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Hello,
I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfh... as a guide.
Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt
Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels.
Thank you,
Carlos
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Hi Carlos,
Your commands look correct to calculate mean cortical thickness.
To calculate the total volume, pass lh.volume to –in <>, and specify –accumulate on the command line: https://secure-web.cisco.com/1GYp9YVgT3IIE67jb48sFXaEizpNOJyZRUgKL5vDUwx_U39...
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Thursday, June 15, 2023 11:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Calculate cortical thickness of a volumetric ROI
External Email - Use Caution Hello,
I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1o-JKFzt6ZOjW1TJu1947tOOT6wRYrM8aQyd70edsXmZHxF...https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness as a guide.
Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt
Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels.
Thank you,
Carlos
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Thank you for your response. If I wanted to calculate the surface area of this cortical ROI, would i pass lh.area.pial into <in>? Do i still use --accumulate flag?
Thank you,
Carlos
On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use CautionHi Carlos,
Your commands look correct to calculate mean cortical thickness.
To calculate the total volume, pass lh.volume to –in <>, and specify –accumulate on the command line: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1VurGVMn29VBCV4gEY-1urMHf0Tc2Q5K6l_Q9RtFkHSD4bo... https://secure-web.cisco.com/1GYp9YVgT3IIE67jb48sFXaEizpNOJyZRUgKL5vDUwx_U39xxjrLMFBNhTxtj7sMD3dgS4Fi-KQqcsDOLk6tnscZfUR_d5_jnsH4q5mi8mxDjYdGmFfVO1DWbCEAFdW3FZXJddre4EsMQe72s-ietR9ptbeXYa5yp5WL-1KVIwGGK_F8BHpxojM6BS4lqEhT8Mg2Z_-YJa27XiX1WhmK9jYL1vaM4PQ4Fe8kcDmkB24698-WNPLqid3met5WuTLAWwkKUA6ELeeuG394Gl8yHGA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer *Sent:* Thursday, June 15, 2023 11:36 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Calculate cortical thickness of a volumetric ROI
External Email - Use Caution *Hello,
I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pXTMCre1AsCZTEIbgrEJaknmPI8CmxkcdA4Wms31XfrQ9E... https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness as a guide.
Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject:
- mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1
--interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt
Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels.
Thank you,
Carlos
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kSW-H4eUaW3OtU0i2-CqQmMsu1Q6KUtGyLTepmS1g-CYno... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1GKAiZ6Cdl-ekuAUAfp91WTtjoWhyizezCix7xtuByRLM6C... < https://secure-web.cisco.com/1GKAiZ6Cdl-ekuAUAfp91WTtjoWhyizezCix7xtuByRLM6C... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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yes
On 7/14/2023 4:15 PM, Carlos Alcocer wrote:
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Thank you for your response. If I wanted to calculate the surface area of this cortical ROI, would i pass lh.area.pial into <in>? Do i still use --accumulate flag?
Thank you,
Carlos
On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use Caution Hi Carlos, Your commands look correct to calculate mean cortical thickness. To calculate the total volume, pass lh.volume to –in <>, and specify –accumulate on the command line: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1DDTL1H0F9hIBx5r0aRIx1iSc1JDgwIzAL3-aHeCtTY8ZMZU3i74kY1kzq7c6FZqQfl970EO2R2e5gYJp-aFH_q2VMczUgoG-lZRzFGRne6sQyGEUlncj5g5XzZ1M8zxuaBy9VIzFx_6N4IFWrl2ctqmGM98d8QQhraHC-NE4ZPIaji5oQHxLJ9WoPJeT5Kp8zaxTXb5DBU2C05NvWnWgCziycC0_cLeEXvyGjNxet7U0mA_WgecLccPBVZwSEhuC2D8sEJ2fUndB4avKcTs-qQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats <https://secure-web.cisco.com/1GYp9YVgT3IIE67jb48sFXaEizpNOJyZRUgKL5vDUwx_U39xxjrLMFBNhTxtj7sMD3dgS4Fi-KQqcsDOLk6tnscZfUR_d5_jnsH4q5mi8mxDjYdGmFfVO1DWbCEAFdW3FZXJddre4EsMQe72s-ietR9ptbeXYa5yp5WL-1KVIwGGK_F8BHpxojM6BS4lqEhT8Mg2Z_-YJa27XiX1WhmK9jYL1vaM4PQ4Fe8kcDmkB24698-WNPLqid3met5WuTLAWwkKUA6ELeeuG394Gl8yHGA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats> Best, Yujing *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer *Sent:* Thursday, June 15, 2023 11:36 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Calculate cortical thickness of a volumetric ROI * External Email - Use Caution * Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EB-U2Jx1U7i-BfFjJDhu_Gr2p1WYpjLDWE-cRb1Fqd5BrksD23wewWRUrM6WJBp9WPPM1ClY6SB3inGWq9ofqn4UX-BUy7c62PR9fr8xB_bdW_3LmLiFftxkRNHDMd1qb94rEs3G84oKA7WkT2V2LrvbWapoY0jrq4hoFLs6z4EkJeeEO0gzAtEknb8SRtpUN6sSmNzWI4otkYtA_NlFH6aYDiPLQ8xEhkgRFM4gzBQLPw1TJUv_JQIAZrDB_5Ezw_BvsU8E9Dh7EpqhvmMdkQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness <https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qfhbWsl0xhAi5bYwjQG5MHh7ZBs9ADbhhnZ29DoSVWVVo5AquAm8aIde3IMQMJt9EBOhJ7ZoVI_JUHIYeCdpKAP5_-cZrBLflOE536wS6M31OKaD4bqQsKfG_furvWZ4uDamocw-yUSMKK2QadGa8bUJRw5TZn9pFhy_5xypbEQZ2g25BUdE17bxwUOwwlW1dD_5ekqmwY3sClBqLaWqGJVepW7LfU0bIa2D_8DfcDkx7Bkbp-YS_5h1d5YXXY_pOh7wAebQPQQmZxXhkixsQKQBwYfdv0BEthv-Pp5S9oQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1SFYJBbW8ZHHyZthXxIKPzdTdkxRYttfc0-eIRyYthw81Unb1E3pUXFraFUMSoZwJiiQMA8a34S4MiCUzvAWdW7H-qhGy6D2WZ2Xk14ZGpcqS7ZMQXU9J8vaPgByYe4xhUGY13n9JNRLKK9DpJmE2wt3DRoOkjCbPHlt4ImhFkQTsxgFl8jK0WpqGC1w-uZSyZ82UuPKuQT8d1EEEDZtcGgyiRg23J97vRqhUwINYKLmF2qc-JwY1r9hp9XBsTVIoFPlnAUBm54Tt3YYCeRIx6A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1kSW-H4eUaW3OtU0i2-CqQmMsu1Q6KUtGyLTepmS1g-CYnoiDhc68d-7ZWNcxVinUbc_sNzuRkwSi4H3G2tfr5nEAwIWRDbiuk-GN4tH1XXNLygvNUSHBrboWHffZMR1zSLzJrvYxaW6BDc1jSom8KRkyJ3KrFViMVQo69AI-cNdjgDKO71gY_VnNGDW3JYsUPnC7dCkLd3QOGK77X3EpIkLVeGa0_yH5sjrDYlhcm7BhQg0AIh5_BGf1sigcHlZmbC0r4wFu6K39dR0x4Pj14Tdly6CA4PssRTuz78YYGJnkqVbAdMa5gL40bI8lpvQM/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. 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Huang, Yujing