Re: [HCP-Users] error running hcp_fix

2018-06-05 Thread Glasser, Matthew 
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

2018-06-05 Thread Marta Moreno 
 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

2018-06-05 Thread Glasser, Matthew 
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

2018-06-05 Thread Marta Moreno 
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

2018-05-31 Thread Marta Moreno 
‘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

2018-05-30 Thread Marta Moreno 
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

2018-05-27 Thread Marta Moreno 
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

2018-05-27 Thread Timothy Coalson 
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

2018-05-27 Thread Marta Moreno 
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

2018-05-27 Thread Glasser, Matthew 
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

2018-05-27 Thread Marta Moreno 
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 > > 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 >> > 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 > wrote:
 
 Perhaps you are running out of memory.
 
 Peace,
 
 Matt.
 
 From: > on behalf of Marta Moreno 
 >
 Date: Saturday, May 26, 2018 at 1:50 PM
 To: HCP Users >
 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 
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
 
>>>

Re: [HCP-Users] error running hcp_fix

2018-05-27 Thread steve 
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  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 > > 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 >> > wrote:
>>> 
>>> Perhaps you are running out of memory.
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> From: >> > on behalf of Marta Moreno 
>>> >
>>> Date: Saturday, May 26, 2018 at 1:50 PM
>>> To: HCP Users >> >
>>> 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 
>>> 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
> 


---
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.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural 

Re: [HCP-Users] error running hcp_fix

2018-05-26 Thread Marta Moreno 
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  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 > > wrote:
>> 
>> Perhaps you are running out of memory.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: > > on behalf of Marta Moreno 
>> >
>> Date: Saturday, May 26, 2018 at 1:50 PM
>> To: HCP Users > >
>> 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 
>> 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

2018-05-26 Thread Marta Moreno 
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  wrote:
> 
> Perhaps you are running out of memory.
> 
> Peace,
> 
> Matt.
> 
> From:  > on behalf of Marta Moreno 
> >
> Date: Saturday, May 26, 2018 at 1:50 PM
> To: HCP Users  >
> 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 
> 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

2018-05-26 Thread Glasser, Matthew 
Perhaps you are running out of memory.

Peace,

Matt.

From: 
>
 on behalf of Marta Moreno 
>
Date: Saturday, May 26, 2018 at 1:50 PM
To: HCP Users 
>
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
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users