I want to insert a label table in the final connectivity matrix.
I generated the connectivity matrices and I am using the DKT parcellation files generated from freesurfer for the in_rois in 3dNetCorr script using the following command:
Hi Paul,
I made the label table with ROIs and the 3dNetCorr. Can you please let me know why the arrangement of labels in the output file is not correct. it should look like this for correct plotting with fat_mat_sel.py
However, my output files are generated in this form and I have to rearrange the labels manually for each file. Can you please let me know where I am making a mistake?
Yes, I did they way to told me. I used the following command to make a table. @MakeLabelTable -lab_file …/DKT.txt 1 0 -labeltable sub.niml.lt -dset DKT_resample+orig
then pass it to 3dNetCorr as
3dNetCorr -prefix netcorr -mask mask_GM_resam+orig.BRIK -ts_out -fish_z -inset errts_DKT_fs+orig -in_rois DKT_resample+orig -output_mask_nonnull -push_thru_many_zeros -ts_wb_corr -ts_wb_strlabel sub.niml.lt
I tried your commands on dsets here, and the output *netcc files looked fine.
I don’t you if perhaps there is a bad character in that D*txt file? You can check with:
file_tool -show_bad_all -infiles DKT.txt
Sidenote: this should not be included in the 3dNetCorr command:
sub.niml.lt
That option does not take an argument:
-ts_wb_strlabel :by default, '-ts_wb_{corr,Z}' output files are named
using the int number of a given ROI, such as:
WB_Z_ROI_001+orig.
with this option, one can replace the int (such as
'001') with the string label (such as 'L-thalamus')
*if* one has a labeltable attached to the file.
I don’t see that affecting the 3dNetCorr stuff, though.
what do you get? Just the first ~10 lines or so would be good enough to see what is happening-- mainly, does the label in the second column of output look reasonable, or does it have some kind of newline character or something in it?
In the test I did running similar commands to yours on my computer, the top of the output looked like:
… but the aforementioned “file_tool” usage seems to have solved the issue.
–pt
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