Issue about Automask

Submitted by phil1022 on

YAN Chao-Gan

Wed, 04/01/2015 - 15:59

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Hi,

Automask sometimes fail on particular subjects. Have many subjects you have automask process failed? If you can not discard that subject, I will suggest, 1) try use automask in AFNI; 2) skip automask for that particular subject.

Best,

Chao-Gan

phil1022

Wed, 04/01/2015 - 17:09

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Dear Chao-Gan,
    Thank you very much for your rapid reply. I just want to know, is it suitable to skip the automask step? I had processed a bunch of subjects without encountering this problem until I started with another data set. I truly tried that subject by random therefore I do not know the percentage. However, I think he is a good subject that I would prefer not to discard.

    Thanks again for your help.

    Sincerely,
    Xiao-Song

On Wed, Apr 1, 2015 at 11:59 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi,

Automask sometimes fail on particular subjects. Have many subjects you have automask process failed? If you can not discard that subject, I will suggest, 1) try use automask in AFNI; 2) skip automask for that particular subject.

Best,

Chao-Gan


Online version of this post: http://www.rfmri.org/comment/3617#comment-3617


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YAN Chao-Gan

Thu, 04/02/2015 - 01:19

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Hi Xiao-Song,
Skip automask for that subject is OK. Automasks are used to generate group mask. Missing one subject should be OK.

Best,

Chao-Gan

On Wed, Apr 1, 2015 at 1:10 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by Xiaosong He (phil1022)
Dear Chao-Gan,
    Thank you very much for your rapid reply. I just want to know, is it suitable to skip the automask step? I had processed a bunch of subjects without encountering this problem until I started with another data set. I truly tried that subject by random therefore I do not know the percentage. However, I think he is a good subject that I would prefer not to discard.

    Thanks again for your help.

    Sincerely,
    Xiao-Song

On Wed, Apr 1, 2015 at 11:59 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi,

Automask sometimes fail on particular subjects. Have many subjects you have automask process failed? If you can not discard that subject, I will suggest, 1) try use automask in AFNI; 2) skip automask for that particular subject.

Best,

Chao-Gan


Online version of this post: http://www.rfmri.org/comment/3617#comment-3617


Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co
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Online version of this post: http://www.rfmri.org/comment/3619#comment-3619


Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
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phil1022

Thu, 04/02/2015 - 12:59

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Thank you!!!
Bests!

Xiao-Song

On Wed, Apr 1, 2015 at 9:20 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)
Hi Xiao-Song,
Skip automask for that subject is OK. Automasks are used to generate group mask. Missing one subject should be OK.

Best,

Chao-Gan

On Wed, Apr 1, 2015 at 1:10 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by Xiaosong He (phil1022)
Dear Chao-Gan,
    Thank you very much for your rapid reply. I just want to know, is it suitable to skip the automask step? I had processed a bunch of subjects without encountering this problem until I started with another data set. I truly tried that subject by random therefore I do not know the percentage. However, I think he is a good subject that I would prefer not to discard.

    Thanks again for your help.

    Sincerely,
    Xiao-Song

On Wed, Apr 1, 2015 at 11:59 AM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi,

Automask sometimes fail on particular subjects. Have many subjects you have automask process failed? If you can not discard that subject, I will suggest, 1) try use automask in AFNI; 2) skip automask for that particular subject.

Best,

Chao-Gan


Online version of this post: http://www.rfmri.org/comment/3617#comment-3617


Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co
Mail comment ID: http://www.rfmri.org/mailcomment/redirect/%3C31.1993.3617.1427903961.be1b26a76f4a098532548c7369c98c55%40www.rfmri.org%3E


Online version of this post: http://www.rfmri.org/comment/3619#comment-3619


Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co
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Online version of this post: http://www.rfmri.org/comment/3620#comment-3620


Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs
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Dear Chao-Gan, Sorry to bother you. In a particular subject, I have encountered an error during the automask step. The error messages looked like this: Generating AutoMasks begin... Reading images from "/Users/PhilHe/Desktop/MRI_data//fcMRI_temp/FunImgAR/con_01/rafcMRI.nii" etc. Attempted to access Xout(0); index must be a positive integer or logical. Error in w_ClipLevel (line 50) clip=Xout(ncut); Error in w_Automask (line 33) clip_fixed=w_ClipLevel(0.5, MeanAbsVolume); Error in DPARSFA_run>(parfor body) (line 1778) w_Automask(InputDir, OutputFile); Error in parallel_function (line 473) F(base, limit); Error in DPARSFA_run (line 1768) parfor i=1:AutoDataProcessParameter.SubjectNum Error in DPARSFA>pushbuttonRun_Callback (line 1670) [Error]=DPARSFA_run(handles.Cfg); Error in gui_mainfcn (line 96) feval(varargin{:}); Error in DPARSFA (line 30) gui_mainfcn(gui_State, varargin{:}); Error while evaluating uicontrol Callback I checked the 'rafcMRI.nii' which looked normal. I notice that the ncut became 0 when I executed the w_ClipLevel command line by line. I have not idea why because based on the commands, and the values generated previously, it should not be 0. My matlab is 2014a and I am using the up-to-date SPM8 and REST. Thank you very much in advance. Sincerely, Xiaosong He