionals, i.e. is it possible to establish an > increase or decrease of FA in significant regions according to time ? > > 3) Should the covariates (age, gender...) be demeaned or centered ? > > 4) Has the accurate time variable to be in years absolutely or could it > be also in days ? > > > Best regards, > > Matthieu > > > 2015-09-29 17:11 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: > >> Hi Matthieu, >> >> use lme_mass_fit_vw and the y is a simple vector. I would mask the image >> before doing this and only pass the brain voxels (to increase speed and >> reduce comparisons). >> >> Best, Martin >> >> >> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote: >> >> Hi Martin, >> >> I understand for the multiple comparisons problem. But if I consider a >> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for >> estimation), how could I consider a correction for multiple comparisons in >> this univariate case ? >> >> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass >> univariate case ? If yes, how do I have to format my 3D FA volume as input >> of the LME toolbox ? >> >> Best regards, >> >> Matthieu >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> 2015-09-29 16:34 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >> >>> Hi Matthieu, >>> >>> yes, multiple comparisons are a problem for any mass univariate >>> approach. You can use the FDR2 correction (in the lme matlab tools) which >>> is less conservative than standard FDR. You can also work in specific ROI's >>> and average there, to reduce the number of comparisons. >>> >>> Best, Martin >>> >>> >>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote: >>> >>> Hi Martin, >>> >>> Thank you for your answer. >>> >>> However, I would like to consider FA maps as a mass-univariate problem >>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my >>> voxels aren't independant, are they ? So, how to correct for multiple >>> comparisons then ? >>> >>> Best regards, >>> >>> Matthieu >>> >>> 2015-09-29 15:04 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Matthieu, >>>> >>>> if all your images are perfectly registered, you can do LME on a >>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other >>>> ROI measure. >>>> >>>> Best, Martin >>>> >>>> >>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote: >>>> >>>> Dear experts, >>>> >>>> I would like to know if it is possible to make a longitudinal study >>>> with LME toolbox from volume FA maps registered in a common space ? >>>> >>>> I don't have T1 images so the recon-all process couldn't be processed. >>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels >>>> format, could it be in good way for LME ? >>>> >>>> Thanks for helping ! >>>> >>>> Best regards, >>>> >>>> Matthieu >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -- >>>> Martin Reuter, PhD >>>> Assistant Professor of Radiology, Harvard Medical School >>>> Assistant Professor of Neurology, Harvard Medical School >>>> A.A.Martinos Center for Biomedical Imaging >>>> Massachusetts General Hospital >>>> Research Affiliate, CSAIL, MIT >>>> Phone: +1-617-724-5652 >>>> Web : http://reuter.mit.edu >>>> >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Martin Reuter, PhD >>> Assistant Professor of Radiology, Harvard Medical School >>> Assistant Professor of Neurology, Harvard Medical School >>> A.A.Martinos Center for Biomedical Imaging >>> Massachusetts General Hospital >>> Research Affiliate, CSAIL, MIT >>> Phone: +1-617-724-5652 >>> Web : http://reuter.mit.edu >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> 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. >> >> >

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longitudinal stream: adding a time point
by Adam, Ruth 08 Oct '15

08 Oct '15

Dear all, We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points) and instead register the third time point to the pre-existing template. What is the best way to do so? Is there a way to force recon-all to use a specific template? Many thanks! Best, ruthi

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Freesurfer October 2015