External Email - Use Caution
Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows:
1. I first create the registration file using bbregister with the following command:
bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
2. Here, the goal is to generate the .dat registration file.
3. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards,
Shraddha [cid:3033bc8c-0a28-47a6-aa01-2a43edc2a75b]
Hi Shraddha
Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window
cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Pandey, Shraddha Sent: Thursday, December 26, 2024 7:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
External Email - Use Caution Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows:
1. I first create the registration file using bbregister with the following command:
bash
bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
1. Here, the goal is to generate the .dat registration file. 2. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command: mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards,
Shraddha [cid:image001.png@01DB5842.6C357490]
External Email - Use Caution
Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons:
1. When I overlay lh.white on the original volume, I notice some misregistration (see the figure below). 2. To address this, I applied the transformationvolume.dat file generated from bbregister, which I used to create the surface with mri_vol2surface.
However, the transformed lh.white surface generated using the transformationvolume.dat file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your help. Shraddha
[cid:06aa7968-bdc4-439f-b728-520b3c3d7e3f] [cid:116c6e6b-0817-4830-9d35-60d16324fa97] ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Friday, December 27, 2024 9:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
Hi Shraddha
Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window
cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Pandey, Shraddha Sent: Thursday, December 26, 2024 7:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
External Email - Use Caution
Dear Free Surfer Experts,
I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows:
1. I first create the registration file using bbregister with the following command:
bash
bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
1. Here, the goal is to generate the .dat registration file. 2. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data.
However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates).
I would greatly appreciate any insights into why this might be occurring and how to resolve the issue.
Thank you for your time and assistance!
Regards,
Shraddha
[cid:image001.png@01DB5842.6C357490]
What kind of image is that? FS will only work on T1-weighted. I'm surprised it did that good.
On 1/3/2025 2:12 PM, Pandey, Shraddha wrote:
External Email - Use Caution
Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons:
- When I overlay |lh.white| on the original volume, I notice some misregistration (see the figure below).
- To address this, I applied the |transformationvolume.dat| file generated from |bbregister|, which I used to create the surface with |mri_vol2surface|.
However, the transformed |lh.white| surface generated using the |transformationvolume.dat| file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your help. Shraddha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu *Sent:* Friday, December 27, 2024 9:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
Hi Shraddha
Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window
cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Pandey, Shraddha *Sent:* Thursday, December 26, 2024 7:25 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
* External Email - Use Caution *
Dear Free Surfer Experts,
I am currently working on generating a surface from a volume using the |mri_vol2surf| tool. The process I am following is as follows:
- I first create the registration file using |bbregister| with the following command:
bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
- Here, the goal is to generate the |.dat| registration file.
- Next, I use this |.dat| file in |mri_vol2surf| to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the |bbregister| command is flash data, and the input volume for |mri_vol2surf| is a paramagnetic volume that has been registered with the Flash data.
However, the surface output generated by |mri_vol2surf| contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates).
I would greatly appreciate any insights into why this might be occurring and how to resolve the issue.
Thank you for your time and assistance!
Regards,
Shraddha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi, Thank you for your response. The images in the first figure represent the paramagnetic files (output from the Chi Separation algorithm). The lh.white surface, registered using the transformationvolume.dat file, has been overlaid on the paramagnetic volume (2nd Figure). Thanks, Shraddha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, January 6, 2025 9:12 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1DHHZZqbPVJc8QIPuaS2as282S5cxR3I9uCXilc8nYZZTeKg_UMtwFuZZBr3b9QZNw34NUkoTkQF-Eck-RK6gLvxGjS6UqNVqkXN6kZX0SwMaxUxvIzZuCEfnWyBx2AVwT0qSI3oPvw5REIybFHI_pYRQPWuC1HSDG0kWURuInx7UqczsPAQfck0uR3nkut1hag86RoO6UhTgQVxgORNPs-I0ouUlxdhGJKYW-2eUV6vrpPbwTN8N7PCMysYuhGMTcsMSqCgybEfQTYhFLbl_I0bXKoHk4l_xKguBf4x_hmU3hkvZtocnWldtqUpcAzP6PDlBNh8-JJMpkXt4_Yi3Gw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification What kind of image is that? FS will only work on T1-weighted. I'm surprised it did that good.
On 1/3/2025 2:12 PM, Pandey, Shraddha wrote: External Email - Use Caution Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons:
1. When I overlay lh.white on the original volume, I notice some misregistration (see the figure below). 2. To address this, I applied the transformationvolume.dat file generated from bbregister, which I used to create the surface with mri_vol2surface.
However, the transformed lh.white surface generated using the transformationvolume.dat file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your help. Shraddha
[cid:part1.gZtQI51H.497KNzaK@mgh.harvard.edu] [cid:part2.RUOjCmJR.drhbvDBq@mgh.harvard.edu] ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu Sent: Friday, December 27, 2024 9:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
Hi Shraddha
Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window
cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Pandey, Shraddha Sent: Thursday, December 26, 2024 7:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output
External Email - Use Caution
Dear Free Surfer Experts,
I am currently working on generating a surface from a volume using the mri_vol2surf tool. The process I am following is as follows:
1. I first create the registration file using bbregister with the following command:
bash
bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
1. Here, the goal is to generate the .dat registration file. 2. Next, I use this .dat file in mri_vol2surf to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the bbregister command is flash data, and the input volume for mri_vol2surf is a paramagnetic volume that has been registered with the Flash data.
However, the surface output generated by mri_vol2surf contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates).
I would greatly appreciate any insights into why this might be occurring and how to resolve the issue.
Thank you for your time and assistance!
Regards,
Shraddha
[cid:part3.w07RwhVX.fdRjQF08@mgh.harvard.edu]
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1g2zyXq_tSlOwLy4acAPd3j0rcdMg-fsLeRaQRxk7LYqxTv...
You have to give it a t1-weighted image.
On 1/7/2025 10:31 AM, Pandey, Shraddha wrote:
External Email - Use Caution
Hi, Thank you for your response. The images in the first figure represent the paramagnetic files (output from the Chi Separation algorithm). The |lh.white| surface, registered using the |transformationvolume.dat| file, has been overlaid on the paramagnetic volume (2nd Figure). Thanks, Shraddha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, January 6, 2025 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important https://secure-web.cisco.com/1DHHZZqbPVJc8QIPuaS2as282S5cxR3I9uCXilc8nYZZTeKg_UMtwFuZZBr3b9QZNw34NUkoTkQF-Eck-RK6gLvxGjS6UqNVqkXN6kZX0SwMaxUxvIzZuCEfnWyBx2AVwT0qSI3oPvw5REIybFHI_pYRQPWuC1HSDG0kWURuInx7UqczsPAQfck0uR3nkut1hag86RoO6UhTgQVxgORNPs-I0ouUlxdhGJKYW-2eUV6vrpPbwTN8N7PCMysYuhGMTcsMSqCgybEfQTYhFLbl_I0bXKoHk4l_xKguBf4x_hmU3hkvZtocnWldtqUpcAzP6PDlBNh8-JJMpkXt4_Yi3Gw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
What kind of image is that? FS will only work on T1-weighted. I'm surprised it did that good.
On 1/3/2025 2:12 PM, Pandey, Shraddha wrote:
* External Email - Use Caution * Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons: 1. When I overlay |lh.white| on the original volume, I notice some misregistration (see the figure below). 2. To address this, I applied the |transformationvolume.dat| file generated from |bbregister|, which I used to create the surface with |mri_vol2surface|. However, the transformed |lh.white| surface generated using the |transformationvolume.dat| file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your help. Shraddha ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> *Sent:* Friday, December 27, 2024 9:33 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output Hi Shraddha Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Pandey, Shraddha *Sent:* Thursday, December 26, 2024 7:25 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output * External Email - Use Caution * Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the |mri_vol2surf| tool. The process I am following is as follows: 1. I first create the registration file using |bbregister| with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1 2. Here, the goal is to generate the |.dat| registration file. 3. Next, I use this |.dat| file in |mri_vol2surf| to generate the surface with the following command: mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" The input MRI for the |bbregister| command is flash data, and the input volume for |mri_vol2surf| is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by |mri_vol2surf| contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards, Shraddha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1g2zyXq_tSlOwLy4acAPd3j0rcdMg-fsLeRaQRxk7LYqxTvZnDFgu4g3spmOLv-ooZNxsSh2F2fXiA60pC0BU27LjasPAKRuUFZStIc-9DwHZ8IiSt73p3oGfDUkhlg88EbBnURcYepgPrOxU-RpDPtoddlOLLrzCJgjO2Zge9LXK4aWbTRZO1xaVj3tYbQba6fKqlGquU1814zQ6kG7dEQeChec211qJLpol2up4gpcbUp4ZzRH6PzUrr3b4NoWtPM-I--l7KGmdY0iXvwWLMTcCY8v16DbKTiYqIA3MlSOVTo9Enj2AF3PYv677toMhl6aICA3Pznj1a1NdoIABCw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm not sure what is happening here. First, what is input_volume? Based on your commands, it should be the same as input_mri Second, what thresholds are you using on the overlay? It could be that you just need to reduce the threshold and those gray bits will turn red. Note that this does not necessarily mean it is right (see first concern)
On 12/26/2024 7:25 PM, Pandey, Shraddha wrote:
External Email - Use Caution
Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the |mri_vol2surf| tool. The process I am following is as follows:
I first create the registration file using |bbregister| with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1
Here, the goal is to generate the |.dat| registration file.
Next, I use this |.dat| file in |mri_vol2surf| to generate the surface with the following command:
mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface"
The input MRI for the |bbregister| command is flash data, and the input volume for |mri_vol2surf| is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by |mri_vol2surf| contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards,
Shraddha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce R.,PHD -
Pandey, Shraddha