[HCP-Users] Workbench v1.3.1 Released - a few bug fixes and new features

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
June 5, 2018
Connectome Workbench v1.3.1 Released
Announcing version 1.3.1 of Connectome 
Workbench 
(WB) brain visualization and analysis software, which fixes a few bugs and adds 
a few features from the recent v1.3.0 release, is now available for 64-bit Mac 
OSX, Windows, and Linux. The Workbench distribution includes wb_view, a 
GUI-based visualization platform, and wb_command, a command-line program for 
performing a variety of algorithmic tasks using volume, surface, and 
grayordinate data.
Changes in Workbench v1.3.1
wb_view:
New Features

  *   Scene numbers using a file added next to files in scene "list files" 
window
  *   Scenes "replace all" no longer shows tab highlight outline in captured 
previews
  *   Builds with older QT5 no longer have very large overlay toolbox by default


Bug Fixes

  *   fixed wb_view crash when loading label volumes
  *   Settings synchronized across overlay settings windows that refer to the 
same file


wb_command:
New Features

  *   -*-roi-from-extrema commands give warnings when output has no maps
  *   -volume-set-space now has a -file option to take space information from 
another volume
  *   -volume-math copies timestep from input files


Bug Fixes

  *   bash completion for wb_shortcuts should now work reliably
  *   wb_shortcuts -cifti-demean should not give warnings about extensions for 
temporary files

Installation for improved tab completion for wb_command:
The below instructions are OPTIONAL, they are not required for workbench to 
function properly.  They are intended for users that use wb_command manually in 
the bash shell.

These instructions are only for people who downloaded workbench as a zip file, 
installation through a package manager such as neurodebian performs similar 
steps automatically.

For relatively modern versions of the "bash" shell, workbench now provides tab 
completions for wb_command options and file extensions (the default OS X bash 
is too old, you would need to use homebrew, macports, or similar).

The easiest way to install them is to copy the file "bashcomplete_wb_command" 
from the workbench folder into /etc/bash_completion.d/, if you have admin 
rights.  If you do not have admin rights, you can make a copy of 
"bashcomplete_wb_command" in your home directory, but renamed to 
".bash_completion" (the dot on the front is important).  Ignore the 
"bashcomplete_wb_shortcuts" file, the wb_shortcuts completions are also inside 
the "bashcomplete_wb_command" file.  The file is located here, depending on OS:

Ubuntu/Debian Linux: workbench/exe_linux64/bashcomplete_wb_command
Centos/RedHat Linux: workbench/exe_rh_linux64/bashcomplete_wb_command
Windows: workbench/bin_windows64/bashcomplete_wb_command
OS X: workbench/macosx64_apps/bashcomplete_wb_command

Once this is done, open a NEW terminal window, type "wb_command -file-info" but 
don't press enter, instead press tab, and the line should change to "wb_command 
-file-information".  If it does not, then it is likely that the OS's 
"bash-completion" package is not installed.


WB v1.3.1 is compatible with the WB v1.0 tutorial and the processed 1200 
Subjects Group Average Data available to download at 
http://humanconnectome.org/connectome/get-connectome-workbench.html and on the 
 ConnectomeDB HCP project 
page. Access to both 
datasets require ConnectomeDB login and signature of the HCP Open Access Data 
Use Terms.

To download the  WB v1.3.1 
source code from GitHub: 
follow the link, click Releases (near the top center of the page), then under 
v1.3.1, click the “Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to 
the hcp-users discussion list (sign up 
here).

Best,
The WU-Minn HCP Consortium

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org


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[HCP-Users] perceptually uniform sequential colormaps?

[Harms, Michael]

Hi guys,
Which of the colormaps currently in Workbench are perceptually uniform and 
monotonically increasing in lightness?

In the interest of supporting some of the recent colormaps with considerable 
thought behind them, what about including the viridis, plasma, inferno, and 
magma colormaps from Matplotlib into Workbench?

http://medvis.org/2016/02/23/better-than-the-rainbow-the-matplotlib-alternative-colormaps/
https://matplotlib.org/users/colormaps.html

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu


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Re: [HCP-Users] error running hcp_fix

[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>>, 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
email: 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>>, 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
email: 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>>
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 
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: 

Re: [HCP-Users] error running hcp_fix

[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  >
> 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>>, 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 
> 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 > >
>> Date: Sunday, May 27, 2018 at 3:22 PM
>> To: "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 
>>>  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);
 
 

Re: [HCP-Users] error running hcp_fix

[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>>, 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
email: 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>>
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 
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.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 

Re: [HCP-Users] error running hcp_fix

[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  >
> Date: Sunday, May 27, 2018 at 3:22 PM
> To: "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 
>>  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