AFNI Message Board

History of AFNI updates  

|
November 16, 2021 05:38AM
>>It seems that the memory crash happened when 3dMVM was trying to save the results to the output file. One easy solution is to break the input files into a few >>chunks. For example, suppose there are 90 slices along the Z-axis, use 3dZcutup to create 3 separate files: one for slices 1-30, one for 31-60, and one for >>61-90. Do this in a loop for all the input files. Then run 3dMVM for each of the three chunks separately. In the end glue them back with 3dZcat.

Thanks good idea! If you mean that it crashes when trying to save the resulting residuals. I do get the output files, but not the output-residuals files.


>>FWIW, there is no such an approach that could be considered "standard". You're trying to draw a rigorous line in the sand, but there are so many factors up >>for debate.

I understand your position here and I agree. And from previous debates I think I got that your approach (which I like) is to report "everything" that is reasonable and interesting and be open about the stats (publish all scores, effect sizes, p-values).

But, AFNI, SPM and FSL are used by researchers who want's to publish. And you want to communicate your results to the journal that you submit to. When using SPM you can check a box and it automatically gives you results that are FWE corrected (usually feels less conservative but that's another discussion). Then you simply write, these results came form SPM, they are FWE corrected/adjusted. And the reviewer will understand this and see the results as "significant". We have to calculate smoothness (or residuals) and run simulations and them look at a cluster table. Then read some papers and documentation to realize that the cluster sizes are only reasonable with p-values below 0.002 (from the FMRI Clustering in AFNI: False Positive Rates Redux paper).

Quote

ACF parameters (which are computed by the standard afni_proc.py pipeline), and a voxelwise p=0.001 or p=0.002 is reasonably safe with this method

So, in order to be able to write that the p-values are adjusted/corrected for multiple-comparison / FWE errors you have to do this. Or the permutaiton-testing in 3dttest++ which in my experience is super conservative). The reviwer want's to know (right or wrong) if the findings are significant.

And don't get me wrong, I love AFNI and it feels so much more honest and in control this way. But I also hope you understand that it is kind of frustrating to not have an "offical way" on how to do these things =).

I just hope reviewers are getting a bit more open minded about what a signficiant finding is.

Thanks again Gang!
Subject Author Posted

3dMVM -residuals error

Robin November 06, 2021 03:05PM

Re: 3dMVM -residuals error

Gang November 08, 2021 03:57PM

Re: 3dMVM -residuals error

Robin November 12, 2021 05:12AM

Re: 3dMVM -residuals error

Gang November 15, 2021 10:09AM

Re: 3dMVM -residuals error

Robin November 16, 2021 05:38AM

Re: 3dMVM -residuals error

Gang November 16, 2021 08:14AM

Re: 3dMVM -residuals error

Robin May 04, 2022 07:39AM

Re: 3dMVM -residuals error

rick reynolds May 04, 2022 10:44AM

Re: 3dMVM -residuals error

Robin May 09, 2022 05:03AM

Re: 3dMVM -residuals error

Gang May 10, 2022 07:46AM

Re: 3dMVM -residuals error

Robin May 17, 2022 09:11AM

Re: 3dMVM -residuals error

Gang May 21, 2022 04:28PM

Re: 3dMVM -residuals error

Robin May 24, 2022 07:56AM

Re: 3dMVM -residuals error

Gang May 25, 2022 11:15AM



Sorry, only registered users may post in this forum.

Click here to login