I am running FAT_MVM to see main effect of group with Functional connectivity(FC) matrix.
Each subject has a 195*195 size FC matrix, and I try to do group analysis with 180 subject.
I have followed FAT_MVM demo and apply this same way to my analysis.
and it took 12 hours to get data table. I assume that the reason why it took huge amount time only to make the data table is 195 ROIs and 180 subject. Is this right?
Once I get the data table, I ran
fat_mvm_scripter.py --vars=‘Group Scanner Age Sex Race HAMD YMRS’
–log_file=TEST01_MVMprep.log
–table=TEST01_MVMtbl.txt
–prefix=TEST01
and I got TEST01_scri.tcsh. And finally I ran
tcsh TEST01_scri.tcsh
But any result is not provided with the following messages
[b]***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now…
Congratulations! The above results are saved in file TEST02_MVM.txt[/b]
There is no result between line “Reading input files now…” and line “Congratulations! The above results are saved in file TEST02_MVM.txt[” and also TEST02_MVM.txt has nothing and file size is zero byte.
For #1: I believe yes, the size of group and matrices are combining to make a large data table. You can see how many bytes it takes up with “ls -l …” on the file name. 12 hours does surprise me a little bit, though.
For #2: I am not certain. My first thought would be that 3dMVM is running out of memory on your computer, but then there would have been a “killed” message in the terminal, I should think.
To test this out, if you run the fat_mvm* commands with just 5 subjects, say, does that still happen? (Just picking a very small group size, so that we can see whether it is the data, which I doubt, or a memory/size of model issue, which I still suspect.)
I have removed ‘glt’ parts to reduce computation cost, but still same empty result has shown.
As your suggestion, I tried to reduce the subject number to just 5 subjects and run it again. But still same empty result.
Also I tried remove covariates as followings,
[b]***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now…
Congratulations! The above results are saved in file TEST03_MVM.txt[/b]
Finally, I tried to reduce ROI number to only one ROI (ROI_001-ROI_002, ROI_001-ROI_003,…, ROI_001-ROI_200) on every 5 subjects with having covariates back,
But still it is giving empty result.
Is this some kinds of version issue? I tried to do above processing on both python 2.7.16 and 3.7.3.
I’m not sure what would be the problem. Python 2.7 is good.
I’ll send you instructions for uploading the 5 subject (but not just single ROI) case, and take a look.
–pt
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.