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:

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Hi 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.

However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs.

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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