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]
email: [email protected]
> On May 27, 2018, at 4:24 PM, Glasser, Matthew <[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>
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>>
>> ---------------------------------------------------------------------------
>> 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>
>> ---------------------------------------------------------------------------
>>
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>>
>>
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>>
>>
>
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