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 email: mmor...@nyspi.columbia.edu > On Jun 5, 2018, at 1:32 PM, Glasser, Matthew <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 >>>>>> <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 >>>>> <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 >>>> <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 <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
