[Freesurfer] segfault
Dear Sir/Madam, I am a new user of freesurfer and had the following error when I tried in tkmedit tool to make a snapshot of the volume. Please find below the contents of the file .xdebug_tkmedit Best Regards, Ruthger Righart ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... tkmedit started: Tue Sep 21 14:22:11 2010 tkmedit.bin 1001 1001-M36-T1.mgz $Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5 $ Set user home dir to /Network/Servers/isd06363.isd.med.uni-muenchen.de/Shared Items/homefolder/rrighart Set subject home dir to /Volumes/ext_rrighart/CADASILData/1001 Using interface file /Applications/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Segfault Verifying volume xDebug stack (length: 4) 03: Volm_SaveToSnapshot( this=0x38c6600 ) 03: Verifying volume 02: SnapshotVolume () 02: Saving snapshot 01: main() 01: Entering main loop 00: 00: ___ Freesurfer mailing list Freesurfer@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] PPC or Intel
Will FreeSurfer work with a PPC processor? Thanks, Colin ___ Freesurfer mailing list Freesurfer@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] RAM question
I realize that FreeSurfer requires at least 4 GB RAM, and I'm in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] RAM question
It should just run slowly doug O'Shea, Colin (NIH/NIMH) [V] wrote: I realize that FreeSurfer requires at least 4 GB RAM, and I’m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] RAM question
Wow. I think you are in a dangerous direction. FreeSurfer will work in PPC only in older MacOSX version. The 4GB will not help you so much. I would suggest a new computer. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Tue, Sep 21, 2010 at 10:29, O'Shea, Colin (NIH/NIMH) [V] colin.o'sh...@nih.gov colin.o%27sh...@nih.gov wrote: I realize that FreeSurfer requires at least 4 GB RAM, and I’m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@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@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.
Re: [Freesurfer] RAM question
Hi Colin how much RAM do you have now? If there's not enough it will probably just fail. cheers Bruce On Tue, 21 Sep 2010, O'Shea, Colin (NIH/NIMH) [V] wrote: I realize that FreeSurfer requires at least 4 GB RAM, and I'm in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] RAM question
to clarify: we are pretty sure it will either fail or run slowly, or both :) Bruce On Tue, 21 Sep 2010, Douglas N Greve wrote: It should just run slowly doug O'Shea, Colin (NIH/NIMH) [V] wrote: I realize that FreeSurfer requires at least 4 GB RAM, and I?m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mri_label2label problem?
what does the original label look like? Can you convert one of the predefined labels (eg, lh.V1.label) to see if the same thing happens? doug Pye, Brandon (NIH/NIMH) [F] wrote: Hey guys, We are using mri_label2label to convert a label created from a cluster (using mri_surfcluster) from an average subject to each individual subject. We have 6 individual labels that we are converting. All of the analysis is done using surface data. I use the command in the generalized form listed below: Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh 5 of the 6 labels transfer well, but a 6th label translated to the correct anatomical location, but the number of labeled vertices is greatly reduced after the translation. This problem persists across all subjects. There doesn't appear to be much interior to the label, just a lot of the outline of the label (i.e. If the outline of the label is yellow and the interior is blue, I see a lot of yellow and not much blue, as if there are a bunch of small islands). The region on them most inferior part of the lateral surface approximately where the temporal and occipital lobes meet. Any ideas what might be going on? Thanks, - Brandon Pye Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 402-3893 Fax: (301) 402-0921 brandon@nih.gov ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] PPC or Intel
yes. use either the tiger or leopard powerpc download, available here: http://surfer.nmr.mgh.harvard.edu/fswiki/Download n. On Tue, 2010-09-21 at 09:29 -0400, O'Shea, Colin (NIH/NIMH) [V] wrote: Will FreeSurfer work with a PPC processor? Thanks, Colin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] RAM question
the visualization tools will work with just 1GB (or less) ram. its the recon-all stream that consumes a lot of memory. 2GB might work on when processing some subjects, but 4GB is best. it will fail midway through the processing stream if there is not enough memory (during mri_ca_register). n. On Tue, 2010-09-21 at 09:29 -0400, O'Shea, Colin (NIH/NIMH) [V] wrote: I realize that FreeSurfer requires at least 4 GB RAM, and I’m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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] isxconcat question
I got the following error when running isxconcat-sess: ERROR: cannot find /space/grouch/3/users/ext/fsaverage/mri.2mm/subcort.mask.mgz I've never seen this before, but this is my first time using isxconcat in fsfast v. 5. Anyone know how to fix it? ___ Freesurfer mailing list Freesurfer@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] changing f.nii nframes
Dear Free Surfers, I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316. I could not find a tool that could change the nframes value (mri_convert can adjust many other things but not this one it seems). Any suggestions? Bests, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
