Hello,<br><div><br></div><div>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.</div>

<div><br></div><div><br></div><div>1. For Version 4.5, I path the freesurfer directories as follows (identical to before installing new program):</div><div><br></div><div>setenv FREESURFER_HOME /Applications/freesurfer</div>
<div>setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir</div>
<div>source $FREESURFER_HOME/SetUpFreeSurfer.csh</div><div><br></div><div><br></div><div>--------- freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 --------</div><div>Setting up environment for FreeSurfer/FS-FAST (and FSL)</div>

<div>FREESURFER_HOME     /Applications/freesurfer</div><div>FSFAST_HOME              /Applications/freesurfer/fsfast</div><div>FSF_OUTPUT_FORMAT  nii</div><div>SUBJECTS_DIR              /MRIData/Root/freesurfer/TRDsubjects_dir</div>

<div>MNI_DIR                         /Applications/freesurfer/mni</div><div><br></div><div>The issue is that now various commands are no longer found in version 4.5.</div><div>For example when typing tkmedit, tksurfer or qdec, I get the following type of error:</div>

<div><br></div><div>tkmedit.bin: Command not found.</div><div><br></div><div><br></div><div>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 Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license?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.</div>

<div><br></div><div><br></div><div>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:</div>

<div><br></div><div>Resolution: 0  S( 512 512 352 )  T( 512 512 352 )</div><div> Iteration(f): 1 (subsample 200) mri_robust_template(3271) malloc: *** mmap(size=1048576) failed (error code=12)*** error: can&#39;t allocate region</div>

<div><div>*** set a breakpoint in malloc_error_break to debug</div><div>MRIalloc(512, 512, 352): could not allocate 1048576 bytes for 258th slice</div><div><br></div><div>Cannot allocate memory</div><div>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</div>

<div><br></div><div>recon-all -s SS002 exited with ERRORS at Fri Nov  4 10:04:46 EDT 2011</div></div><div><br></div><div>Any ideas on what might be causing this error? I have 4 GB memory.</div><div><br></div><div>thanks,</div>
<div>Jennifer Addicks</div><div>University of Ottawa</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div>