FAT_MVM no result issue

Hi,

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.

  1. To get data table, I ran

fat_mvm_prep.py -p TEST01 -c all_subj_Cross_Bandpass_3Group.csv
-m ‘Cross_Bandpass_Craddock/*P1_000.netcc’

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?

  1. 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.

Why 3dMVM is not giving any result?

Jung

Hi, Jung-

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.)

–pt

Hi Paul,

Thanks for your response.

In my TEST01_scri.tcsh,


3dMVM -prefix TEST01_MVM
-bsVars “Group+Scanner+Age+Sex+Race+HAMD+YMRS”
-wsVars “ROI”
-qVars “Age,HAMD,YMRS”
-dataTable @TEST01_MVMtbl.txt

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,

3dMVM -prefix TEST03_MVM
-bsVars “Group”
-wsVars “ROI”
-dataTable @TEST02_MVMtbl_5Subj.txt

But still it gave me the empty result.

[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.

Thanks

Jung

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