Error In Spm_jobman
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v1.5 REST v1.4 REST v1.3 REST v1.2 REST v1.1 DynamicBC DPARSF CourseMultimedia Course: Data Processing of Resting-State fMRI Demonstrational Data for Resting-State fMRI FAQ AboutYu-feng Zang Site history Search this site: Username: * Password: * Create new account Request new password Navigation Recent posts Help of restfmri.netDownloads Statistics Howto Start a topic from an abstract in PubMed I have a question! Home › Forums › Resting-state fMRI topics Resting-State analyis using the DPARSF toolbox - Error at Slice timing Tue, 01/29/2013 - 23:09 — kvoigt Hello, I just started to do my first resting-state analysis https://www.nitrc.org/forum/forum.php?thread_id=6901&forum_id=1144 using the REST toolbox. Unfortunatley, I have already an error at an early preprocessing step, namely slice timing. It does the slice time correction for the first subject, but it immediately stops when the analysis for the second subject should actually start. I am using a Mac OS X (Version 10.8.2), Matlab 2012b, SPM8, REST (Version 1.8). What might be the problem? The following error http://www.restfmri.net/forum/node/1351 message occurs: Warning: Run spm_jobman('initcfg'); beforehand > In spm_jobman at 107 In DPARSF_run at 364 In DPARSF>pushbuttonRun_Callback at 976 In gui_mainfcn at 96 In DPARSF at 43 ------------------------------------------------------------------------ Running job #1 ------------------------------------------------------------------------ Running 'Slice Timing' SPM8: spm_slice_timing (v4310) 15:58:50 - 29/01/2013 ======================================================================== Your TR is 2.1 Failed 'Slice Timing' Improper assignment with rectangular empty matrix. In file "/Users/katharinavoigt/Documents/MATLAB/spm8/spm_slice_timing.m" (v4310), function "spm_slice_timing" at line 232. In file "/Users/katharinavoigt/Documents/MATLAB/spm8/config/spm_run_st.m" (v2312), function "spm_run_st" at line 25. The following modules did not run: Failed: Slice Timing Error using cfg_util (line 835) Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message) ------------------ Running job #1 ------------------ Error in spm_jobman (line 217) Error in DPARSF_run (line 365) Error in DPARSF>pushbuttonRun_Callback (line 976) Error in gui_mainfcn (line 96) Error in DPARSF (line 43) Error while evaluating uicontrol Callback Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: The given Fi
setting up lab in St Andrews I've consistently run into a DICOM Import Error that causes the process to http://akiraoconnor.org/2011/12/08/spm-dicom-import-error/ terminate about half-way through. I finally fixed the problem today after a quick search on the SPM mailing list. The error I was receiving was as follows: Running ‘DICOM https://www.jiscmail.ac.uk/cgi-bin/webadmin?A3=ind1305&L=SPM&E=quoted-printable&P=1000032&B=--Apple-Mail%3D_CC849512-9CAA-4FB8-86B8-B8A0FCE8F1F3&T=text%2Fhtml;%20charset=iso-8859-1&pending= Import' Changing directory to: D:Akira Cue Framing 2011PP03 Failed ‘DICOM Import' Error using ==> horzcat CAT arguments dimensions are not consistent. In file "C:spm8spm_dicom_convert.m" (v4213), function "spm_dicom_convert" at line error in 61. In file "C:spm8configspm_run_dicom.m" (v2094), function "spm_run_dicom" at line 32. The following modules did not run: Failed: DICOM Import ??? Error using ==> cfg_util at 835 Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error error in spm_jobman message) ------------ Running job #[X] ------------ Error in ==> spm_jobman at 208 ??? Error while evaluating uicontrol Callback This was a little mysterious, as the appropriate number of nifti files appeared to be left after the process terminated unexpectedly. The following link suggested an SPM code tweak that might fix it: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1106&L=SPM&P=R49499&1=SPM&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 The proposed fix from John Ashburner simply requires changing line 61 of spm_dicom_convert.m from: out.files = [fmos fstd fspe]; to: out.files = [fmos(:); fstd(:); fspe(:)]; Works like a charm! Posted in fMRI, pre-processing, SPM, Tweaks.Tagged SPM. Leave a reply Cancel reply CommentYou may use these HTML tags and attributes:
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on matlab, it's putting a shortest path so when debugging you can see that it opens a new cfg_util that is actually the same file but didn't keep the same variables with the persistent variables jobs and c0.Thank you for your help Dennis, Benjamin Yvernault Le 7 mai 2013 à 17:48, Dennis Thompson a écrit :Isuspectthat you have an issue with incorrect paths in Linux. Matllab cannot find the cfg_util.m file which islocatedin{SPMPATH}/matlabbatch/cfg_util.m Also I think that there might be a very old bug in your script.line 10 in your script should mostlikelybe "clearmatlabbatch" the "jobs" data structure was discontinued in the switch from spm5 to spm8 On Tue, May 7, 2013 at 2:51 PM, Benjamin Yvernault <[log in to unmask]> wrote: Hello, I have an issue with spm_jobman.m running on linux. I have a matlab script that used SPM8 and VBM8 and the spm_jobman. When I used it on my mac, the script is working fine but when I am using with the same SPM8 folder on linux, I have an error : Undefined function 'list' for input arguments of type 'cell'. Error in cfg_repeat/list (line 112) [id1 stop1] = list(citems{k}, spec, tropts); Error in cfg_util>local_getcjid2subs (line 1196) cjid2subsin = list(cjin, exspec, tropts); Error in cfg_util>local_initjob (line 1367) [ucj ucjid2subs] = cellfun(@local_getcjid2subs, ucj, 'UniformOutput', false); Error in cfg_util (line 678) [jobs(cjob) mod_job_idlist] = local_initjob(jobs(cjob), job, jobdedup); Error in spm_jobman (line 174) cjob = cfg_util('initjob', mljob); Error in script (line 171) spm_jobman('interactive',matlabbatch); I attached the script.m that is creating the matlabbatch and calling spm_jobman. It looks like something is wrong with Linux and spm. I started debugging it and I saw that the line : spm_jobman('initcfg'); is not doing the same thing on mac and linux. It looks like calling the function cfg_util.m twice on linux doesn't keep the previous jobs and c0. I check if it was a problem with an update for spm but it's the latest one and I am using the same script, same spm8/VBM8. Does someone know what is wrong? Thank you for your help, Benjam