Re: [Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-07-20 Thread Douglas N. Greve
   External Email - Use Caution


yes

On 7/14/2023 4:15 PM, Carlos Alcocer wrote:


External Email - Use Caution

Thank you for your response. If I wanted to calculate the surface area 
of this cortical ROI, would i pass lh.area.pial into ? Do i still 
use --accumulate flag?


Thank you,

Carlos

On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing 
 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-boun...@nmr.mgh.harvard.edu
 *On Behalf Of *Carlos Alcocer
*Sent:* Thursday, June 15, 2023 11:36 AM
*To:* Freesurfer support list 
*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

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<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>
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Re: [Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-07-14 Thread Carlos Alcocer
External Email - Use Caution

Thank you for your response. If I wanted to calculate the surface area of
this cortical ROI, would i pass lh.area.pial into ? Do i still use
--accumulate flag?

Thank you,

Carlos

On Thu, Jun 15, 2023 at 5:17 PM Huang, Yujing 
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/1VurGVMn29VBCV4gEY-1urMHf0Tc2Q5K6l_Q9RtFkHSD4boTU7uMNAd9KSB9eY23wb5F5JkZVhaKJ0aehfz-K1kXaPch5YcDhLo5NOKxM_huiMH0dpH5Y2hnfxkP-WVuCU6m7-1MwV0y6qQNmYPwMr3GEaRVIbLjBKZY1ASWWOW-eS7P-SKIOQ4nJY7cm4rE-x8RdyQWmQZQ0GZkq8ZeS8dHvTUWQ7jhT3QK13LbHNncTYLUhxMjeydJBdlBjqGqG8bCjQ-hdGTadf6DXCo6Bn559C9L2HGyX4hX0oSp1WBQiKqRR7g5GiWpdZHJb_-ZB/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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer
> *Sent:* Thursday, June 15, 2023 11:36 AM
> *To:* Freesurfer support list 
> *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/1pXTMCre1AsCZTEIbgrEJaknmPI8CmxkcdA4Wms31XfrQ9ENPg5XK0K7sTORK5BoKjzRhCLOEl7f2o4k5zolqfiJGu4xLzdTBbsb07maqI0XVXkw4LfzMdpk3SGUrc2PWBF9e-LbCA4129qWNpBZNMpoI1267ojoE_RAylNZI1f6HwDLSSFlDZn2-fH02MtRk_Dw9qrx1HguntVrowlahx0zmqnjD8VZO4auFqCeUKkbpvZUE1opoJiGsMq0hcJpokWUHiCJB2FjGjH4k-m_qK6TsRHpfTVQ8Nce43QMsEP9uIE7hVI9G-v4inWZNV0OO/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
>
>
>
>
>
>
> ___
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> 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
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Re: [Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-06-15 Thread Huang, Yujing
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: 
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-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Alcocer
Sent: Thursday, June 15, 2023 11:36 AM
To: Freesurfer support list 
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-JKFzt6ZOjW1TJu1947tOOT6wRYrM8aQyd70edsXmZHxFfSxuL3l1zg5IzyvSdP1JQp_mPCmI8cEpNXq6NaN7IX5-daXLwUILAwXzYdFrX5Ys5YU4uwVHT59dfb-1LvILukycXfPsJ6VUIe0DIW5lrGV9YtqYZC3ng3aZTzx8pYLbTbxYXYTUnvDFmNBtughuA0vLeKTtnoDjzRyW_ZFJ6k8sYvaxpiGdMtftC4YEeY_1ev0l6yMpLrOaK6UGNYAE0JWlzu-oKaDsgxCYp-PQ/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



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[Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-06-15 Thread Carlos Alcocer
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 
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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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 
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 .
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continue to communicate over unencrypted e-mail. 


[Freesurfer] Calculate cortical thickness of a volumetric ROI

2023-06-07 Thread Carlos Alcocer
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 
https://secure-web.cisco.com/1SRB1kl1prYOxcV3133JRM9O5Bj21w9M9aZYfcod7MM5GHwsDfBpkAJGh0Rs610J3N7kmx2WIaftk4KvSgiCc24mytynSAJYbOtgdbThjndntDX62ycHQTnGr8XWqmgIlVYB94HendZy03fCZG5yog4ttjg6kDqoW7EMD3euPhVAH7RWYjLA4o21LgNH2gGJ8OiUAGmi9PDXP978HKFgSGmlgfGg_ZJWDmZ0AywDyaN3_J1mfdwUSoJGMkUKKRrSzZmQSwHFkS0pWWyNllEn3RWBzI56yvVh7FGRHcpVI7U_3QPzsgdfeYX5LRKxg_kwErt-McsKT97BlE8Lj5Yo9xQ/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
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline 
 .
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.