Great. Added now. 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: [email protected] email: [email protected]
> On Jun 5, 2018, at 1:38 PM, Glasser, Matthew <[email protected]> wrote: > > 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 <[email protected] > <mailto:[email protected]>> > Date: Tuesday, June 5, 2018 at 12:36 PM > To: Matt Glasser <[email protected] <mailto:[email protected]>> > Cc: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>>, HCP Users > <[email protected] <mailto:[email protected]>>, > Timothy Coalson <[email protected] <mailto:[email protected]>>, "Harwell, John" > <[email protected] <mailto:[email protected]>> > 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: [email protected] <mailto:[email protected]> > email: [email protected] <mailto:[email protected]> >> On Jun 5, 2018, at 1:32 PM, Glasser, Matthew <[email protected] >> <mailto:[email protected]>> wrote: >> >> What do you have on line 94 of the FIX settings.sh? >> >> Matt. >> >> From: Marta Moreno <[email protected] >> <mailto:[email protected]>> >> Date: Tuesday, June 5, 2018 at 12:28 PM >> To: Matt Glasser <[email protected] <mailto:[email protected]>> >> Cc: "[email protected] <mailto:[email protected]>" >> <[email protected] <mailto:[email protected]>>, HCP Users >> <[email protected] <mailto:[email protected]>>, >> Timothy Coalson <[email protected] <mailto:[email protected]>>, "Harwell, John" >> <[email protected] <mailto:[email protected]>> >> 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: [email protected] <mailto:[email protected]> >> email: [email protected] <mailto:[email protected]> >>> On May 27, 2018, at 4:24 PM, Glasser, Matthew <[email protected] >>> <mailto:[email protected]>> 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 <[email protected] >>> <mailto:[email protected]>> >>> Date: Sunday, May 27, 2018 at 3:22 PM >>> To: "[email protected] <mailto:[email protected]>" >>> <[email protected] <mailto:[email protected]>> >>> Cc: Matt Glasser <[email protected] <mailto:[email protected]>>, HCP >>> Users <[email protected] <mailto:[email protected]>> >>> 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, [email protected] >>>> <mailto:[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 >>>>> <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
