Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

exporting surfaces
by abel cruz vadell 09 Mar '07

09 Mar '07

Hi everyone When FreeSurfer construct the surface from the volume, does it maintain it original orientation or FreeSurfer makes internally any reorientation when normalizes the volume with Talairach? My goal is export the inflated surfaces to fusion them with another information outside the FreeSurfer and I need to know wich will be the orientation of the resulted surfaces and if I can change that orientation. Could I export both hemispheres in only one file and not splitted in two files (rigth and left)? Thanks Abel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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reorient MRI volume
by abel cruz vadell 08 Mar '07

08 Mar '07

Hi everyone I have MPRAGE MRI volume acquired sagitaly and I need to convert it to axial. Could I do this task with any tool of FreeSurfer? Could I export back the result in analyze format? Thanks in advance Abel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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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

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