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SPM  July 2009

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Subject:

Realignment failure when using spm_jobman

From:

Eric Mansfield <[log in to unmask]>

Reply-To:

Eric Mansfield <[log in to unmask]>

Date:

Thu, 23 Jul 2009 17:46:57 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (28 lines) , realignlog.txt (1 lines) , realigntest.m (184 lines)

Hello,
I've been attempting to run "Realign and Unwarp" using the spm_jobman 
function. I've consistently encountered the error detailed the in the attached 
txt-file. The process that caused the error to occur is as follows:

1) in the unix command window: matlab -nodisplay <spmjob.m >log.txt

2) spmjob.m contains:
addpath('/usr/local/packages/MATLAB/spm8/');
which spm
%spm('defaults','fmri') Attempted to use to turn off plotting
spm_jobman('initcfg');
spm_jobman
('run_nogui','/home/eric/experiments/ATD.02/Analysis/Conn/20080709_34595/re
aligntest.m');

3) Realigntest.m is a batch file created in the SPM8 batch utility. I have 
created similar files for coregistration, segmentation, normalization and 
smoothing. These files have all worked.

I would be grateful for any insight on how to get "Realign and Unwarp" to run 
from the command line.

Thank you,
Eric Mansfield
Duke University



< M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 ---------------------------------------------------------- Your MATLAB license will expire in 40 days. Please contact your system administrator or The MathWorks to renew this license. ---------------------------------------------------------- To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> /usr/local/packages/MATLAB/spm8/spm.m >> >> >> ----------------------------------------------------------------------- Running job #1 ----------------------------------------------------------------------- Running 'Realign & Unwarp' {Warning: Unable to open display.} > In spm at 605 In spm at 536 In spm_figure at 640 In spm_figure at 216 In spm_uw_show at 83 In spm_uw_estimate at 416 In spm_run_realignunwarp at 89 In matlabbatch/private/cfg_run_cm at 29 In cfg_util>local_runcj at 1350 In cfg_util at 686 In spm_jobman at 194 {Warning: Unable to open display.} > In spm at 605 In spm at 536 In spm at 565 In spm_figure at 641 In spm_figure at 216 In spm_uw_show at 83 In spm_uw_estimate at 416 In spm_run_realignunwarp at 89 In matlabbatch/private/cfg_run_cm at 29 In cfg_util>local_runcj at 1350 In cfg_util at 686 In spm_jobman at 194 {Warning: Unable to open display.} > In spm at 605 In spm at 536 In spm at 622 In spm_figure at 643 In spm_figure at 216 In spm_uw_show at 83 In spm_uw_estimate at 416 In spm_run_realignunwarp at 89 In matlabbatch/private/cfg_run_cm at 29 In cfg_util>local_runcj at 1350 In cfg_util at 686 In spm_jobman at 194 {Warning: Unable to open display.} > In spm at 605 In spm_figure at 644 In spm_figure at 216 In spm_uw_show at 83 In spm_uw_estimate at 416 In spm_run_realignunwarp at 89 In matlabbatch/private/cfg_run_cm at 29 In cfg_util>local_runcj at 1350 In cfg_util at 686 In spm_jobman at 194 {Warning: Unable to open display.} > In spm at 605 In spm at 536 In spm at 565 In spm_uw_show at 101 In spm_uw_estimate at 416 In spm_run_realignunwarp at 89 In matlabbatch/private/cfg_run_cm at 29 In cfg_util>local_runcj at 1350 In cfg_util at 686 In spm_jobman at 194 procedure terminated abnormally: Error using ==> set Width and height must be > 0Computing mask.. Failed 'Realign & Unwarp' Reference to non-existent field 'beta'. In file "/usr/local/packages/MATLAB/spm8/spm_uw_apply.m" (v1358), function "spm_uw_apply" at line 226. In file "/usr/local/packages/MATLAB/spm8/config/spm_run_realignunwarp.m" (v2337), function "spm_run_realignunwarp" at line 106. The following modules did not run: Failed: Realign & Unwarp >> >> >> >> >>
%----------------------------------------------------------------------- % Job configuration created by cfg_util (rev $Rev: 2787 $) %----------------------------------------------------------------------- %% matlabbatch{1}.spm.spatial.realignunwarp.data.scans = {                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170001.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170002.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170003.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170004.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170005.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170006.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170007.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170008.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170009.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170010.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170011.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170012.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170013.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170014.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170015.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170016.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170017.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170018.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170019.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170020.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170021.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170022.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170023.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170024.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170025.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170026.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170027.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170028.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170029.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170030.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170031.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170032.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170033.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170034.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170035.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170036.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170037.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170038.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170039.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170040.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170041.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170042.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170043.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170044.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170045.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170046.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170047.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170048.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170049.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170050.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170051.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170052.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170053.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170054.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170055.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170056.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170057.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170058.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170059.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170060.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170061.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170062.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170063.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170064.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170065.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170066.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170067.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170068.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170069.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170070.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170071.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170072.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170073.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170074.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170075.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170076.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170077.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170078.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170079.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170080.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170081.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170082.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170083.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170084.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170085.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170086.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170087.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170088.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170089.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170090.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170091.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170092.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170093.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170094.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170095.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170096.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170097.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170098.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170099.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170100.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170101.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170102.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170103.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170104.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170105.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170106.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170107.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170108.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170109.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170110.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170111.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170112.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170113.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170114.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170115.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170116.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170117.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170118.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170119.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170120.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170121.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170122.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170123.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170124.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170125.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170126.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170127.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170128.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170129.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170130.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170131.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170132.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170133.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170134.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170135.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170136.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170137.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170138.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170139.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170140.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170141.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170142.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170143.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170144.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170145.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170146.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170147.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170148.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170149.img,1'                                                        '/home/esm5/experiments/ATD.02/Analysis/Conn/20080709_34595/run0170150.img,1'                                                        }; %% matlabbatch{1}.spm.spatial.realignunwarp.data.pmscan = ''; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.quality = 0.9; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.sep = 4; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.fwhm = 5; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.rtm = 0; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.einterp = 2; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.ewrap = [0 0 0]; matlabbatch{1}.spm.spatial.realignunwarp.eoptions.weight = {''}; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.basfcn = [12 12]; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.regorder = 1; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.lambda = 100000; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.jm = 0; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.fot = [4 5]; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.sot = 1; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.uwfwhm = 4; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.rem = 1; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.noi = 5; matlabbatch{1}.spm.spatial.realignunwarp.uweoptions.expround = 'Average'; matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.uwwhich = [2 1]; matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.rinterp = 4; matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.wrap = [0 0 0]; matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.mask = 1; matlabbatch{1}.spm.spatial.realignunwarp.uwroptions.prefix = 'u';

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