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
Fax: (312) 563-4660
Email: Douglas_Merkitch@rush.edu





On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@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_Merkitch@rush.edu <mailto:Douglas_Merkitch@rush.edu>





On Nov 29, 2016, at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@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_Merkitch@rush.edu <mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>







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