Freesurfer March 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
79 discussions

smoothing error...?
by Cameron Ellis 08 Mar '07

08 Mar '07

Hi, After sphreical resampling I attempted to smooth the spherical surface which seemed to work fine but when I try to perform a group average using the smoothed surface I receive this error: troy:cameo[99] isxavg-re-sess -group Controlssh+smvsnh -sf sessidcontrolsshvsnh -df sesspar -a retrievalSPMHRF_sphere -c sh+smvsnh -space sphsmooth Log file is /autofs/space/troy_003/users/retrievalnewest/log/isxavg-re-sess-retrievalSPMHRF_sphere-sh+smvsnh.log Thu Mar 8 14:17:54 EST 2007 --------------------------------------------------- /autofs/space/troy_003/users/retrievalnewest isxavg-re -i /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C2/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C3/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C4/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C5/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C6/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C7/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C8/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C10/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C11/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C12/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C13/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C14/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C15/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C16/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C17/bold/retrievalSPMHRF_sphere/sphsmooth/h -i /autofs/space/troy_003/users/retrievalnewest/SM0C18/bold/retrievalSPMHRF_sphere/sphsmooth/h -cmtx retrievalSPMHRF_sphere/sh+smvsnh.mat -avg Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/avg -std Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/std -sig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/sig -t Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/t -minsig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/minsig -iminsig Controlssh+smvsnh/bold/retrievalSPMHRF_sphere/sphsmooth-rfx/sh+smvsnh/iminsig --------------------------------------------------- cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory@: Expression Syntax. ERROR: nslices of /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_sphere/sphsmooth/h ERROR: troy:cameo[100] I noticed that the smoothed spherical surface volume contains 1 more slice than the original resampled spherical volume, 7 instead of 6 in the h-lh-offset.bhdr file. Can someone explain to me why this would be, if this is related to this error, and offer a suggestion for correcting this? Thanks for anyone's assistance in advance! (working in stable environment) Cameron

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omnibus contrast / paint-sess
by Sheeva Azma 08 Mar '07

08 Mar '07

Hello, I am trying to create and view an omnibus contrast for one subject. When I type the appropriate command: paint-sess -analysis SNgamma -contrast omnibus -space sph -spacedir sphsm20 -d . -s sub28a -subject sub28_recon I get the following error: ----------------------------------------------------------------- paint-sess logfile is /autofs/space/perun_004/users/sheeva/fMRIanal/log/paint-sess.log ----------------------------------------------------------------- setenv SUBJECTS_DIR /space/perun/3/users/cylix/Subjects INFO: painting onto white grep: /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/session.info: No such file or directory SpaceDir is sphsm20 SpaceSubDir is sphsm20 INFO: setting srcsubject to ico ------ lh hemisphere ------ Thu Mar 8 13:12:00 EST 2007 SpaceDir is sphsm20 INFO: Painting onto sub28_recon ERROR: cannot find any files with /autofs/space/perun_004/users/sheeva/fMRIanal/sub28a/bold_SN/SNgamma/sphsm20/omnibus/sig-lh It seems that stxgrinder-sess created fsig, f, iminsig, and minsig files, but did not create t or sig files. This only occurred for the omnibus -- it didn't happen with the other contrasts. I don't know if I should be doing something differently for the omnibus as compared to the other contrasts -- any insight would be greatly appreciated. Thank you! Sheeva Azma FREESURFER_HOME: /usr/local/freesurfer/stable Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070308 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: perun SUBJECTS_DIR: /space/perun/3/users/cylix/Subjects PWD: /autofs/space/perun_004/users/sheeva/fMRIanal

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longitudinal analysis error
by Chacko Cherian 07 Mar '07

07 Mar '07

Hello all, I got an error while running longitudinal analysis using recon-all -long and the process exited with errors. THis is the error message: mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007 Could someone give me suggestions on what could have gone wrong..thanks in advance. Regards Chacko. ____________________________________________________________________________________ We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list. http://tv.yahoo.com/collections/265

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missing cerebellum
by Derin Cobia 07 Mar '07

07 Mar '07

I noticed that one of our subjects made it through the processing stream (successfully) with the cerebellum missing, thus creating a bad aseg.mgz. I filled it back in, and was wondering if I needed to reprocess it completely under autorecon2 and 3 again, or just run -aseg and whatever else it needed. Thanks. -Derin

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aseg2feat
by oxro03＠yahoo.com 07 Mar '07

07 Mar '07

Hi Doug & others, It seems that aseg2feat takes lower level .feat directories to get stats on annotations. It does not seem to work for higher level g.feat directories. Is there a way around it? cheers, Sandy --------------------------------- Don't be flakey. Get Yahoo! Mail for Mobile and always stay connected to friends.

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remote access
by Leila BH 07 Mar '07

07 Mar '07

Hello, I tried to do remote access from my windows xp computer to the linux one, I follows the steps described in the freesurfer web pages. The remote access seems work correctly, but when I try to run freesurfer (tksurfer) it does not work, this is the error: Someone can help me?? I already installed vncviewer, the vncserver.glx and xf4vnc. Thanks in advance Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /root surfer: all rgb files written to /root surfer: Reading header info from /usr/local/freesurfer/subjects/chuv44/mri/T1.mgz surfer: vertices=155533, faces=311062 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl: this isn't a Tk applicationunknown color name "Black" surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OriginalVSetLoaded 1: can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_InflatedVSetLoaded 0: can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_WhiteVSetLoaded 0: can't read "glEnableGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0: can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 0: can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0: can't read "glEnableGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0: can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0: can't read "glEnableGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0: can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0: can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable surfer: Error sending tcl command UpdateLinkedVarGroup all: invalid command name "UpdateLinkedVarGroup" % Received X error! Error code : 164 Request code : 151 Minor code : 2 Error text : 'GLXBadLargeRequest' Received X error! Error code : 164 Request code : 151 Minor code : 2 Error text : 'GLXBadLargeRequest'

2 1

Nifti
by Marek Kosinski 07 Mar '07

07 Mar '07

Hi, I am using MRIConvert tool of lcni.uoregon.edu to convert Simens ima files to FSL Nifti format. After converting the files every time when I want to do anything with freesurfer I get the following error message: niiRead(): unsupported timing pattern in Test.nii.gz and, when use mri_convert of freesurfer to convert siemens ima files to any format I get the following error can't open file TEST.1.1.ima (low = 1, this = 1, high = 1) actually the first file in the folder is TEST.1.001.ima.. I think mri_convert has a problem with zeros at the end of the file name. It just ignores them. Is there a way to get rid of this problems? Thanks a lot Cheers ___________________________________________________________ Telefonate ohne weitere Kosten vom PC zum PC: http://messenger.yahoo.de

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missing library
by Furlong, Carolyn 06 Mar '07

06 Mar '07

Hi I'm new to freesurfer, I have downloaded version v3.0.4 and I have tried to run the fully automated command line recon-all and have received an error message stating: ## mri-watershed error while loading shared libraries libstdc++s0.6 cannot open shared subject file: no such file or directory ## orig.mgz and T1.mgz appear to be fine but I have not produced brainmask.mgz, the skull strip doesn't seem to be working at all. Should I install a missing library? if so how? Thanks Carolyn

2 1

Reference volumes
by Martin Kavec 04 Mar '07

04 Mar '07

Hi, I am wondering, whether there has been any publication, or any other resource, with reference volumes of ALL the segmented subcortical structures for different age categories. I tried to search the mailinglist archives, but no success. Thanks, Martin -- ********************************** Senior Research Associate in Neuroradiology MRI Unit of the Department of Radiology Erasme Hospital Lennik Street 808 B-1070 Brussels BELGIUM tel: +32-2-555-4325 fax: +32-3-555-3994 email: kavec(a)messi.uku.fi ********************************** ----------------------------------------------- Find a way, or make one!

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Runtime for -subcortseg
by Martin Kavec 04 Mar '07

04 Mar '07

Hi, anybody knows, how long does it take to run one subcortical segmentation on a MacPro? It take about 6 hours on my MacBook Pro, so I would expect it should finish faster on the workstation. Could anybody suggest me a hardware configuration, on which it could be about 4 hours? Last question, is/can be/will be the freesurfer's code parallelized? Thanks in advance, Martin -- ********************************** Senior Research Associate in Neuroradiology MRI Unit of the Department of Radiology Erasme Hospital Lennik Street 808 B-1070 Brussels BELGIUM tel: +32-2-555-4325 fax: +32-3-555-3994 email: kavec(a)messi.uku.fi ********************************** ----------------------------------------------- Find a way, or make one!

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Freesurfer March 2007