External Email - Use Caution
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.
[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
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 Caution
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.
image.png
However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs.
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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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?
https://secure-web.cisco.com/1ZYHetRdabKD5Gn8wP94XZVZjn_XX6XdJZKa6bucFiAr21huJro6ox9lac4YlPrc2dVki0RPbYFnmtTvJ3HDwI1dL7ShrdmucVLE9mTbYI6LX7x8TcCRNuaNytDRfeqiw6plsD_MKSadvweG6eAs6om74jc7WOTtlpSiFALlmosv7qOaBYfYCU5DbCeONYsx4R1ri5M4QmxO-jMgHK0NvKJ4rs7UaveiLBPEwulSrmJWN72r3dIUXMtXrMQac8ZiD0OLzWsQsjWN9emiGRaaq932LlGbT-hBj4gfYnrKuBemOxxTMb5Mt4JTl1SldtN3pOww5wPUBAYXp952w4yFPfg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. http://secure-web.cisco.com/1AMwE-LgpKCY2jqJkefJThQ0px8FHL2zvty0vwk2mYRvv9Ns... https://secure-web.cisco.com/1zKfeim9uhnQE2rFbB7CbKtLLqli-two35ZClZ0OU2bheLI8TBNY1hflr1LJfIuyglAHNDe5cbCwqwj8fDacDFzPGmqXzfoQT1_-7kQlDCGjV-a_vpOU0mxmvCgN7JvF6_74a4Erye8qGL3E2KXDhSiXeY1tWo8rHnxHa-tyvzUjv5uQJGXe6_sS1MoBjaUtMhUENQ2A60IYbEXLqFleV85NGiAsXPfKmLk4WyussDpJ5FM1MlbBPyx7aFZNNw0oIGKs9LbJ6hQSM13QEdyk6llzuZLrL30SIMKxPAmQ6-Qq34NTD_hu9g_8YsB9_fqql1ItSC6CnxyaFsiRcIm3ZYg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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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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)?
On 5/31/2022 7:26 PM, Benjamin Deck wrote:
External Email - Use Caution
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.png
However, if I click in a different region, the ROI seems to be non-existent.
image.png Wondering if I am doing something wrong with my mri_concat command?
https://secure-web.cisco.com/1ZYHetRdabKD5Gn8wP94XZVZjn_XX6XdJZKa6bucFiAr21huJro6ox9lac4YlPrc2dVki0RPbYFnmtTvJ3HDwI1dL7ShrdmucVLE9mTbYI6LX7x8TcCRNuaNytDRfeqiw6plsD_MKSadvweG6eAs6om74jc7WOTtlpSiFALlmosv7qOaBYfYCU5DbCeONYsx4R1ri5M4QmxO-jMgHK0NvKJ4rs7UaveiLBPEwulSrmJWN72r3dIUXMtXrMQac8ZiD0OLzWsQsjWN9emiGRaaq932LlGbT-hBj4gfYnrKuBemOxxTMb5Mt4JTl1SldtN3pOww5wPUBAYXp952w4yFPfg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.avast.com https://secure-web.cisco.com/1zKfeim9uhnQE2rFbB7CbKtLLqli-two35ZClZ0OU2bheLI8TBNY1hflr1LJfIuyglAHNDe5cbCwqwj8fDacDFzPGmqXzfoQT1_-7kQlDCGjV-a_vpOU0mxmvCgN7JvF6_74a4Erye8qGL3E2KXDhSiXeY1tWo8rHnxHa-tyvzUjv5uQJGXe6_sS1MoBjaUtMhUENQ2A60IYbEXLqFleV85NGiAsXPfKmLk4WyussDpJ5FM1MlbBPyx7aFZNNw0oIGKs9LbJ6hQSM13QEdyk6llzuZLrL30SIMKxPAmQ6-Qq34NTD_hu9g_8YsB9_fqql1ItSC6CnxyaFsiRcIm3ZYg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink
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 Caution 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. image.png However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs. 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. 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Douglas N. Greve