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Hi there,
Thank you for your response.
I'm not quite sure what you mean in your question. But here is a case where I can click on a region that is associated with an ROI.
[image: image.png]
However, if I click in a different region, the ROI seems to be non-existent.
[image: image.png] Wondering if I am doing something wrong with my mri_concat command?
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On Tue, May 31, 2022 at 6:13 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
when you click on something that should have an ROI, what value do you get?
On 5/30/2022 12:37 PM, Benjamin Deck wrote:
External Email - Use CautionHi freesurfer experts,
I am attempting to create a custom LUT from a parcellation I created.
I have projected the labels into the subject's volume space and then concatenated all of these volumtes together using:
mri_concat --sum --f vols.txt --o sub_vols.mgz
When I visualize these on the subject's t1w the number of ROIs looks approximately correct (n~105). However, my custom LUT seems to be incorrect. Not sure how that is. I used the FreesurferLUT as my template and added new colors and changed names of each row to match my file names (excluding the .mgz).
Here is my custom LUT
0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 5 5 5 5 2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 25 5 25 0 3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 25 100 40 0 4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 70 130 180 0 5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 100 100 0 0 6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 196 58 250 0 7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 100 25 0 0 8 Net_12_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 120 70 50 0 9 Net_13_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 220 20 10 0 10 Net_13_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 220 20 100 0 11 Net_13_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 180 40 120 0 12 Net_13_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 122 186 220 0 13 Net_13_ROIs_3_lh_native_sm6_sm6_dil2_lh_vol 140 20 140 0 14 Net_13_ROIs_3_rh_native_sm6_sm6_dil2_rh_vol 12 48 255 0 15 Net_13_ROIs_4_lh_native_sm6_sm6_dil2_lh_vol 20 30 140 0 ------and it goes on for 105 indices.
here is my list of volumes
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 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_3_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_3_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz -------and so on.
Below I show that you can load each volume onto the brain and pick individual colors.
[image: image.png]
However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs.
[image: image.png]
Any guidance on this odd behavior would be much appreciated.
Thanks, Ben
OS: Windows--WSL2 Ubuntu 18
FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
-- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University*
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