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pshuk

August 17, 2012 01:47PM

Registered: 11 years ago
Posts: 147

Hi,
My gen_group_command is not outputting the desired output. Can someone please help me out?

I have 2 Grps: ET and CT and two conditions: diff_vis and diff_nv

Now data is in one folder and files are named as SUIT.ET....diff_nv.nii and SUIT.ET....diff_vis.nii and similarly for CT group.

Here is what my script looks like:

----------------------------------------------
#!/usr/bin/env tcsh

# set test and group identifiers
set test = 3dANOVA3
set grp1 = ET
set grp2 = CT
set task = diff

# set data directories
set data_dir = /mnt/Processing1/Priyank/KRISTINA/ANOVA/Anal_data
set anal_dir = /mnt/Processing1/Priyank/KRISTINA/ANOVA/new_Anal

gen_group_command.py -command $test \
-write_script cmd.A3.SUIT.${grp1}_${grp2}.$task \
-prefix $anal_dir/outA3.Typ5.SUIT.${task}.${grp1}-${grp2} \
-dsets $data_dir/SUIT.${grp1}.*.${task}*.nii \
-subs_betas \
"#0" "#0" \
-dsets $data_dir/SUIT.${grp2}.*.${task}*.nii \
-subs_betas \
"#0" "#0" \
-set_labels $grp1 $grp2 \
-options \
-fa Grp_${grp1}_${grp2} \
-fb $task \
-amean 1 ${grp1}_mean \
-amean 2 ${grp2}_mean \
-bmean 1 diff_nv_mean \
-bmean 2 diff_vis_mean \
-fab intr_grp_diff \
-adiff 1 2 ${grp1}_vs_${grp2}

-------------------------------------------------------------------------------------

and here is what it generates:

------------------------------------
#!/bin/tcsh

# apply any data directories with variables
set data1 = /mnt/Processing1/Priyank/KRISTINA/ANOVA/Anal_data

# note: factor A is group, B is condition, C is subject

3dANOVA3 -type 5 \
-alevels 2 \
-blevels 2 \
-clevels 28 \
-dset 1 1 1 "$data1/SUIT.ET.16119.diff_nv.nii[#0]" \
-dset 1 2 1 "$data1/SUIT.ET.16119.diff_nv.nii[#0]" \
-dset 1 1 2 "$data1/SUIT.ET.16119.diff_vis.nii[#0]" \
-dset 1 2 2 "$data1/SUIT.ET.16119.diff_vis.nii[#0]" \
-dset 1 1 3 "$data1/SUIT.ET.18541.diff_nv.nii[#0]" \
-dset 1 2 3 "$data1/SUIT.ET.18541.diff_nv.nii[#0]" \
-dset 1 1 4 "$data1/SUIT.ET.18541.diff_vis.nii[#0]" \
-dset 1 2 4 "$data1/SUIT.ET.18541.diff_vis.nii[#0]" \
-dset 1 1 5 "$data1/SUIT.ET.18817.diff_nv.nii[#0]" \
-dset 1 2 5 "$data1/SUIT.ET.18817.diff_nv.nii[#0]" \
-dset 1 1 6 "$data1/SUIT.ET.18817.diff_vis.nii[#0]" \
-dset 1 2 6 "$data1/SUIT.ET.18817.diff_vis.nii[#0]" \
-dset 1 1 7 "$data1/SUIT.ET.18825.diff_nv.nii[#0]" \
-dset 1 2 7 "$data1/SUIT.ET.18825.diff_nv.nii[#0]" \
-dset 1 1 8 "$data1/SUIT.ET.18825.diff_vis.nii[#0]" \
-dset 1 2 8 "$data1/SUIT.ET.18825.diff_vis.nii[#0]" \
-dset 1 1 9 "$data1/SUIT.ET.19146.diff_nv.nii[#0]" \
-dset 1 2 9 "$data1/SUIT.ET.19146.diff_nv.nii[#0]" \
-dset 1 1 10 "$data1/SUIT.ET.19146.diff_vis.nii[#0]" \
-dset 1 2 10 "$data1/SUIT.ET.19146.diff_vis.nii[#0]" \
-dset 1 1 11 "$data1/SUIT.ET.19223.diff_nv.nii[#0]" \
-dset 1 2 11 "$data1/SUIT.ET.19223.diff_nv.nii[#0]" \
-dset 1 1 12 "$data1/SUIT.ET.19223.diff_vis.nii[#0]" \
-dset 1 2 12 "$data1/SUIT.ET.19223.diff_vis.nii[#0]" \
-dset 1 1 13 "$data1/SUIT.ET.20002.diff_nv.nii[#0]" \
-dset 1 2 13 "$data1/SUIT.ET.20002.diff_nv.nii[#0]" \
-dset 1 1 14 "$data1/SUIT.ET.20002.diff_vis.nii[#0]" \
-dset 1 2 14 "$data1/SUIT.ET.20002.diff_vis.nii[#0]" \
-dset 1 1 15 "$data1/SUIT.ET.20433.diff_nv.nii[#0]" \
-dset 1 2 15 "$data1/SUIT.ET.20433.diff_nv.nii[#0]" \
-dset 1 1 16 "$data1/SUIT.ET.20433.diff_vis.nii[#0]" \
-dset 1 2 16 "$data1/SUIT.ET.20433.diff_vis.nii[#0]" \
-dset 1 1 17 "$data1/SUIT.ET.20725.diff_nv.nii[#0]" \
-dset 1 2 17 "$data1/SUIT.ET.20725.diff_nv.nii[#0]" \
-dset 1 1 18 "$data1/SUIT.ET.20725.diff_vis.nii[#0]" \
-dset 1 2 18 "$data1/SUIT.ET.20725.diff_vis.nii[#0]" \
-dset 1 1 19 "$data1/SUIT.ET.20778.diff_nv.nii[#0]" \
-dset 1 2 19 "$data1/SUIT.ET.20778.diff_nv.nii[#0]" \
-dset 1 1 20 "$data1/SUIT.ET.20778.diff_vis.nii[#0]" \
-dset 1 2 20 "$data1/SUIT.ET.20778.diff_vis.nii[#0]" \
-dset 1 1 21 "$data1/SUIT.ET.20821.diff_nv.nii[#0]" \
-dset 1 2 21 "$data1/SUIT.ET.20821.diff_nv.nii[#0]" \
-dset 1 1 22 "$data1/SUIT.ET.20821.diff_vis.nii[#0]" \
-dset 1 2 22 "$data1/SUIT.ET.20821.diff_vis.nii[#0]" \
-dset 1 1 23 "$data1/SUIT.ET.20988.diff_nv.nii[#0]" \
-dset 1 2 23 "$data1/SUIT.ET.20988.diff_nv.nii[#0]" \
-dset 1 1 24 "$data1/SUIT.ET.20988.diff_vis.nii[#0]" \
-dset 1 2 24 "$data1/SUIT.ET.20988.diff_vis.nii[#0]" \
-dset 1 1 25 "$data1/SUIT.ET.20996.diff_nv.nii[#0]" \
-dset 1 2 25 "$data1/SUIT.ET.20996.diff_nv.nii[#0]" \
-dset 1 1 26 "$data1/SUIT.ET.20996.diff_vis.nii[#0]" \
-dset 1 2 26 "$data1/SUIT.ET.20996.diff_vis.nii[#0]" \
-dset 1 1 27 "$data1/SUIT.ET.21065.diff_nv.nii[#0]" \
-dset 1 2 27 "$data1/SUIT.ET.21065.diff_nv.nii[#0]" \
-dset 1 1 28 "$data1/SUIT.ET.21065.diff_vis.nii[#0]" \
-dset 1 2 28 "$data1/SUIT.ET.21065.diff_vis.nii[#0]" \
-dset 2 1 1 "$data1/SUIT.CT.12203.diff_nv.nii[#0]" \
-dset 2 2 1 "$data1/SUIT.CT.12203.diff_nv.nii[#0]" \
-dset 2 1 2 "$data1/SUIT.CT.12203.diff_vis.nii[#0]" \
-dset 2 2 2 "$data1/SUIT.CT.12203.diff_vis.nii[#0]" \
-dset 2 1 3 "$data1/SUIT.CT.13246.diff_nv.nii[#0]" \
-dset 2 2 3 "$data1/SUIT.CT.13246.diff_nv.nii[#0]" \
-dset 2 1 4 "$data1/SUIT.CT.13246.diff_vis.nii[#0]" \
-dset 2 2 4 "$data1/SUIT.CT.13246.diff_vis.nii[#0]" \
-dset 2 1 5 "$data1/SUIT.CT.13306.diff_nv.nii[#0]" \
-dset 2 2 5 "$data1/SUIT.CT.13306.diff_nv.nii[#0]" \
-dset 2 1 6 "$data1/SUIT.CT.13306.diff_vis.nii[#0]" \
-dset 2 2 6 "$data1/SUIT.CT.13306.diff_vis.nii[#0]" \
-dset 2 1 7 "$data1/SUIT.CT.13493.diff_nv.nii[#0]" \
-dset 2 2 7 "$data1/SUIT.CT.13493.diff_nv.nii[#0]" \
-dset 2 1 8 "$data1/SUIT.CT.13493.diff_vis.nii[#0]" \
-dset 2 2 8 "$data1/SUIT.CT.13493.diff_vis.nii[#0]" \
-dset 2 1 9 "$data1/SUIT.CT.13672.diff_nv.nii[#0]" \
-dset 2 2 9 "$data1/SUIT.CT.13672.diff_nv.nii[#0]" \
-dset 2 1 10 "$data1/SUIT.CT.13672.diff_vis.nii[#0]" \
-dset 2 2 10 "$data1/SUIT.CT.13672.diff_vis.nii[#0]" \
-dset 2 1 11 "$data1/SUIT.CT.16301.diff_nv.nii[#0]" \
-dset 2 2 11 "$data1/SUIT.CT.16301.diff_nv.nii[#0]" \
-dset 2 1 12 "$data1/SUIT.CT.16301.diff_vis.nii[#0]" \
-dset 2 2 12 "$data1/SUIT.CT.16301.diff_vis.nii[#0]" \
-dset 2 1 13 "$data1/SUIT.CT.16343.diff_nv.nii[#0]" \
-dset 2 2 13 "$data1/SUIT.CT.16343.diff_nv.nii[#0]" \
-dset 2 1 14 "$data1/SUIT.CT.16343.diff_vis.nii[#0]" \
-dset 2 2 14 "$data1/SUIT.CT.16343.diff_vis.nii[#0]" \
-dset 2 1 15 "$data1/SUIT.CT.19424.diff_nv.nii[#0]" \
-dset 2 2 15 "$data1/SUIT.CT.19424.diff_nv.nii[#0]" \
-dset 2 1 16 "$data1/SUIT.CT.19424.diff_vis.nii[#0]" \
-dset 2 2 16 "$data1/SUIT.CT.19424.diff_vis.nii[#0]" \
-dset 2 1 17 "$data1/SUIT.CT.19527.diff_nv.nii[#0]" \
-dset 2 2 17 "$data1/SUIT.CT.19527.diff_nv.nii[#0]" \
-dset 2 1 18 "$data1/SUIT.CT.19527.diff_vis.nii[#0]" \
-dset 2 2 18 "$data1/SUIT.CT.19527.diff_vis.nii[#0]" \
-dset 2 1 19 "$data1/SUIT.CT.19874.diff_nv.nii[#0]" \
-dset 2 2 19 "$data1/SUIT.CT.19874.diff_nv.nii[#0]" \
-dset 2 1 20 "$data1/SUIT.CT.19874.diff_vis.nii[#0]" \
-dset 2 2 20 "$data1/SUIT.CT.19874.diff_vis.nii[#0]" \
-dset 2 1 21 "$data1/SUIT.CT.19960.diff_nv.nii[#0]" \
-dset 2 2 21 "$data1/SUIT.CT.19960.diff_nv.nii[#0]" \
-dset 2 1 22 "$data1/SUIT.CT.19960.diff_vis.nii[#0]" \
-dset 2 2 22 "$data1/SUIT.CT.19960.diff_vis.nii[#0]" \
-dset 2 1 23 "$data1/SUIT.CT.20219.diff_nv.nii[#0]" \
-dset 2 2 23 "$data1/SUIT.CT.20219.diff_nv.nii[#0]" \
-dset 2 1 24 "$data1/SUIT.CT.20219.diff_vis.nii[#0]" \
-dset 2 2 24 "$data1/SUIT.CT.20219.diff_vis.nii[#0]" \
-dset 2 1 25 "$data1/SUIT.CT.21087.diff_nv.nii[#0]" \
-dset 2 2 25 "$data1/SUIT.CT.21087.diff_nv.nii[#0]" \
-dset 2 1 26 "$data1/SUIT.CT.21087.diff_vis.nii[#0]" \
-dset 2 2 26 "$data1/SUIT.CT.21087.diff_vis.nii[#0]" \
-dset 2 1 27 "$data1/SUIT.CT.22895.diff_nv.nii[#0]" \
-dset 2 2 27 "$data1/SUIT.CT.22895.diff_nv.nii[#0]" \
-dset 2 1 28 "$data1/SUIT.CT.22895.diff_vis.nii[#0]" \
-dset 2 2 28 "$data1/SUIT.CT.22895.diff_vis.nii[#0]" \
-fa Grp_ET_CT -fb diff -amean 1 ET_mean -amean 2 CT_mean -bmean 1 \
diff_nv_mean -bmean 2 diff_vis_mean -fab intr_grp_diff -adiff 1 2 \
ET_vs_CT \
-bucket \
/mnt/Processing1/Priyank/KRISTINA/ANOVA/new_Anal/outA3.Typ5.SUIT.diff.ET-CT

--------------------------

Now as you can see after dset, each 2 lines have different b values but same file. Can anyone help, please?

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Subject	Author	Posted
gen_group_command help	pshuk	August 17, 2012 01:47PM
Re: gen_group_command help	rick reynolds	August 17, 2012 04:27PM
Re: gen_group_command help	pshuk	August 17, 2012 04:48PM
Re: gen_group_command help	rick reynolds	August 17, 2012 09:28PM
Re: gen_group_command help	pshuk	August 20, 2012 04:05PM
Re: gen_group_command help	pshuk	August 20, 2012 04:39PM
Re: gen_group_command help	Daniel Glen	August 20, 2012 05:52PM
Re: gen_group_command help	pshuk	August 21, 2012 07:53AM
Re: gen_group_command help	pshuk	August 21, 2012 08:22AM
Re: gen_group_command help	rick reynolds	August 21, 2012 09:42AM
Re: gen_group_command help	pshuk	August 21, 2012 09:54AM
Re: gen_group_command help	rick reynolds	August 21, 2012 10:03AM