Hi - we've seen this in the past with specific combinations of matlab version and workbench version. I'm not quite sure if the very latest versions of both have the issue or not. Cheers.
> On 27 May 2018, at 02:32, Marta Moreno <[email protected]> wrote: > > I found the following error, please advice: (before is giving me some > warnings about different functions that has same name as a Matlab builtin, I > have pasted the output from last warning and first error). > > Which are the files that needs to be included in ‘CIFTIMatlabReaderWriter’ > for the settings.sh? > > Warning: Function subsref has the same name as a MATLAB builtin. We suggest > you > rename the function to avoid a potential name conflict. > > In path (line 109) > In fix_3_clean (line 45) > /bin/bash: /usr/local/workbench/bin_macosx64: is a directory > Error using read_gifti_file_standalone (line 20) > [GIFTI] Loading of XML file > /private/var/folders/j2/__433pcd02l1cw9qkydkqs5h0000gn/T/tp6555679429695603.gii > failed. > > Error in gifti (line 71) > this = read_gifti_file_standalone(varargin{1},giftistruct); > > Error in ciftiopen (line 31) > cifti = gifti([tmpfile '.gii']); > > Error in fix_3_clean (line 46) > BO=ciftiopen('Atlas.dtseries.nii',WBC); > > Thanks! > > -L > > >> On May 26, 2018, at 6:55 PM, Marta Moreno <[email protected] >> <mailto:[email protected]>> wrote: >> >> You were right, now the problem is gone but still cannot find my >> clean.dtseries >> >> Here is the output, I could not find any error in .ica folder: >> hcp_fix RS_fMRI_1.nii.gz 2000 >> processing FMRI file RS_fMRI_1 with highpass 2000 >> running highpass >> running MELODIC >> running FIX >> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica >> create edge masks >> run FAST >> registration of standard space masks >> extract features >> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using >> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and >> threshold 10 >> FIX Applying cleanup using cleanup file: >> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set >> to 1 >> >> Please advice. >> >> Thanks! >> >> -L >> >> >>> On May 26, 2018, at 2:52 PM, Glasser, Matthew <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> Perhaps you are running out of memory. >>> >>> Peace, >>> >>> Matt. >>> >>> From: <[email protected] >>> <mailto:[email protected]>> on behalf of Marta Moreno >>> <[email protected] <mailto:[email protected]>> >>> Date: Saturday, May 26, 2018 at 1:50 PM >>> To: HCP Users <[email protected] >>> <mailto:[email protected]>> >>> Subject: [HCP-Users] error running hcp_fix >>> >>> Dear experts, >>> >>> I am getting the following error. Please advice: >>> >>> hcp_fix RS_fMRI_1.nii.gz 2000 >>> processing FMRI file RS_fMRI_1 with highpass 2000 >>> running highpass >>> running MELODIC >>> running FIX >>> FIX Feature extraction for Melodic output directory: RS_fMRI_1_hp2000.ica >>> create edge masks >>> run FAST >>> registration of standard space masks >>> extract features >>> FIX Classifying components in Melodic directory: RS_fMRI_1_hp2000.ica using >>> training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and >>> threshold 10 >>> FIX Applying cleanup using cleanup file: >>> RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup >>> set to 1 >>> sh: line 1: 10513 Killed: 9 >>> /Applications/MATLAB_R2017b.app/bin/matlab -nojvm -nodisplay -nodesktop >>> -nosplash -r "addpath('/usr/local/fix1.065'); >>> addpath('/usr/local/fsl/etc/matlab'); fix_3_clean('.fix',0,1,2000)" >> >>> .fix.log 2>&1 >>> >>> Thanks, >>> >>> -L >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] <mailto:[email protected]> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] <mailto:[email protected]> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
