AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
vokuneye
January 17, 2018 02:52PM
Hello,
I'm having trouble with 3dMVM.
I've found that for my current study - a large analysis of seed based resting state connectivity I am having difficulty running 3dMVM.
My extensive attempts at debugging suggest that the issue was that I didn't have a wsVar *though if you think it may be something else let me know*

As a workaround I put in a dummy wsVariable by copying each subjects dataset twice. This does enable me to get the 3dMVM program to finish running.

I wanted to know if there if:

1. Is there another solution to running 3dMVM without wsVars
2. Is this workaround statistically sound, I am not sure if doubling up on the subjects would artificially inflate df or something else in the statistics of the 3dMVM program.

Below are samples of the scripts.

#./P3.MVM1_BD41R 2>&1 | tee output.P3.MVM1_BD41R
3dMVM_rcc -prefix P3_MVM1_BD41R -jobs 64 \
-bsVars 'P3Lev+Age' \
-wsVars 'wsDummy' \
-qVars 'Age' \
-qVarCenters '38.38' \
-num_glt 6 \
-gltLabel 1 HCvNone -gltCode 1 'P3Lev : 1*HC -1*None' \
-gltLabel 2 HCvMod -gltCode 2 'P3Lev : 1*HC -1*Mod' \
-gltLabel 3 HCvSev -gltCode 3 'P3Lev : 1*HC -1*Sev' \
-gltLabel 4 NonevMod -gltCode 4 'P3Lev : 1*None -1*Mod' \
-gltLabel 5 NonevSev -gltCode 5 'P3Lev : 1*None -1*Sev' \
-gltLabel 6 ModvSev -gltCode 6 'P3Lev : 1*Mod -1*Sev' \
-dataTable @BD41R_DataTable.txt \



Subj wsDummy P3Lev Dx Bio Site Race Age Sex Gaf Hand InputFile \
4 1.00 Mod SADP 3 GP CA 19 1 70 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S5366ACM1/BD41R_MNI_RScorr_Z+tlrc \
4 2.00 Mod SADP 3 GP CA 19 1 70 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S5366ACM1/BD41R_MNI_RScorr_Z+tlrc \
55 1.00 Mod SZP 999 GP CA 21 1 65 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S0092JDO1/BD41R_MNI_RScorr_Z+tlrc \
55 2.00 Mod SZP 999 GP CA 21 1 65 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S0092JDO1/BD41R_MNI_RScorr_Z+tlrc \
86 1.00 HC HC 0 GP AA 46 2 80 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S1122IJG3/BD41R_MNI_RScorr_Z+tlrc \
86 2.00 HC HC 0 GP AA 46 2 80 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S1122IJG3/BD41R_MNI_RScorr_Z+tlrc \
93 1.00 HC HC 0 GP AA 32 2 95 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S4090DGW1/BD41R_MNI_RScorr_Z+tlrc \
93 2.00 HC HC 0 GP AA 32 2 95 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S4090DGW1/BD41R_MNI_RScorr_Z+tlrc \
94 1.00 HC HC 0 GP AA 49 2 90 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S5446BQT8/BD41R_MNI_RScorr_Z+tlrc \
94 2.00 HC HC 0 GP AA 49 2 90 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S5446BQT8/BD41R_MNI_RScorr_Z+tlrc \
......




We have a parallel computing adapted version of 3dMVM we use to run faster installed on our university's high performance computing cluster.


Thanks in advance,
Victoria
Reply Quote
RSS
Subject Author Posted

running 3dMVM without wsVars????

vokuneye January 17, 2018 02:52PM

Re: running 3dMVM without wsVars????

gang January 17, 2018 04:59PM

Re: running 3dMVM without wsVars????

vokuneye January 17, 2018 05:58PM

Re: running 3dMVM without wsVars????

vokuneye January 17, 2018 06:19PM

Re: running 3dMVM without wsVars????

discoraj January 17, 2018 06:22PM