DPARSFA issues (edited)

Submitted by farras on

YAN Chao-Gan

Wed, 04/09/2014 - 23:13

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Please check the slice timing parameters, seems they are not correct -- especially for slice order. "Failed 'Slice Timing' Improper assignment with rectangular empty matrix."

Best,

Chao-Gan

Hi Chao-Gan,
Thank you for responding. I have used the same slice timing parameters in the past with no issues. How do I double check the parameters from the fMRI images? I used the following parameters:
SliceNumber: 33
TR: 2
TA: 1.9394
SliceOrder: [1x33 double]
ReferenceSlice: 33

I have 197 volumes (time points) for each subject. Does the text file usually accompanying a subject's fMRI session have the needed information?

Thanks again.

Thanks!


On Wed, Apr 9, 2014 at 7:13 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)

Please check the slice timing parameters, seems they are not correct -- especially for slice order. "Failed 'Slice Timing' Improper assignment with rectangular empty matrix."

Best,

Chao-Gan


Online version of this post: http://www.rfmri.org/comment/3066#comment-3066


Hi Farras,

What's the Slice Order exactly?  [1:2:33,2:2:32]?

I am suspecting your total slice number is not 33. Could you have a check on your data? You can use MRIcroN to open it, and then click "CTRL + I" and look at the slice information.

Best,

Chao-Gan

Hi Chao-Gan,
You are correct. My number of slices was indeed wrong. From the *.txt file associated with T1 image I found it (39). For slice order I used [1:39] as this seems to be the case from the *.txt file. [1:2:39, 2:2:39] caused problems. The program is running as I type this email.

Thanks.


On Thu, Apr 10, 2014 at 10:49 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 Farras,

What's the Slice Order exactly?  [1:2:33,2:2:32]?

I am suspecting your total slice number is not 33. Could you have a check on your data? You can use MRIcroN to open it, and then click "CTRL + I" and look at the slice information.

Best,

Chao-Gan


Online version of this post: http://rfmri.org/comment/3068#comment-3068


Sorry, the email I sent earlier appears to be posted incomplete. Here's the complete message I got from Matlab:

Warning: Run spm_jobman('initcfg'); beforehand

In spm_jobman at 107 In DPARSFA_run at 393

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

Running job #1 ------------------------------------------------------------------------

Running 'Slice Timing' SPM8: spm_slice_timing (v3756) 17:35:27 - 09/04/2014

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

Your TR is 2.4 Failed 'Slice Timing' Improper assignment with rectangular empty matrix.

In file "/home/faa2016/Documents/MATLAB/myToolboxes/spm8/spm_slice_timing.m" (v3756), function "spm_slice_timing" at line 232. In file "/home/faa2016/Documents/MATLAB/myToolboxes/spm8/config/spm_run_st.m" (v2312), function "spm_run_st" at line 25.

The following modules did not run: Failed: Slice Timing 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 (line 394) Any help will be most appreciated.

-- Farras Abdelnour farras.abdelnour@gmail.com http://sacklerinstitute.academia.edu/FarrasAbdelnour