Please help: Error related to 'Realign: Estimate & Reslice'

Submitted by Floating on Sat, 06/04/2016 - 08:51

Dear Expert,

While I was running DPARSF, I ran into this error:

Starting parallel pool (parpool) using the 'local' profile ... Warning: Found 2 pre-existing communicating job(s) created by pool that are running. You can use 'delete(myCluster.Jobs)' to remove all jobs

created with profile local. To create 'myCluster' use 'myCluster = parcluster('local')'.

connected to 2 workers.

Realign Setup:10111 OK

Realign Setup:20312 OK

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 756

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 756

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Running 'Realign: Estimate & Reslice'

Failed 'Realign: Estimate & Reslice'

Attempted to access V.dim(4); index out of bounds because numel(V.dim)=3.

In file "C:\Users\zlin\Documents\MATLAB\marsbar-0.44\spm99\spm_write_vol.m" (???), function "spm_write_vol" at line 22.

In file "C:\Users\zlin\Documents\MATLAB\spm8\spm_reslice.m" (v4179), function "reslice_images" at line 230.

In file "C:\Users\zlin\Documents\MATLAB\spm8\spm_reslice.m" (v4179), function "spm_reslice" at line 122.

In file "C:\Users\zlin\Documents\MATLAB\spm8\config\spm_run_realign_estwrite.m" (v4152), function "spm_run_realign_estwrite" at line 39.

The following modules did not run:

Failed: Realign: Estimate & Reslice

Error using cfg_util (line 835)

Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the

exact #job as displayed in this error message)

------------------

Running job #1

------------------

Error in spm_jobman (line 217)

Error in DPARSFA_run>(parfor body) (line 756)

Error in DPARSFA_run (line 715)

parfor i=1:AutoDataProcessParameter.SubjectNum

Error in DPARSF_run (line 95)

[Error] = DPARSFA_run(Cfg);

Error in DPARSF>pushbuttonRun_Callback (line 1117)

[Error]=DPARSF_run(handles.Cfg);

Error in gui_mainfcn (line 95)

feval(varargin{:});

Error in DPARSF (line 50)

gui_mainfcn(gui_State, varargin{:});

Error while evaluating uicontrol Callback

I used the exact procedure as before but for some reasons it didn't work this time. Any help or suggestion would be greatly appreciated! My matlab version is matlab2014a, using DPARSF 3.1, SPM8.

Thank you very much,

Floating

Re: [RFMRI] Please help:

Hi Floating,

Seems there is something wrong with your data. Are you using 4D NifTI data? Please make sure the data is correct.

Best,

Chao-Gan

On Sat, Jun 4, 2016 at 4:51 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:

[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By Ziyong Lin (Floating)
Dear Expert,

While I was running DPARSF, I ran into this error:

Starting parallel pool (parpool) using the 'local' profile ... Warning: Found 2 pre-existing communicating job(s) created by pool that are running. You can use 'delete(myCluster.Jobs)' to remove all jobs

created with profile local. To create 'myCluster' use 'myCluster = parcluster('local')'.

connected to 2 workers.

Realign Setup:10111 OK

Realign Setup:20312 OK

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 756

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 756

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Running 'Realign: Estimate & Reslice'

Failed 'Realign: Estimate & Reslice'

Attempted to access V.dim(4); index out of bounds because numel(V.dim)=3.

In file "C:\Users\zlin\Documents\MATLAB\marsbar-0.44\spm99\spm_write_vol.m" (???), function "spm_write_vol" at line 22.

In file "C:\Users\zlin\Documents\MATLAB\spm8\spm_reslice.m" (v4179), function "reslice_images" at line 230.

In file "C:\Users\zlin\Documents\MATLAB\spm8\spm_reslice.m" (v4179), function "spm_reslice" at line 122.

In file "C:\Users\zlin\Documents\MATLAB\spm8\config\spm_run_realign_estwrite.m" (v4152), function "spm_run_realign_estwrite" at line 39.

The following modules did not run:

Failed: Realign: Estimate & Reslice

Error using cfg_util (line 835)

Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the

exact #job as displayed in this error message)

------------------

Running job #1

------------------

Error in spm_jobman (line 217)

Error in DPARSFA_run>(parfor body) (line 756)

Error in DPARSFA_run (line 715)

parfor i=1:AutoDataProcessParameter.SubjectNum

Error in DPARSF_run (line 95)

[Error] = DPARSFA_run(Cfg);

Error in DPARSF>pushbuttonRun_Callback (line 1117)

[Error]=DPARSF_run(handles.Cfg);

Error in gui_mainfcn (line 95)

feval(varargin{:});

Error in DPARSF (line 50)

gui_mainfcn(gui_State, varargin{:});

Error while evaluating uicontrol Callback

I used the exact procedure as before but for some reasons it didn't work this time. Any help or suggestion would be greatly appreciated! My matlab version is matlab2014a, using DPARSF 3.1, SPM8.

Thank you very much,

Floating

Online version of this post: http://rfmri.org/content/please-help-error-related-realign-estimate-reslice

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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Mail comment ID: http://rfmri.org/mailcomment/redirect/%3C31.2319.0.1465030293.735910a5a3153f419326524b40632756%40www.rfmri.org%3E

Chao-Gan YAN, Ph.D.

Principal Investigator
Deputy Director, MRI Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China

Initiator

DPABI, DPARSF, PRN and The R-fMRI Network (RFMRI.ORG)

http://rfmri.org/yan

http://scholar.google.com/citations?user=lJQ9B58AAAAJ

Thank you so much for your

Thank you so much for your quick reply! I am extremely grateful.

The data format is img and hdr. I have used the same data before... When I did slice timing, there was another error:

connected to 2 workers.

Removing First 5 Time Points: 10143 OKRemoving First 5 Time Points: 10151 OKRemoving First 5 Time Points: 10152 OK

Removing First 5 Time Points: 10141 OKRemoving First 5 Time Points: 10142 OKRemoving First 5 Time Points: 10153 OK

Slice Timing Setup:10143 OK

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 693

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Slice Timing Setup:10141 OK

Warning: Run spm_jobman('initcfg'); beforehand

> In spm_jobman at 107

In DPARSFA_run>(parfor body) at 693

In parallel_function>make_general_channel/channel_general at 927

In remoteParallelFunction at 38

------------------------------------------------------------------------

Running job #1

------------------------------------------------------------------------

Running 'Slice Timing'

SPM8: spm_slice_timing (v4310) 05:20:59 - 04/06/2016

========================================================================

Your TR is 2.0

Running 'Slice Timing'

SPM8: spm_slice_timing (v4310) 05:20:59 - 04/06/2016

========================================================================

Your TR is 2.0

Failed 'Slice Timing'

Maximum recursion limit of 500 reached. Use set(0,'RecursionLimit',N) to change the limit. Be aware that exceeding your available stack space can crash MATLAB and/or your computer.

In file "C:\Users\zlin\Documents\MATLAB\marsbar-0.44\spm2\spm_create_image.m" (???), function "spm_create_image" at line 0.