Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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

2 1

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

2 1

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.

2 1

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

2 1

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!

2 3

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!

2 1

preproc inorm question
by Cameron Ellis 02 Mar '07

02 Mar '07

Hi all, If I were to perform a surface-based analysis, resampling to spherical space, and I did not want to smooth in the volume, would I need to preprocess my data again without smoothing or could I just specify the motion corrected volume in in a new analysis. I think the answer is: I could just specify the motion corrected volume, however, since the global mean for intensity normalization is calculated at the end of preprocessing after smoothing and exists in the fmcsm.meanval file, will there be a problem with the inorm in later stages, will it be performed etc. if I just specify the fmc volume in a new analysis? Thanks, Cameron

2 3

tksurfer window too small
by Joongnam Yang 02 Mar '07

02 Mar '07

Hi all, When I displayed a flattened image of the entire cortex (lh.full.patch.flat) on the tksurfer window, the image was too big for the tksurfer window, meaning the falttened image is chopped out. Is there any way that I can display the entire flattened image on the tksurfer window? Thanks. Nam.

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