Thanks, but with newer versions is not working either because R software packages such as 'kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' version 1.6.7 or 'randomForest' version 4.6.12, are incompatible with R 3.3 or 3.5. At least based on my experience. So could you please let me know which is the R version I need to install to have it compatible with workbench and also compatible with R software packages listed above that are needed to run hcp_fix? I am using a MAC pro, with workbench v1.3.
This is becoming a nightmare so I would really appreciate your help. Thanks!, -L > On May 27, 2018, at 3:04 AM, [email protected] wrote: > > 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] >> <mailto:[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 >>> <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 >> > > > --------------------------------------------------------------------------- > 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] <mailto:[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
