Hello again, I did, in fact, encounter another error that resulted in only the first mri/orig/001.mgz and not the mr/orig/002.mgz file to be written. Below is the command line and terminal output:
======= recon-all -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 -s 1039 Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039 \n mri_convert /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz \n mri_convert.bin /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001... Starting DICOMRead2() dcmfile = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 dcmdir = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE Ref Series No = 5 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: -1.2 0 0 Vs: -1 0 0 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = ROW (dicom read) Loading pixel data TR=9.23, TE=3.72, TI=450.00, flip angle=13.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz... if: Expression Syntax. ======= I did a quick search of the mail archives involving Mac and dyld variables, and it seems like this may be something that you may provide a fix for? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> On Nov 29, 2016, at 3:36 PM, Z K <zkauf...@nmr.mgh.harvard.edu<mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: Hello Douglas, Any chance you can upload the two data files 005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 and 4355-0006-00001: https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeEkINY_hAxr--w&e= Ide like to try and reproduce this. Thanks. -Zeke On 11/29/2016 04:20 PM, Douglas Merkitch wrote: Hello Doug, Command line & terminal output: recon-all -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 -s 1039 ERROR: cannot find /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca I do have the following similarly-named files in the v6 beta average directory: RB_all_2008-03-26.mni152.2mm.lta RB_all_2016-05-10.vc700.gca RB_all_withskull_2016-05-10.vc700.gca Thanks for the prompt response! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> <mailto:douglas_merki...@rush.edu> On Nov 29, 2016, at 3:12 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: can you send your command line and full terminal output? On 11/29/2016 04:10 PM, Douglas Merkitch wrote: Hello experts, I was attempting to test out the freesurfer v6 beta and encountered the following error during dicom conversion: "ERROR: cannot find /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca". I'm currently running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5. Any help would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 <tel:%28312%29%20563-3853> Fax: (312) 563-4660 <tel:%28312%29%20563-4660> Email: douglas_merki...@rush.edu<mailto:douglas_merki...@rush.edu> <mailto:douglas_merki...@rush.edu> <mailto:douglas_merki...@rush.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=waImhwQq0O8LHAlIun2v95CPShQ-yUCVzQzvOhsqD9s&e= -- Douglas N. 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