Hello Bruce & Doug, There are no spaces in the filenames (just a lot of underscores and dashes!).
I don't think it's a permissions issue because it is able to write the first of the two files that I input (regardless of which one I feed it first), but fails to write the second file (what would be 002.mgz). My current work around is to set it up as two different subjects for the dicom conversion and then copy and rename one of the T1 outputs to 002.mgz. I am currently processing this subject through the recon-all -all pipeline after employing this work around, which suggests to me that it's not a permissions issue? 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 4:15 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote: Do you have write permission into that folder, ie, /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can you run it with -debug as the first argument and send the terminal output? On 11/29/2016 05:00 PM, Douglas Merkitch wrote: 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> <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> <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> <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> <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> <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> <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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