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) 563-3853tel:%28312%29%20563-3853 Fax: (312) 563-4660tel:%28312%29%20563-4660 Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 4:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@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_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edumailto:zkaufman@nmr.mgh.harvard.edu mailto: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....
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.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto: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.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.