what's the equivalent for 3dTsmooth for 1D files?

AFNI Message Board
1

Hello,

I was wondering how I can make the same 3dTsmooth -hamming 7 with 1D files…?

for example:

3dTsmooth
-hamming 7
-prefix ${run}_fft_00101_smooth
${run}_fft_00101+tlrc

I would like to perform the same analysis ROI-based with 1D file using as input a file like ${run}_Zscore_wholef_fft_00101.1D

How can I do it?

thanks

Andrea

2

Hi Andrea,

It should work fine on 1D files, except that it will
typically need to transpose them on input, e.g.

3dTsmooth
-hamming 7 \
-prefix ${run}_fft_00101_smooth.1D
${run}_Zscore_wholef_fft_00101.1D'

The trailing ' (which attaches ’ to the
input file name) signals to perform a
transpose upon read.

  • rick
3

Thanks so much Rick,

I'm working on a script for .1D files but I still have some problems with the following steps before the 3dTsmooth

1dcat
{run}_{ROI}_Zscore_wholef_fft.1D'{4..49}' > {run}_{ROI}_Zscore_wholef_fft_00101_cat.1D

here for 1dcat it's not working, AFNI tells me that it can't read {run}_{ROI}_Zscore_wholef_fft.1D do you have any idea on how to solve it?????

3dTsmooth
-hamming 7
-prefix {run}_fft_00101_smooth \ {run}_Zscore_wholef_fft_00101_cat.1D'

1deval -expr 'log(a)'
-a ${run}_fft_00101_smooth.1D \

${run}_fft_log_00101.1D

Thanks so much

Andrea

here just an example of the {run}_{ROI}_Zscore_wholef_fft.1D file
2.38419e-07
0.502789
1.32364
6.11228
8.03104
5.58127
9.56688
3.63077
6.88422
4.56747
2.00472
10.6795
4.45426
7.42745
5.16626
3.63999
7.23981
5.03277
7.85348
8.21632
2.52845
6.38424
2.33118
1.18754
3.06448
2.58301
4.94544
2.47241
1.94483
3.21577
5.06239
2.72484
5.97873
2.93036
2.69855
0.394818
3.97423
4.44977
4.93802
5.4856
0.766626
3.01214
4.64581
3.9289
2.58138
2.35655
6.5292
2.03464
4.37471
7.42455
5.15667
5.09453
4.3846
5.60204
3.8387
2.0363
2.05727
3.21342
5.42977
2.97605
2.08322
1.17347
2.41729
2.3898
2.71716
2.85595
2.73546
3.90572
0.685085
1.80392
1.75101
1.31732
1.93598
4.76443
3.95733
5.14024
3.71706
2.47241
2.14501
1.69829
4.46711
3.91821
0.825044
3.76483
3.44378
1.4594
1.67269
2.78942
2.5832
2.401
0.763827
3.53354
5.51884
4.0849
2.09696
0.522183
2.5577
0.524742
4.23096
3.10874
3.00147
0.333293
3.163
3.48439
2.22506
2.49604
2.12767
4.23324
5.97559
2.59378
1.0844
2.30523
3.17885
0.770797
2.20064
1.70561
4.09368
2.34081
3.39363
2.22444
1.13506
2.03793
0.898973
1.33451
1.07976
0.00035882

4

Hi Andrea,

The command looks good. What does file_tool say about the file?

file_tool -test -infile ${run}_${ROI}_Zscore_wholef_fft.1D

  • rick
5

Hello Rick,

AFNI says: file_tool -test -infile rest_ROI_LPGy38vox_Zscore_whole_fft.1D
rest_ROI_LPGy38vox_Zscore_whole_fft.1D has 0 bad characters

rest_ROI_LPGy38vox_Zscore_whole_fft.1D file type: UNIX

6

Hi Andrea,

That output looks good, which suggests that perhaps when
running the script, the file is not in the directory that you expect
it to be in. Running your 1dcat command on that file with the
posted contents works fine for me.

If it is still not working, would you please post the exact
error message?

Thanks,

  • rick
7

Thanks for your help Rick,

I guess the problem is solved now.