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) 563-3853tel:%28312%29%20563-3853 Fax: (312) 563-4660tel:%28312%29%20563-4660 Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
On Nov 29, 2016, at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Hello Douglas,
Any chance you can upload the two data files 005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 and 4355-0006-00001:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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) 563-3853tel:%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 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edumailto: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
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> 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 3:36 PM, Z K <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.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.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.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.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.
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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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
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_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 4:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto: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.edu mailto: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.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@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.ed... >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.ed...
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.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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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Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca ) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca && ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options ) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt ) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd )
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env ) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir ) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat ) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat ) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat ) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat ) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat ) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat ) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat ) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 )
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz ) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz \n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz \n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) ) then if: Expression Syntax.
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 4:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote: 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_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu mailto: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 mailto: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 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 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 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 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 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...
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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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It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca ) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca && ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options ) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt ) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd )
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env ) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir ) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat ) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat ) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat ) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat ) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat ) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat ) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat ) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 )
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz ) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz \n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz \n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) ) then if: Expression Syntax.
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
On Nov 29, 2016, at 4:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
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_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 4:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu > mailto: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.edu mailto:greve@nmr.mgh.harvard.edu > mailto: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.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@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 >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> mailto: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... >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> >> >> 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. >> > > > > _______________________________________________ > 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.ed... > > > > _______________________________________________ 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.ed...
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.
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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hmmm it is a dicom file. Could it be that the lack of file extension gives it problems?
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 5:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote: Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca ) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca && ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options ) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt ) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd )
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env ) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log ) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh ) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir ) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log ) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat ) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat ) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat ) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat ) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat ) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat ) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat ) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 )
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz ) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz \n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz \n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 != mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 ) ) then if: Expression Syntax.
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 4:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote: 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_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 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 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 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 mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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...
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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
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Actually, it is the lack of a dot (".") in the file name. This is a short-coming of recon-all. I'm really surprised that it took this long to manifest itself. The short-term fix is to convert the files to mgz, then pass the mgz files to recon-all.
On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
Hmmm it is a dicom file. Could it be that the lack of file extension gives it problems?
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
On Nov 29, 2016, at 5:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca
) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca
&& ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options
) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt
) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd
)
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir
) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat
) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat
) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat
) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat
) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat
) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat
) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat
) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
)
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz
) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz
\n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz
\n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) ) then if: Expression Syntax.
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
On Nov 29, 2016, at 4:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
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_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 4:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > > > > > > On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu > mailto:zkaufman@nmr.mgh.harvard.edu > mailto:zkaufman@nmr.mgh.harvard.edu > mailto: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.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto: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.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> mailto: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.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@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 >>>>> 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.ed... >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto: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... >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>>> >>>> >>>> >>>> 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. >>>> >>> >>> >>> >>> _______________________________________________ >>> 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 >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>> >>> >>> >>> >>> >> _______________________________________________ >> 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 >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> >> >> >> >> >> 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. >> > > > > _______________________________________________ > 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.ed... > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Well, at least it is an easy work around. Thanks for all the detective work!
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Nov 30, 2016, at 11:39 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, it is the lack of a dot (".") in the file name. This is a short-coming of recon-all. I'm really surprised that it took this long to manifest itself. The short-term fix is to convert the files to mgz, then pass the mgz files to recon-all.
On 11/30/2016 11:41 AM, Douglas Merkitch wrote: Hmmm it is a dicom file. Could it be that the lack of file extension gives it problems?
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 5:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote: Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca
) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca
&& ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options
) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt
) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd
)
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir
) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat
) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat
) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat
) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat
) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat
) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat
) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat
) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
)
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz
) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz
\n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz
\n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) ) then if: Expression Syntax.
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
On Nov 29, 2016, at 4:48 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 run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote: 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_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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 mailto:Douglas_Merkitch@rush.edu mailto: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 mailto:zkaufman@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
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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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto: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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-- 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.
Doug, can you do me a favor and check to see if this modified version of recon-all works on your data?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all
On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
Hmmm it is a dicom file. Could it be that the lack of file extension gives it problems?
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
On Nov 29, 2016, at 5:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca
) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca
&& ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options
) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt
) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd
)
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir
) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat
) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat
) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat
) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat
) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat
) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat
) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat
) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
)
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz
) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz
\n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz
\n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) ) then if: Expression Syntax.
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
On Nov 29, 2016, at 4:48 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
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_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
On Nov 29, 2016, at 4:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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.edu mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > mailto:Douglas_Merkitch@rush.edu > > > > > > On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu > mailto:zkaufman@nmr.mgh.harvard.edu > mailto:zkaufman@nmr.mgh.harvard.edu > mailto: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.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto:Douglas_Merkitch@rush.edu >>> mailto: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.edu mailto:greve@nmr.mgh.harvard.edu >>> mailto:greve@nmr.mgh.harvard.edu >>> mailto: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.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@rush.edu >>>>> mailto:Douglas_Merkitch@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 >>>>> 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.ed... >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto:greve@nmr.mgh.harvard.edu >>>> mailto: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... >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>>> >>>> >>>> >>>> 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. >>>> >>> >>> >>> >>> _______________________________________________ >>> 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 >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>> >>> >>> >>> >>> >> _______________________________________________ >> 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 >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> >> >> >> >> >> 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. >> > > > > _______________________________________________ > 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.ed... > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto: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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Doug,
That modified version of recon-all worked like a charm! Both T1s were converted without error. I'll go ahead and run it through recon-all -all just as an extra test.
Thanks again!
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu
On Nov 30, 2016, at 12:07 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Doug, can you do me a favor and check to see if this modified version of recon-all works on your data?
https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
On 11/30/2016 11:41 AM, Douglas Merkitch wrote: Hmmm it is a dicom file. Could it be that the lack of file extension gives it problems?
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 5:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is not recognizing that the input is a dicom file. Is 4355-0005-00001 a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote: Here is the command/output with the -debug flag:
recon-all -debug -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_test set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 5 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 )
set flag = $argv[1] ; shift ; set flag = -i shift
switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 3 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 shift if ( ! -e "$InputVol" ) then if ( ! -e /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( -d "$InputVol" ) then if ( -d /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then if ( ! -r "$InputVol" ) then if ( ! -r /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 pushd $InVolDir > /dev/null pushd /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 )
set flag = $argv[1] ; shift ; set flag = -s shift
switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = 1039_test shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename 1039_test breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 )
goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params
if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then
if ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) then if ( 0 || 0 ) then
if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then
if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then
pushd $SUBJECTS_DIR > /dev/null pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test
if ( $TH3Flag ) set TH3Opt = "-th3" if ( 1 ) set TH3Opt = -th3 set TH3Opt = -th3 if ( ! $TH3Flag ) set TH3Opt = "-no-th3" if ( ! 1 ) set TH3Opt = -no-th3
if ( $longitudinal ) then if ( 0 ) then
set haslong = `echo $subjid | grep ".long."` set haslong = `echo $subjid | grep ".long."` grep .long. echo 1039_test set hasxhemi = `echo $subjid | grep xhemi` set hasxhemi = `echo $subjid | grep xhemi` grep xhemi echo 1039_test if ( "$haslong" != "" && "$hasxhemi" == "" ) then if ( != && == ) then
endif endif
if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps ) then endif endif
if ( $DoCreateBaseSubj && -e $subjdir ) then if ( 0 && -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then
if ( $#InputList == 0 ) then if ( 2 == 0 ) then
if ( -e $subjdir ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then mkdir -p $subjdir mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test endif endif else else
if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then
if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca
) then
if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca
&& ( 0 || 0 ) ) then
foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif if ( ! -e $avgtif ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $GCSHemi ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs if ( ! -e $CPAtlas ) then if ( ! -e /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
) then end end
if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then
if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 1 == 1 && 0 == 1 ) then
mkdir -p $subjdir/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options
) then
if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif
if ( $#NotifyFile != 0 ) then if ( 0 != 0 ) then
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg ) then if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then
if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then
if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then
if ( $#SurfRegToSubj ) then if ( 0 ) then
if ( $DoParallel == 1 && $#hemilist == 1 ) then if ( 0 == 1 && 2 == 1 ) then
goto check_params_return ; goto check_params_return
set StartTime = `date` ; set StartTime = `date` date set tSecStart = `date '+%s'` ; set tSecStart = `date '+%s'` date +%s
if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0 if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0 setenv REQUIRE_FS_MATCH 0
set bstampfile0 = $FREESURFER_HOME/build-stamp.txt set bstampfile0 = /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt
) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae endif endif rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/patchdir.txt if ( $?PatchDir ) then if ( 1 ) then echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt echo endif endif cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt
if ( $DoMakefile ) then if ( 0 ) then
if ( $DoTime ) then if ( 0 ) then
echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T
pushd $FREESURFER_HOME > /dev/null pushd /Applications/freesurfer_v6beta_16Nov2016 set freesurfer_home_true = `pwd` ; set freesurfer_home_true = `pwd` pwd popd > /dev/null popd echo "Actual FREESURFER_HOME $freesurfer_home_true" echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016
set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M
if ( $DoSuperClean ) then if ( 0 ) then
cd $subjdir cd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri scripts surf tmp label touch stats touch trash mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch
if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd
)
echo "\n\n#---------------------------------" >> $CF echo \n\n#--------------------------------- echo "# New invocation of recon-all `date` " >> $CF echo # New invocation of recon-all `date` date
set ENVF = $subjdir/scripts/recon-all.env set ENVF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env if ( -e $ENVF ) mv -f $ENVF $ENVF.bak if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
) mv -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo $inputargs >> $ENVF echo -debug -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_test uname -a >> $ENVF uname -a echo "" >> $ENVF echo limit >> $ENVF limit echo "" >> $ENVF echo printenv >> $ENVF printenv endif endif
if ( $DoVersionsOnly ) then if ( 0 ) then
if ( $#LF == 0 ) then if ( 0 == 0 ) then set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME ) set LF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) if ( -e $LF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log
) then else else skip_new_invo: skip_new_invo:
date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all echo $inputargs >> $LF echo -debug -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_test
if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid 1039_test echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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 limit >> $LF limit if ( -e /usr/bin/free ) then if ( -e /usr/bin/free ) then if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "" >> $LF echo /usr/bin/top -l 1 | grep PhysMem >> $LF /usr/bin/top -l 1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid grep PhysMem echo "" >> $LF echo endif endif if ( $?PBS_JOBID ) then if ( 0 ) then
set cmd = ( which bc ) set cmd = ( which bc ) $cmd > & /dev/null which bc if ( $status ) then if ( 0 ) then
echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /Applications/freesurfer_v6beta_16Nov2016/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info mri_relabel_hypointensities -all-info >> $LF mri_relabel_hypointensities -all-info
echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCA $GCA" >> $LF echo GCA RB_all_2016-05-10.vc700.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2016-05-10.vc700.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/average echo "GCS $GCS" >> $LF echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs echo "#######################################" >> $LF echo ####################################### skip_all_info: skip_all_info:
if ( $DoVersionsOnly ) exit 0 ; if ( 0 ) exit 0
set ErrorFile = $subjdir/scripts/recon-all.error set ErrorFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error rm -f $ErrorFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error
if ( $#DoneFile == 0 ) then if ( 0 == 0 ) then set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done rm -f $DoneFile rm -f /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done endif endif
if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh set bailfile = ( ) ; set bailfile = ( ) if ( $#hemilist == 1 ) then if ( 2 == 1 ) then
set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh set IsRunningFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh
) set bailfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 0 ) then echo "------------------------------" > $IsRunningFile echo ------------------------------ echo "SUBJECT $subjid" >> $IsRunningFile echo SUBJECT 1039_test echo "HEMI $hemilist" >> $IsRunningFile echo HEMI lh rh echo "DATE `date`" >> $IsRunningFile echo DATE `date` date echo "USER $user" >> $IsRunningFile echo USER glennstebbins echo "HOST `hostname`" >> $IsRunningFile echo HOST `hostname` hostname echo "PROCESSID $$ " >> $IsRunningFile echo PROCESSID 33721 echo "PROCESSOR `uname -m`" >> $IsRunningFile echo PROCESSOR `uname -m` uname -m echo "OS `uname -s`" >> $IsRunningFile echo OS `uname -s` uname -s uname -a >> $IsRunningFile uname -a echo $VERSION >> $IsRunningFile echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ if ( $?PBS_JOBID ) then if ( 0 ) then endif endif
set CSDF = $subjdir/scripts/csurfdir set CSDF = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( $DoCleanCSDF ) rm -vf $CSDF if ( 0 ) rm -vf /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir if ( -e $CSDF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir
) then
if ( $#SF == 0 ) then if ( 0 == 0 ) then set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) set SF = ( /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) if ( -e $SF ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log
) then else else echo "status file for recon-all" >> $SF echo status file for recon-all date >> $SF date
if ( "`uname -s`" == "Linux" ) then if ( `uname -s` == Linux ) then uname -s
if ( $#WaitForFile != 0 ) then if ( 0 != 0 ) then
if ( ! $RunIt ) then if ( ! 1 ) then
if ( $DoCleanSeed ) then if ( 0 ) then if ( $DoCleanCW256 ) then if ( 0 ) then if ( $DoCleanTal ) then if ( 0 ) then if ( $DoCleanLta ) then if ( 0 ) then if ( $DoCleanPFH ) then if ( 0 ) then if ( $DoCleanBM ) then if ( 0 ) then if ( $DoCleanASeg ) then if ( 0 ) then if ( $DoCleanWM ) then if ( 0 ) then if ( $DoCleanCP ) then if ( 0 ) then if ( $DoCleanTWM ) then if ( 0 ) then if ( $DoCleanBFSE ) then if ( 0 ) then if ( $DoCleanXopts ) then if ( 0 ) then if ( $DoCleanT2 ) then if ( 0 ) then if ( $DoCleanFLAIR ) then if ( 0 ) then
set seedfile = $subjdir/scripts/seed-pons.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat if ( $#PonsSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat
) set PonsSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-cc.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat if ( $#CCSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat
) set CCSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-lh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat if ( $#LHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat
) set LHSeedCRS = `cat $seedfile | grep -v #` set seedfile = $subjdir/scripts/seed-rh.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat if ( $#RHSeedCRS ) then if ( 0 ) then if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat
) set RHSeedCRS = `cat $seedfile | grep -v #`
set seedfile = $subjdir/scripts/seed-ws.crs.man.dat set seedfile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat if ( $#WSSeedPoint ) then if ( 0 ) then if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v #` if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat
) set WSSeedPoint = `cat $seedfile | grep -v #`
set ControlPointsFile = $subjdir/tmp/control.dat set ControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat if ( -e $ControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat
) then
set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat set DefaultTWMControlPointsFile = /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat if ( $UseTWMControlPoints ) then if ( 0 ) then
if ( -e $DefaultTWMControlPointsFile ) then if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat
) then endif endif
if ( $DoConformWidth256 ) then if ( 0 ) then
if ( $DoShowEdits ) then if ( 0 ) then
if ( $longitudinal ) then if ( 0 ) then
if ( $#InputList != 0 ) then if ( 2 != 0 ) then @ nth = 1 ; @ nth = 1 foreach InputVol ( $InputList ) foreach InputVol ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
/Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
)
if ( $nth == 1 ) then if ( 1 == 1 ) then
set firstInput = ( $InputVol ) set firstInput = ( /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) set rows = `mri_info --nrows $InputVol |& tail -n 1` set rows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set cols = `mri_info --ncols $InputVol |& tail -n 1` set cols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 set slices = `mri_info --nslices $InputVol |& tail -n 1` set slices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 tail -n 1 else else
set nthid = `printf %03d.mgz $nth` set nthid = `printf %03d.mgz $nth` printf %03d.mgz 1 set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) set cmd = ( 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_test/mri/orig/001.mgz
) $PWD | & tee -a $LF /bin/pwd tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log echo \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_test/mri/orig/001.mgz
\n tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd \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_test/mri/orig/001.mgz
\n if ( $RunIt ) then if ( 1 ) then $fs_time $cmd | & tee -a $LF 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_test/mri/orig/001.mgz tee -a /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log 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_test/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_test/mri/orig/001.mgz... if ( $status ) goto error_exit ; if ( 0 ) goto error_exit endif endif @ nth = $nth + 1 ; @ nth = 1 + 1 end end
if ( $nth == 1 ) then if ( 2 == 1 ) then
set nrows = `mri_info --nrows $InputVol |& tail -n 1` set nrows = `mri_info --nrows $InputVol |& tail -n 1` mri_info --nrows /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set ncols = `mri_info --ncols $InputVol |& tail -n 1` set ncols = `mri_info --ncols $InputVol |& tail -n 1` mri_info --ncols /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 set nslices = `mri_info --nslices $InputVol |& tail -n 1` set nslices = `mri_info --nslices $InputVol |& tail -n 1` mri_info --nslices /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 tail -n 1 if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != $slices ) ) then if ( ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) || ( mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001
!= mri_info: could not parse extension from /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001
) ) then if: Expression Syntax.
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
On Nov 29, 2016, at 4:48 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 run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote: 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_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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 mailto:Douglas_Merkitch@rush.edu mailto: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 mailto:zkaufman@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu mailto:Douglas_Merkitch@rush.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto: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.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto: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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- 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...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
Hi Doug
do you have any spaces in your filenames? That can cause this kind of thing. It's hard to tell from your email
cheers Bruce On Tue, 29 Nov 2016, 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 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.... _FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz 7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeE kINY_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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... stinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkz z7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=waImhwQq0O8LHAlIun2v95CPShQ-yU CVzQzvOhsqD9s&e=
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto: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... d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0G gWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=5c8BG0jWHPLzpY6NB7Qaxm6jR1KlRb-uxt-ubzqrV9U&e=
www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed... utgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrF kzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=q36YAeWf40aDIu00LgaqEQKGoZ6i ygWUhdUQLvWflDo&e=
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Hello,
Sorry for the confusion - the problem was that, while I had changed the $FREESURFER_HOME variable in the mac terminal, I still had the older freesurfer version sourced in my .bashrc file. Once I updated that file, the conversion went on without error.
Thanks again for the prompt response and I apologize for my error.
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 3:20 PM, Douglas Merkitch <Douglas_Merkitch@rush.edumailto:Douglas_Merkitch@rush.edu> 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
On Nov 29, 2016, at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto: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
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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.htmlhttp://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.
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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.
freesurfer@nmr.mgh.harvard.edu
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