3dISC: 1D files

Monira · March 12, 2022, 2:48am

Hello!

I have a potentially obvious question about viewing results from 3dISC.

I ran my subjects (who underwent surface-based analysis) through 3dISC, and the results were in a 1D file format. From what I could find, 1D files are simple text files with numbers. I was wondering if there is any way to view the results/project them on(to) a surface?

I hope I explained that well and I really appreciate any help you can provide.

Thank you!

Monira

ptaylor · March 14, 2022, 5:29pm

Hi-

Can you please share your 3dISC command? Is the output *.1D file output on a standard mesh, say, after running FreeSurfer’s recon-all and @SUMA_Make_Spec_FS?

–pt

Monira · March 15, 2022, 1:23am

Thank you so much for your reply!

Yes, of course.

This is my 3dISC command:

3dISC -prefix ISCSURFlh -jobs 12
-r2z
-model ‘Motion+grp+(1|Subj1)+(1|Subj2)’
-qVars Motion
-gltCode Motion ‘0 1 0 0’
-gltCode G11 ‘1 0 1 0’
-gltCode G12 ‘1 0 0 1’
-gltCode G22 ‘1 0 -1 -1’
-gltCode G11vG22 ‘0 0 2 1’
-gltCode G11vG12 ‘0 0 0 -1’
-gltCode G12vG22 ‘0 0 1 2’
-dataTable @surf.txt > log_surf.txt

This is what part of my table looks like:

Subj1 Subj2 Motion grp InputFile
1089006 1089018 0.1253305 G11 TCorr1089006.1089018.niml.dset
1089006 1089050 0.1009067 G11 TCorr1089006.1089050.niml.dset
1089006 1089066 0.0870002 G11 TCorr1089006.1089066.niml.dset
1089006 1089601 0.10536935 G11 TCorr1089006.1089601.niml.dset
1089006 1089634 0.09412235 G11 TCorr1089006.1089634.niml.dset
1089006 1089680 0.1120105 G11 TCorr1089006.1089680.niml.dset
1089006 1089682 0.120178 G11 TCorr1089006.1089682.niml.dset
1089006 1089685 0.119129 G11 TCorr1089006.1089685.niml.dset
1089006 1089062 0.09126035 G12 TCorr1089006.1089062.niml.dset
1089006 1089087 0.08332125 G12 TCorr1089006.1089087.niml.dset
1089006 1089097 0.08747375 G12 TCorr1089006.1089097.niml.dset
1089006 1089603 0.08613485 G12 TCorr1089006.1089603.niml.dset
1089006 1089604 0.08637945 G12 TCorr1089006.1089604.niml.dset
1089006 1089606 0.09596995 G12 TCorr1089006.1089606.niml.dset
1089006 1089609 0.0836139 G12 TCorr1089006.1089609.niml.dset
1089006 1089633 0.1012745 G12 TCorr1089006.1089633.niml.dset
1089006 1089645 0.09306725 G12 TCorr1089006.1089645.niml.dset
1089006 1089654 0.1047328 G12 TCorr1089006.1089654.niml.dset
1089006 1089669 0.1106133 G12 TCorr1089006.1089669.niml.dset
1089006 1089671 0.09624425 G12 TCorr1089006.1089671.niml.dset
1089006 1089684 0.0895185 G12 TCorr1089006.1089684.niml.dset \

This is what part of the output looks like (when I open it using a text editor):

<AFNI_3D_dataset

self_idcode = “XYZ_h4030g89l1tCc2r8t2QFis”

ni_type = “14*float”

ni_dimen = “198812,1,1”

ni_delta = “1,1,1”

ni_origin = “0,0,0”

ni_axes = “R-L,A-P,I-S”

ni_stat = “none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21)”

>

-0.123013 -0.454147 0.011494 1.07172 0.00448478 0.72294 -0.00440214 -0.55643 0.0158961 1.11764 -0.000625908 -0.130131 0.00888692 0.94121
-0.244991 -0.641665 0.0115402 0.78008 0.0165223 1.74746 0.0246254 2.14462 -0.0130852 -0.680176 0.00104036 0.16615 -0.00810314 -0.629211
-0.194382 -0.786399 -0.0120027 -1.16716 0.00828653 1.63985 0.0107162 1.53187 -0.022719 -1.66433 -0.00595319 -1.202 -0.00242971 -0.271457
-0.412207 -0.577503 0.0795327 2.87082 0.0763674 3.83462 0.0666492 2.91674 0.0128835 0.379281 -0.00218432 -0.204278 0.0097182 0.423253
-0.0550254 -0.212325 0.0105073 0.97452 0.0143703 2.71235 0.00547534 0.746515 0.005032 0.351593 -0.00425265 -0.81896 0.00889497 0.947853
0.063097 0.160802 -0.00658965 -0.432457 0.0228027 2.37518 0.0167762 1.42889 -0.0233658 -1.17429 -0.0118063 -1.81386 0.00602655 0.452989
-0.516918 -1.37069 0.0277571 1.86705 0.0179815 2.05686 0.0152892 1.38252 0.0124679 0.633577 0.00236109 0.357204 0.00269232 0.20581

Thank you so much for your help!

Monira

ptaylor · March 15, 2022, 2:08am

Hi, Monira-

Thanks for sharing that information. From this line in the *.1D file header you shared:


# ni_dimen = "198812,1,1"

… I assume that that is on a std.141.* mesh, too, so I think you should be able to overlay it in the SUMA GUI. The only thing I don’t see is the hemisphere information there (normally, ‘rh’ or ‘lh’ is kept in a surface file name, for ease of remembering which hemi it is from).

Let’s say it was the left hemisphere data. Then you should be able to open SUMA, such as for a subject with subject ID “SUBJ”:


suma -spec std.141.SUBJ_lh.spec -sv SUBJ_SurfVol.nii &

… and then hit Ctrl+s to open the Surface Controller.

→ click on “Load Dset” in the lower left panel.
→ In the new panel, click in the filename “Filter” for selecting dsets to display, at the top.
→ change the file to show “*1D” dsets, like the one you have output.
→ select that from the Files listed there.
… and how does that seem?

–pt

Monira · March 16, 2022, 7:19pm

Thank you so much for all your help! It’s working great!

Also, is there a way to view the different contrasts I added in my ISC model? It seems that I am only able to do that on the subjects who underwent volume-based analysis.

Thank you again! I really appreciate it!

Monira

ptaylor · March 17, 2022, 5:43pm

Yes, if you have multiple volumes in the dataset you are overlaying (the one in color, that you selected from the Load Dset list), then you should be able to go to the "I"ntensity and "T"hreshold items to the right of the colorbar in the Surface Controller to select different items within that dset to display.
I = intensity (basically, the overlaid/displayed volume; determines what color is shown)
T = threshold (the dset for applying thresholding; determines if a node shows color or not)

–pt

Monira · March 21, 2022, 8:49pm

Thank you so much! It worked perfectly.

One last question, SUMA seems to be reading my “t-stat” as type “numeric” (even though they show up under the Ttest(21) column of the results), which is preventing me from changing (or assigning) p- or q-values (the p and q thresholds below the slider show up as “N/A”).

Is there a way around this?

This is what part of the output looks like (when I open it using a text editor):

<AFNI_3D_dataset

self_idcode = “XYZ_h4030g89l1tCc2r8t2QFis”

ni_type = “14*float”

ni_dimen = “198812,1,1”

ni_delta = “1,1,1”

ni_origin = “0,0,0”

ni_axes = “R-L,A-P,I-S”

ni_stat = “none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21);none;Ttest(21)”

>

-0.123013 -0.454147 0.011494 1.07172 0.00448478 0.72294 -0.00440214 -0.55643 0.0158961 1.11764 -0.000625908 -0.130131 0.00888692 0.94121
-0.244991 -0.641665 0.0115402 0.78008 0.0165223 1.74746 0.0246254 2.14462 -0.0130852 -0.680176 0.00104036 0.16615 -0.00810314 -0.629211
-0.194382 -0.786399 -0.0120027 -1.16716 0.00828653 1.63985 0.0107162 1.53187 -0.022719 -1.66433 -0.00595319 -1.202 -0.00242971 -0.271457
-0.412207 -0.577503 0.0795327 2.87082 0.0763674 3.83462 0.0666492 2.91674 0.0128835 0.379281 -0.00218432 -0.204278 0.0097182 0.423253
-0.0550254 -0.212325 0.0105073 0.97452 0.0143703 2.71235 0.00547534 0.746515 0.005032 0.351593 -0.00425265 -0.81896 0.00889497 0.947853
0.063097 0.160802 -0.00658965 -0.432457 0.0228027 2.37518 0.0167762 1.42889 -0.0233658 -1.17429 -0.0118063 -1.81386 0.00602655 0.452989
-0.516918 -1.37069 0.0277571 1.86705 0.0179815 2.05686 0.0152892 1.38252 0.0124679 0.633577 0.00236109 0.357204 0.00269232 0.20581

Thank you so much for your help!

Monira