External Email - Use Caution
Hi
I am reaching out to ask some questions about PetSurfer. I am working with an open access dataset (ADNIDODhttps://secure-web.cisco.com/1CEWzN2wc2OketK1X9ZfAONKbe4S8QwQqJbEzc-uLebpb5iLyurErwDCYU9dEFW55xHYx9mxRJ4s-TL2FlLQIbllPFjbVLzsDC9XaAOLVcJ4BPCYxVvmkzz5WL7fwzqArzCTl7jXbFms57HAQCk9oDJP4GQMaNJVvH81nqovflbZek0w2R3oaUB0mhqThtXW8emd5SLuwtDH-yB4jbuUpPXIGmhqWK4nuHUmS5VDivnVPSbpl_aSskZP9YI7Fci53iSpwXOX2Y1Nyr2El2Z5CzCtcTHkhO9D-2IfdtLGR_36fOtU2NOhKkdimuKm20Kzi1RmvulVh9nVRszjEVAEdDQ/https%3A%2F%2Fadni.loni.usc.edu%2Fupdated-adnidod-datasets-now-available%2F) to analyze neurobiological differences in veterans with a history of TBI. I am hoping to use the PET data (there are the raw dicoms and preprocessed PET data) to segment the choroid plexus using a specific segmentation software.https://secure-web.cisco.com/1UhF7rhtSZAlDXzE9N3KqTGlmagy96emXFw2bQ51_0Eb0Id2KW46vSzKf7ETu9zzm1Gpst_mPycHQcyo6rBIdXvf7z-4eiXpgXXdNvSKMXs83Fn8yIQM0bl4iEqhE9ikLMugZLM74DBsWbuYUr0LMGPF9W4_rPGI2o3obY1rquABvn77UqWu45a9Z8OugwT2Jht8plqvLB8Do-8QSE82Kzh_6w0vAB-9EAE70eLolKeN_CmA5sxKpD3w_HmWp1gudXTjb7_8-vLzLc6wsj7b1mEXdhPccaBPs0N9gH0YdXWjyTo_kDqUkcImT4EYRcUEtUmrRsaw6eI6wkAbDwhPCng/https%3A%2F%2Fgithub.com%2FEhsanTadayon%2Fchoroid-plexus-segmentation I have already done the segmentation on the T1 images, but am hoping to apply the masks to the preprocessed PET images. I was looking at using the “mri_gtmpvc” command to segment the choroid plexus using the mask I already created but was hoping for some guidance.
There are also several options of preprocessed PET data I can chose from, including “co-registered averaged standardized image and voxel” including “co-registered averaged standardized image and voxel with unform resolution” and “co-registered averaged” or “co-registered dynamic”.
If anyone are willing to help or can connect me to someone how might have time to reply or quickly chat, that would be great. I appreciate the support and am looking forward to using PetSurfer.
Hi, sorry for the many months to get back to you. I have just updated the documentation on https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer to indicate how to use your own segmentations. I'm assuming that you have a volume with choroid plexus labeled that you want to merge into the stream. Take a look and see if that does what you want.
On 9/26/2023 2:42 PM, Emma Tinney wrote:
External Email - Use Caution
Hi
I am reaching out to ask some questions about PetSurfer. I am working with an open access dataset (ADNIDOD https://secure-web.cisco.com/1CEWzN2wc2OketK1X9ZfAONKbe4S8QwQqJbEzc-uLebpb5iLyurErwDCYU9dEFW55xHYx9mxRJ4s-TL2FlLQIbllPFjbVLzsDC9XaAOLVcJ4BPCYxVvmkzz5WL7fwzqArzCTl7jXbFms57HAQCk9oDJP4GQMaNJVvH81nqovflbZek0w2R3oaUB0mhqThtXW8emd5SLuwtDH-yB4jbuUpPXIGmhqWK4nuHUmS5VDivnVPSbpl_aSskZP9YI7Fci53iSpwXOX2Y1Nyr2El2Z5CzCtcTHkhO9D-2IfdtLGR_36fOtU2NOhKkdimuKm20Kzi1RmvulVh9nVRszjEVAEdDQ/https%3A%2F%2Fadni.loni.usc.edu%2Fupdated-adnidod-datasets-now-available%2F) to analyze neurobiological differences in veterans with a history of TBI. I am hoping to use the PET data (there are the raw dicoms and preprocessed PET data) to segment the choroid plexus using aspecific segmentation software. https://secure-web.cisco.com/1UhF7rhtSZAlDXzE9N3KqTGlmagy96emXFw2bQ51_0Eb0Id2KW46vSzKf7ETu9zzm1Gpst_mPycHQcyo6rBIdXvf7z-4eiXpgXXdNvSKMXs83Fn8yIQM0bl4iEqhE9ikLMugZLM74DBsWbuYUr0LMGPF9W4_rPGI2o3obY1rquABvn77UqWu45a9Z8OugwT2Jht8plqvLB8Do-8QSE82Kzh_6w0vAB-9EAE70eLolKeN_CmA5sxKpD3w_HmWp1gudXTjb7_8-vLzLc6wsj7b1mEXdhPccaBPs0N9gH0YdXWjyTo_kDqUkcImT4EYRcUEtUmrRsaw6eI6wkAbDwhPCng/https%3A%2F%2Fgithub.com%2FEhsanTadayon%2Fchoroid-plexus-segmentationI have already done the segmentation on the T1 images, but am hoping to apply the masks to the preprocessed PET images. I was looking at using the “mri_gtmpvc” command to segment the choroid plexus using the mask I already created but was hoping for some guidance.
There are also several options of preprocessed PET data I can chose from, including “co-registered averaged standardized image and voxel” including “co-registered averaged standardized image and voxel with unform resolution” and “co-registered averaged” or “co-registered dynamic”.
If anyone are willing to help or can connect me to someone how might have time to reply or quickly chat, that would be great. I appreciate the support and am looking forward to using PetSurfer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Emma Tinney