Sorry for incremental updates: c) you can pass the -flirt-motioncor flag to recon all to revert to the old way (using flirt)
If your scans are decent quality I would recommend b) as it is unclear if averaging actually helps. -Martin On Tue, 2011-11-08 at 13:45 -0500, Martin Reuter wrote: > Hi Jennifer > > for question 2. You run out of memory. How many within session inputs > are you trying to motion correct? > > You can > a) try downsample your hi-res images before processing > b) try to only select a single input to recon-all instead of averaging > inputs. > > Best, Martin > > > On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote: > > Hello, > > > > > > I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 > > with no issues. I recently installed FreeSurfer 5.1 to a separate > > directory on the same laptop to analyze a new dataset and I am now > > having various issues with both FreeSurfer versions. > > > > > > > > > > 1. For Version 4.5, I path the freesurfer directories as follows > > (identical to before installing new program): > > > > > > setenv FREESURFER_HOME /Applications/freesurfer > > setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > > > > > > > > > --------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii > > SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir > > MNI_DIR /Applications/freesurfer/mni > > > > > > The issue is that now various commands are no longer found in version > > 4.5. > > For example when typing tkmedit, tksurfer or qdec, I get the following > > type of error: > > > > > > tkmedit.bin: Command not found. > > > > > > > > > > Is it possible that, although I installed version 5.1 in a separate > > directory, that some files were deleted or moved in version 4.5? Is my > > 4.5 license no longer valid now that I have installed version 5.1 with > > a new license? It is confusing since some commands appear to function, > > such as mri_convert and recon-all, but anything involving a GUI seems > > not to function. > > > > > > > > > > 2. For version 5.1, I believe the program is successfully installed > > and pathed. I have been able to use it to convert files to mgz, > > tkmedit and tksurfer work fine, however, I get the same error each > > time I run recon-all with each participant (one of which was > > previously successfully processed using version 4.5). The recon-all > > error occurs early during motion correction of the 2 structural runs: > > > > > > Resolution: 0 S( 512 512 352 ) T( 512 512 352 ) > > Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** > > mmap(size=1048576) failed (error code=12)*** error: can't allocate > > region > > *** set a breakpoint in malloc_error_break to debug > > MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th > > slice > > > > > > Cannot allocate memory > > Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel > > Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; > > root:xnu-1228.15.4~1/RELEASE_I386 i386 > > > > > > recon-all -s SS002 exited with ERRORS at Fri Nov 4 10:04:46 EDT 2011 > > > > > > Any ideas on what might be causing this error? I have 4 GB memory. > > > > > > thanks, > > Jennifer Addicks > > University of Ottawa > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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 > > _______________________________________________ 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.
