Re: [HCP-Users] error running hcp_fix
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 mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:36 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" mailto:st...@fmrib.ox.ac.uk>>, HCP Users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>>, "Harwell, John" 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 mailto:glass...@wustl.edu>> wrote: What do you have on line 94 of the FIX settings.sh? Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:28 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" mailto:st...@fmrib.ox.ac.uk>>, HCP Users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>>, "Harwell, John" 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/__433pcd02l1cw9qkydkqs5hgn/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 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 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>" mailto:st...@fmrib.ox.ac.uk>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 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 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 setting
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 email: mmor...@nyspi.columbia.edu > On Jun 5, 2018, at 1:32 PM, Glasser, Matthew wrote: > > What do you have on line 94 of the FIX settings.sh? > > Matt. > > From: Marta Moreno <mailto:mmorenoort...@icloud.com>> > Date: Tuesday, June 5, 2018 at 12:28 PM > To: Matt Glasser mailto:glass...@wustl.edu>> > Cc: "st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>" > mailto:st...@fmrib.ox.ac.uk>>, HCP Users > mailto:hcp-users@humanconnectome.org>>, > Timothy Coalson mailto:tsc...@mst.edu>>, "Harwell, John" > 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/__433pcd02l1cw9qkydkqs5hgn/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 > <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 > <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>" >> mailto:st...@fmrib.ox.ac.uk>> >> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users >> 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 >>> <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 a
Re: [HCP-Users] error running hcp_fix
What do you have on line 94 of the FIX settings.sh? Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:28 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>" mailto:st...@fmrib.ox.ac.uk>>, HCP Users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>>, "Harwell, John" 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/__433pcd02l1cw9qkydkqs5hgn/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 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 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>" mailto:st...@fmrib.ox.ac.uk>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users 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 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/__433pcd02l1cw9qkydkqs5hgn/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 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.R
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/__433pcd02l1cw9qkydkqs5hgn/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 email: mmor...@nyspi.columbia.edu > On May 27, 2018, at 4:24 PM, Glasser, Matthew 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 <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>" > mailto:st...@fmrib.ox.ac.uk>> > Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP Users > 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 >> <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/__433pcd02l1cw9qkydkqs5hgn/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 >>> <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 extr
Re: [HCP-Users] error running hcp_fix
‘randomForest’ >> * removing >> ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’ >> Installation failed: Command failed (1) >> >> Thanks! >> >> -L >> >>> On May 27, 2018, at 9:12 PM, Timothy Coalson >> <mailto:tsc...@mst.edu>> wrote: >>> >>> The way I solved this was to use the very latest R version (cran mirrors >>> contain debian and ubuntu packages, see >>> http://cran.wustl.edu/bin/linux/ubuntu/ >>> <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X >>> binaries: http://cran.wustl.edu/bin/macosx/ >>> <http://cran.wustl.edu/bin/macosx/> ), then install devtools (this is the >>> main reason for installing the latest R, as getting devtools installed in >>> older R is an even bigger pain), and then use "install_version": >>> https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages >>> >>> <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages> >>> >>> Tim >>> >>> >>> On Sun, May 27, 2018 at 3:32 PM, Marta Moreno >> <mailto:mmorenoort...@icloud.com>> wrote: >>> I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of >>> them allowed me to install specified software packages versions required to >>> run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' >>> version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am >>> getting now is regarding this issue. I have pasted the error below: >>> >>> Error in ctreefit(object = object, controls = controls, weights = weights, >>> : >>> no slot of name "remove_weights" for this object of class >>> "TreeGrowControl" >>> Calls: eval -> eval -> -> ctreefit >>> Execution halted >>> >>> Please advice on which R version should I have installed to make it to >>> work. I have downloaded software packages and installing them in R as root >>> as follow: >>> > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', >>> > dependencies=TRUE) >>> Warning message: >>> package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for >>> R version 3.3.3) >>> >>> Thanks! >>> >>> -L >>> >>>> On May 27, 2018, at 4:24 PM, Glasser, Matthew >>> <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 >>> <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>" >>>> mailto:st...@fmrib.ox.ac.uk>> >>>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP >>>> Users >>> <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. >>>
Re: [HCP-Users] error running hcp_fix
d >> >> Please advice on which R version should I have installed to make it to work. >> I have downloaded software packages and installing them in R as root as >> follow: >> > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', >> > dependencies=TRUE) >> Warning message: >> package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R >> version 3.3.3) >> >> Thanks! >> >> -L >> >>> On May 27, 2018, at 4:24 PM, Glasser, Matthew >> <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 >> <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>" >>> mailto:st...@fmrib.ox.ac.uk>> >>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, HCP >>> Users 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 >>>> <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/__433pcd02l1cw9qkydkqs5hgn/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 >>>>> <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 >>>>>>
Re: [HCP-Users] error running hcp_fix
Thanks, Tim! I followed your advice and I am almost there… How did you install randomForest' version 4.6.12? I am getting the following error: install_version("randomForest", version = "4.6-12", repos = "http://cran.us.r-project.org”) (…) /var/tmp//ccP5LbYW.s:2671:2: error: unknown directive .stabn 224,0,0,LBE141 ^ /var/tmp//ccP5LbYW.s:2673:9: error: unsupported directive '.stabs' .stabs "",36,0,0,Lscope8-LFBB8 ^ /var/tmp//ccP5LbYW.s:2697:9: error: unsupported directive '.stabs' .stabs "",100,0,0,Letext0 ^ /var/tmp//ccP5LbYW.s:2835:11: warning: section "__textcoal_nt" is deprecated .section __TEXT,__textcoal_nt,coalesced,pure_instructions ^ ~ /var/tmp//ccP5LbYW.s:2835:11: note: change section name to "__text" .section __TEXT,__textcoal_nt,coalesced,pure_instructions ^ ~ make: *** [rfsub.o] Error 1 ERROR: compilation failed for package ‘randomForest’ * removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/randomForest’ Installation failed: Command failed (1) Thanks! -L > On May 27, 2018, at 9:12 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > The way I solved this was to use the very latest R version (cran mirrors > contain debian and ubuntu packages, see > http://cran.wustl.edu/bin/linux/ubuntu/ > <http://cran.wustl.edu/bin/linux/ubuntu/> , and they also have OS X binaries: > http://cran.wustl.edu/bin/macosx/ <http://cran.wustl.edu/bin/macosx/> ), then > install devtools (this is the main reason for installing the latest R, as > getting devtools installed in older R is an even bigger pain), and then use > "install_version": > https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages > > <https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages> > > Tim > > > On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> wrote: > I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of > them allowed me to install specified software packages versions required to > run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' > version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am > getting now is regarding this issue. I have pasted the error below: > > Error in ctreefit(object = object, controls = controls, weights = weights, : > no slot of name "remove_weights" for this object of class "TreeGrowControl" > Calls: eval -> eval -> -> ctreefit > Execution halted > > Please advice on which R version should I have installed to make it to work. > I have downloaded software packages and installing them in R as root as > follow: > > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', > > dependencies=TRUE) > Warning message: > package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R > version 3.3.3) > > Thanks! > > -L > >> 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
Re: [HCP-Users] error running hcp_fix
The way I solved this was to use the very latest R version (cran mirrors contain debian and ubuntu packages, see http://cran.wustl.edu/bin/linux/ubuntu/ , and they also have OS X binaries: http://cran.wustl.edu/bin/macosx/ ), then install devtools (this is the main reason for installing the latest R, as getting devtools installed in older R is an even bigger pain), and then use "install_version": https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages Tim On Sun, May 27, 2018 at 3:32 PM, Marta Moreno <mmorenoort...@icloud.com> wrote: > I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of > them allowed me to install specified software packages versions required to > run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' > version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am > getting now is regarding this issue. I have pasted the error below: > > Error in ctreefit(object = object, controls = controls, weights = > weights, : > no slot of name "remove_weights" for this object of class > "TreeGrowControl" > Calls: eval -> eval -> -> ctreefit > Execution halted > > Please advice on which R version should I have installed to make it to > work. I have downloaded software packages and installing them in R as root > as follow: > > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', > dependencies=TRUE) > *Warning message:* > *package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available > (for R version 3.3.3)* > > Thanks! > > -L > > On May 27, 2018, at 4:24 PM, Glasser, Matthew <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> > Date: Sunday, May 27, 2018 at 3:22 PM > To: "st...@fmrib.ox.ac.uk" <st...@fmrib.ox.ac.uk> > Cc: Matt Glasser <glass...@wustl.edu>, HCP Users < > 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 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> 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/__433pcd02l1cw9qkydkqs5hgn/ > 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> > 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: R
Re: [HCP-Users] error running hcp_fix
I am using workbench v1.3. I have used R v3.3, R v3.4.and R v3.5. None of them allowed me to install specified software packages versions required to run hcp_fix: ('kernlab' version 0.9.24, 'party' version 1.0.25, 'e1071' version 1.6.7 or 'randomForest' version 4.6.12), so I guess the error I am getting now is regarding this issue. I have pasted the error below: Error in ctreefit(object = object, controls = controls, weights = weights, : no slot of name "remove_weights" for this object of class "TreeGrowControl" Calls: eval -> eval -> -> ctreefit Execution halted Please advice on which R version should I have installed to make it to work. I have downloaded software packages and installing them in R as root as follow: > install.packages('/Users/alayar/Downloads/kernlab_0.9-24.tar', > dependencies=TRUE) Warning message: package ‘/Users/alayar/Downloads/kernlab_0.9-24.tar’ is not available (for R version 3.3.3) Thanks! -L > On May 27, 2018, at 4:24 PM, Glasser, Matthew <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/__433pcd02l1cw9qkydkqs5hgn/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 highpas
Re: [HCP-Users] error running hcp_fix
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/__433pcd02l1cw9qkydkqs5hgn/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
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 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/__433pcd02l1cw9qkydkqs5hgn/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 spa
Re: [HCP-Users] error running hcp_fix
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> 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/__433pcd02l1cw9qkydkqs5hgn/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/h
Re: [HCP-Users] error running hcp_fix
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/__433pcd02l1cw9qkydkqs5hgn/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> 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 > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] error running hcp_fix
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> 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] error running hcp_fix
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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users