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_hp2
>> 000.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
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