Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
> On Oct 19, 2016, at 5:46 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> You could also need to run the add path parts of the command.
>
> Peace,
>
> Matt.
>
> From: nailin yao <ynai...@gmail.com>
> Date: Wednesday, October 19, 2016 at 4:02 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
>
> I tried to run fix_3_clean on matlab directly, and met the error message
> below:
>
>
> fix_3_clean('.fix',0,1,2000)
>
> TR =
>
> 0.7200
>
> /bin/bash: -cifti-convert: command not found
>
> Undefined function 'gifti' for input arguments of type 'char'.
>
> Error in ciftiopen (line 31)
>
> cifti = gifti([tmpfile '.gii']);
>
> Error in fix_3_clean (line 40)
>
> BO=ciftiopen('Atlas.dtseries.nii',WBC);
>
>
> Do you know why? Thank you very much!
>
> Best,
> Nailin
>
> 2016-10-17 20:12 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>> Is it a reproducible error? What happens if you try running the fix_3_clean
>> function with the parameters mentioned below?
>>
>> Peace,
>>
>> Matt.
>>
>> From: nailin yao <ynai...@gmail.com>
>> Date: Monday, October 17, 2016 at 2:58 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] hcp_fix bug
>>
>> Hi Matt,
>>
>> It's not compiled matlab.
>>
>> Best,
>> Nailin
>>
>> 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>>> Is this compiled matlab or not compiled?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of nailin yao
>>> <ynai...@gmail.com>
>>> Date: Monday, October 17, 2016 at 11:13 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] hcp_fix bug
>>>
>>> Hi ,
>>>
>>> I received the bug report when running hcp_fix for the last step:
>>>
>>> running FIX
>>>
>>> FIX Feature extraction for Melodic output directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica
>>>
>>> create edge masks
>>>
>>> run FAST
>>>
>>> registration of standard space masks
>>>
>>> extract features
>>>
>>> FIX Classifying components in Melodic directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
>>> /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
>>> threshold 10
>>>
>>> FIX Applying cleanup using cleanup file:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
>>> motion cleanup set to 1
>>>
>>> sh: line 1: 24221 Bus error (core dumped)
>>> /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
>>> -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
>>> addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
>>> fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
>>>
>>>
>>> Does anyone know what's the problem? Thank you very much!
>>>
>>> Best,
>>> Nailin
>>>
>>> --
>>> Nailin Yao, PhD
>>>
>>> Postdoctoral Associate
>>> Department of Psychiatry, Yale University
>>>
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>>
>>> The materials in this message are private and may contain Protected
>>> Healthcare Information or other information of a sensitive nature. If you
>>> are not the intended recipient, be advised that any unauthorized use,
>>> disclosure, copying or the taking of any action in reliance on the contents
>>> of this information is strictly prohibited. If you have received this email
>>> in error, please immediately notify the sender via telephone or return mail.
>>>
>>
>>
>>
>> --
>> Nailin Yao, PhD
>>
>> Postdoctoral Associate
>> Department of Psychiatry, Yale University
>>
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
>
>
> --
> Nailin Yao, PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you are
> not the intended recipient, be advised that any unauthorized use, disclosure,
> copying or the taking of any action in reliance on the contents of this
> information is strictly prohibited. If you have received this email in error,
> please immediately notify the sender via telephone or return mail.
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