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.
- 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 Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license?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.
- 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
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