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Hi Doug,
Thanks for taking a look.I have attached the LUT and two mgz files.
Ben
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On Tue, Jun 7, 2022 at 1:00 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
yes, send the LUT file
On 6/3/2022 3:03 PM, Benjamin Deck wrote:
External Email - Use CautionHi there,
I created the file via a linux computer by hand. I also checked that there weren't any hidden characters and made sure that the file had spaces instead of tabs like the default LUT file.
again here are my files when I list them:
Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_19_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz
And here is my LUT:
0 unknown 5 5 5 0 1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 25 5 25 0 2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 25 100 40 0 3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 70 130 180 0 4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 100 100 0 0 5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 196 58 250 0 6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 100 25 0 0 7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 120 70 50 0
Could I possibly send you my LUT file? I am really at a loss for what the problem is. Ben
On Fri, Jun 3, 2022 at 1:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
No, there is a problem with your LUT (for the default, there might not be entries for all of your segs which is why you are not seeing them). I don't know what the problem is. Try making it a different way or doing it by hand in linux.
On 6/3/2022 1:20 PM, Benjamin Deck wrote:
External Email - Use CautionResponding re: Douglas Greve
How exactly did you create the LUT? Eg, in windows using notepad? I'm thinking that there might be some hidden characters in there as the color is wrong. I did notice that your first entry had a value of 5 in the last column; usually this is 0 (not sure what it is for). What happens if you switch the LUT to the default? Do you get reasonable colors (even if the names are wrong)?
Reply:
I used a custom python script that creates a LUT for each subject. Then I ran dos2unix to ensure the line endings were appropriate.
If I load the default FS LUT only 2 ROIs are being labeled.
Does this mean that I have an issue with my mri_concat call?
Which is:
mri_concat --sum --f vols.txt --o sub_vols.mgz
Thanks, Ben
-- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University*
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