Well you have the path to the wb_command binary set as a directory instead of to the binary itself. Presumably in the past you had it set to the binary when it was working.
Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:36 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Harwell, John" <jharw...@wustl.edu<mailto:jharw...@wustl.edu>> Subject: Re: [HCP-Users] error running hcp_fix 94 # Set this to the location of the HCP Workbench command for your platform 95 FSL_FIX_WBC='/Applications/workbench/bin_macosx64'; 96 export FSL_FIX_CIFTIRW FSL_FIX_WBC Thanks! ******************************************* Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> email: mmor...@nyspi.columbia.edu<mailto:mmor...@nyspi.columbia.edu> On Jun 5, 2018, at 1:32 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: What do you have on line 94 of the FIX settings.sh? Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:28 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Harwell, John" <jharw...@wustl.edu<mailto:jharw...@wustl.edu>> Subject: Re: [HCP-Users] error running hcp_fix Dear Matt and all, R version 3.4. Matlab version 2017b. Workbench version 1.3. I am using a macOS Sierra version 10.12.6. I have installed all required versions from packages kernlab, party, etc. in R successfully, but after running hcp_fix I get the following error in .fix.log. Please advice (see below): /bin/bash: /Applications/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/tp8475904261983465.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 ******************************************* Leah Moreno, PhD Associate Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> email: mmor...@nyspi.columbia.edu<mailto:mmor...@nyspi.columbia.edu> On May 27, 2018, at 4:24 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: There is no relationship between R and Workbench (or R and matlab). As to a Workbench/matlab incompatibility, we would need to know what version of Workbench and matlab to debug this. Peace, Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Sunday, May 27, 2018 at 3:22 PM To: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>> Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] error running hcp_fix 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, st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk> 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 <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> 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 <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Perhaps you are running out of memory. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Saturday, May 26, 2018 at 1:50 PM To: HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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) st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk> http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
