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help > RE: gPPI Error
Feb 1, 2016 05:02 PM | Andrew Alan - Western University
RE: gPPI Error
Hello Dr McLaren,
Thank you so much for your time, I really appreciate it.
(1) Yes this is what is written on line 369. When I insert:
xY.IC
SPM.xCon(xY.Ic)
size(SPM.xX.xKXs)
size(beta)
I get the following error.
Reference to non-existent field 'IC'.
Error in timeseries_extract (line 366)
Error in PPPI (line 461)
(2) I inserted the line you suggested. I received the following:
VOI has 220 voxels in 2x2x2 space
VOI has 220 voxels in 2x2x2 space. This is in the the same space as the input data and functional mask.
ans =
Columns 1 through 15
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 16 through 30
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 31 through 45
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 46 through 60
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 61 through 75
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 76 through 90
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 91 through 105
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 106 through 120
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 121 through 135
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 136 through 150
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 151 through 165
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 166 through 180
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 181 through 195
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 196 through 210
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 211 through 220
0 0 0 0 0 0 0 0 0 0
Originally posted by Donald McLaren:
Thank you so much for your time, I really appreciate it.
(1) Yes this is what is written on line 369. When I insert:
xY.IC
SPM.xCon(xY.Ic)
size(SPM.xX.xKXs)
size(beta)
I get the following error.
Reference to non-existent field 'IC'.
Error in timeseries_extract (line 366)
Error in PPPI (line 461)
(2) I inserted the line you suggested. I received the following:
VOI has 220 voxels in 2x2x2 space
VOI has 220 voxels in 2x2x2 space. This is in the the same space as the input data and functional mask.
ans =
Columns 1 through 15
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 16 through 30
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 31 through 45
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 46 through 60
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 61 through 75
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 76 through 90
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 91 through 105
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 106 through 120
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 121 through 135
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 136 through 150
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 151 through 165
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 166 through 180
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 181 through 195
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 196 through 210
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Columns 211 through 220
0 0 0 0 0 0 0 0 0 0
Originally posted by Donald McLaren:
(1) This is an odd message that rarely comes up
for this line. I think I've seen it a few times.
Can you verify the line 369 in timeseries_extract is: y=y-spm_FcUtil('Y0',SPM.xCon(xY.Ic),SPM.xX.xKXs,beta);
If this is not the line, can you send me the line?
If this is the line, then the issue is likely xY.Ic. Insert 4 lines above, with the following:
xY.IC
SPM.xCon(xY.Ic)
size(SPM.xX.xKXs)
size(beta)
Then re-run with the output for the subject that failed.
(2) This is the result of having NaN or Inf values in y. At line ~365 and ~373, can you insert the following line:
sum(isnan(y))
This will help to determine if the NaN came in before or after the correction with the omnibus contrast. Then try running it again.
I'm a bit concerned that the VOI size is not the same for these two subjects. How did you generate the VOIs for each subject?
Best,
Donald
Originally posted by Andrew Alan:
Can you verify the line 369 in timeseries_extract is: y=y-spm_FcUtil('Y0',SPM.xCon(xY.Ic),SPM.xX.xKXs,beta);
If this is not the line, can you send me the line?
If this is the line, then the issue is likely xY.Ic. Insert 4 lines above, with the following:
xY.IC
SPM.xCon(xY.Ic)
size(SPM.xX.xKXs)
size(beta)
Then re-run with the output for the subject that failed.
(2) This is the result of having NaN or Inf values in y. At line ~365 and ~373, can you insert the following line:
sum(isnan(y))
This will help to determine if the NaN came in before or after the correction with the omnibus contrast. Then try running it again.
I'm a bit concerned that the VOI size is not the same for these two subjects. How did you generate the VOIs for each subject?
Best,
Donald
Originally posted by Andrew Alan:
Hello Dr. Donald McLaren,
I am having some trouble with an error I received while computing gPPI for two amygdala VOIs.
The right amygdala VOI worked well, using a mask from pickatlas.
However, when I try to compute gPPI for the left amygdala I get the following errors for 2 participants.
1)
Index exceeds matrix dimensions.
Error in timeseries_extract (line 369)
Error in PPPI (line 461)
2)
Error using svd
Input to SVD must not contain NaN or Inf.
Error in timeseries_extract (line 378)
Error in PPPI (line 461)
I checked the mask.mat files created by the first level analysis, and they look the same as those created by other participants in which gPPI was successful.
I also opened the omnibus F -test con-images created by gPPI, and set p=1. There appears to be no missing information that would result from a faulty mask.mat file created in the first level.
When I did an ROI analysis for the amygdala VOI using the omnibus F test, I got a cluster size of 221 with Z=2.71 for the participant I got an error for (another participant I got an error for had a similar cluster size but with a Z=4.21). Then for other participants, which ran properly, the cluster size was 220 with Zs of around 3.71
Any ideas would be much appreciated! Thank you for your time!
I am having some trouble with an error I received while computing gPPI for two amygdala VOIs.
The right amygdala VOI worked well, using a mask from pickatlas.
However, when I try to compute gPPI for the left amygdala I get the following errors for 2 participants.
1)
Index exceeds matrix dimensions.
Error in timeseries_extract (line 369)
Error in PPPI (line 461)
2)
Error using svd
Input to SVD must not contain NaN or Inf.
Error in timeseries_extract (line 378)
Error in PPPI (line 461)
I checked the mask.mat files created by the first level analysis, and they look the same as those created by other participants in which gPPI was successful.
I also opened the omnibus F -test con-images created by gPPI, and set p=1. There appears to be no missing information that would result from a faulty mask.mat file created in the first level.
When I did an ROI analysis for the amygdala VOI using the omnibus F test, I got a cluster size of 221 with Z=2.71 for the participant I got an error for (another participant I got an error for had a similar cluster size but with a Z=4.21). Then for other participants, which ran properly, the cluster size was 220 with Zs of around 3.71
Any ideas would be much appreciated! Thank you for your time!
Threaded View
| Title | Author | Date |
|---|---|---|
| Andrew Alan | Jan 29, 2016 | |
| Donald McLaren | Feb 3, 2016 | |
| Donald McLaren | Feb 3, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Donald McLaren | Feb 1, 2016 | |
| Andrew Alan | Feb 2, 2016 | |
| Andrew Alan | Feb 2, 2016 | |
| Donald McLaren | Feb 2, 2016 | |
| Andrew Alan | Feb 2, 2016 | |
| Andrew Alan | Feb 2, 2016 | |
| Andrew Alan | Feb 1, 2016 | |
| Andrew Alan | Feb 1, 2016 | |