running 3dMVM without wsVars????

vokuneye · January 17, 2018, 7:52pm

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:

Is there another solution to running 3dMVM without wsVars
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 : 1HC -1None’
-gltLabel 2 HCvMod -gltCode 2 ‘P3Lev : 1HC -1Mod’
-gltLabel 3 HCvSev -gltCode 3 ‘P3Lev : 1HC -1Sev’
-gltLabel 4 NonevMod -gltCode 4 ‘P3Lev : 1None -1Mod’
-gltLabel 5 NonevSev -gltCode 5 ‘P3Lev : 1None -1Sev’
-gltLabel 6 ModvSev -gltCode 6 ‘P3Lev : 1Mod -1Sev’
-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

Gang · January 17, 2018, 9:59pm

Is there another solution to running 3dMVM without wsVars

No, you don’t have to have a within-subject variable to run 3dMVM. In other words, option -wsVars is not required in 3dMVM. What error message did you get when you run the script without -wsVars?

vokuneye · January 17, 2018, 10:58pm

There error I get is : Contrasts set to contr.sum for the following variables: P3Lev

Below is the scripts run…same as above but removing the wsVars line and removing the duplicate subjects/datasets from the DataTable

#./P3.MVM2_BD41R 2>&1 | tee output.P3.MVM2_BD41R
3dMVM_rcc -prefix P3_MVM2_BD41R -jobs 64
-bsVars ‘P3Lev+Age’
-qVars ‘Age’
-qVarCenters ‘38.38’
-num_glt 6
-gltLabel 1 HCvNone -gltCode 1 ‘P3Lev : 1HC -1None’
-gltLabel 2 HCvMod -gltCode 2 ‘P3Lev : 1HC -1Mod’
-gltLabel 3 HCvSev -gltCode 3 ‘P3Lev : 1HC -1Sev’
-gltLabel 4 NonevMod -gltCode 4 ‘P3Lev : 1None -1Mod’
-gltLabel 5 NonevSev -gltCode 5 ‘P3Lev : 1None -1Sev’
-gltLabel 6 ModvSev -gltCode 6 ‘P3Lev : 1Mod -1Sev’
-dataTable @BD41R_DataTable_noWSvar.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
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
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
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
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
119 1.00 HC HC 0 GP CA 41 2 91 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Hartford/FunImgARCWF/S8936WFE5/BD41R_MNI_RScorr_Z+tlrc \

…
9923 1.00 Mod SADP 1 CT CA 46 2 51 2 /project/skeedy/BSNIP1/fromHartford/rest_2/Dallas/FunImgARCWF/20080911_143441_S8320IGX1/BD41R_MNI_RScorr_Z+tlrc

vokuneye · January 17, 2018, 11:19pm

Looking at the other output files…I’m guess alone the line Contrasts set to contr.sum for the following variables: P3Lev does not indicate an error.

In the case of my “no wsVar” error…this line repeats over and over and over instead of beginning the computation, until I typically abort.

Example from unsuccessful output w/out wsVar:
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
Contrasts set to contr.sum for the following variables: P3Lev
…

Example from my successful output with the dummy wsVar:

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

Contrasts set to contr.sum for the following variables: P3Lev
[1] “Great, test run passed at voxel (20, 36, 30)!”
[1] “Start to compute 61 slices along Z axis. You can monitor the progress”
[1] “and estimate the total run time as shown below.”
[1] “01/09/18 13:05:53.060”
[1] “Rmpi and parallel loaded successfully”
[1] “INFO: Using 80 Processors”
80 slaves are spawned successfully. 0 failed.
[1] “INFO: Parallel R Cluster Created”
Z slice 1 done: 01/09/18 13:08:51.815
Z slice 2 done: 01/09/18 13:11:32.152
…

discoraj · January 17, 2018, 11:22pm

Hi,
Does it run without the GLT lines?

thanks, Justin