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Hello,
I am Chi-Hyeon, a postdoc at the Martinos Center.
One of my colleagues wants to try to use advance segmentations: brainstem substructures segmentation (https://secure-web.cisco.com/10i08joHQng6yy87_-Iv618kYQPXRW-hpxjKH9kcjO2KOqV...), and limbic segmentation (https://secure-web.cisco.com/1G7Fom1uIgN-gFY6zk_6Hke0zvGSdyKnPlI53oHnUoBSckW...).
Thanks to the instructions, I was able to generate the segmentations but I cannot find the lookup table for the labels for this versions of segmentation. I will need a look-up table to generate binary masks from these segmentations to eventually export PET values from that binary segmentation masks. Please let me know where I could find the labels for these sets of segmentations.
Chi-Hyeon
External Email - Use Caution
For the sclimbic, you can find it in $FREESURFER/models/sclimbic.ctab For the brainstem, the labels are in the main FS table, $FREESURFER/FreeSurferColorLUT.txt I think there are only three labels in the brainstem, so you can load it into freeview to pull out the indices
On 5/22/2023 9:18 AM, Yoo, Chi-Hyeon wrote:
External Email - Use Caution
Hello,
I am Chi-Hyeon, a postdoc at the Martinos Center.
One of my colleagues wants to try to use advance segmentations:brainstem substructures segmentation(*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1UWiwhhMqHQGIdhftZdIRtHjnjeRBMqfoGlnzhRd7aIAZIO... https://secure-web.cisco.com/10i08joHQng6yy87_-Iv618kYQPXRW-hpxjKH9kcjO2KOqVvlM4Qc6B8P72pJrIrntUcBIDuPBxUFDSuywKNrXNNWrbdZrXsSxgWXdoEPhmXB7JwaJrlVx8d_L0LSfOlo9m5jMFn4twQtwfLwsK5oJo934aKdF2khIuQfUlalPoIg-avsUQs3a9TKdsaLFefdCbRaFIhXx10p__FO-768SogKW7klpJdXrGxoFh06FAUb13ze-C_fQi2XwIeDgVatTk8iv7cpT6FFpS0GUg6djw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures), and limbic segmentation(*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ixRmL9K3mai-f5kaHhSzRDv_5vB0T_3iAMndNZwdrDafS9... https://secure-web.cisco.com/1G7Fom1uIgN-gFY6zk_6Hke0zvGSdyKnPlI53oHnUoBSckWK4zMKapZhh9rE4F8g1nZvF3iu0kfPWwr7HWeMhVjuXLtqG9UPfKlrmX3uFCM8wTx9yMP9-pdjEomnWAEulXWCEgdBZo39mNe5NTIyf8qYRiemvlem9Dg8d_5TLp-HaoyHh8Ct5bBnNNLyTPycpN078uE2qtH0pD-UeOlaCiPdVB_3-veu-XPTonlfBXCZHTeOSWvR0Qd1dN46rdpT4MxvXmK_AvWrI4IwwYZvXXQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FScLimbic).
Thanks to the instructions, I was able to generate the segmentations but I cannot find the lookup table for the labels for this versions of segmentation.
I will need a look-up table to generate binary masks from these segmentations to eventually export PET values from that binary segmentation masks.
Please let me know where I could find the labels for these sets of segmentations.
Chi-Hyeon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Gcbi-n1uJFFxeKEcsGXE-c3MEpapn7StLI-DYz_d6I2NCV...
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Yoo, Chi-Hyeon