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Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
* Painted the sulcus of interest on the surface by creating a .label file. * Registered this .label file to fsaverage (mri_label2label) * Converted the .label file to vol (mri_label2vol) * Converted it to a surface file (mri_vol2surf) * Concatenated the data to create an average (mri_concat --mean) * Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (*please see attachment for an example of such surface probability maps*). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
- Painted the sulcus of interest on the surface by creating a .label file.
- Registered this .label file to fsaverage (mri_label2label)
- Converted the .label file to vol (mri_label2vol)
- Converted it to a surface file (mri_vol2surf)
- Concatenated the data to create an average (mri_concat --mean)
- Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes*_: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? _*
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). *_Is there a way to change this to a percentage?_*
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
**
*Kristi Drudik *
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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Hi Kristi
I use mris_spherical_average for this, but I think Doug has something better documented Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Friday, February 19, 2021 11:37 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution
Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* February 19, 2021 10:16 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
* External Email - Use Caution * Good afternoon, I hope this email finds you well. I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (*please see attachment for an example of such surface probability maps*). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I: 1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes*_: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? _* Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). *_Is there a way to change this to a percentage?_* Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi ** *Kristi Drudik * Ph.D. Student, Clinical Psychology Montreal Neurological Institute McGill University Montreal, Canada _______________________________________________ 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/1ubKxTNsCTZVlr84CR43qG2Lz0_CGtXUK_M-Y4erfJWLnfYVDfCSDUXo8IunPh3pQDG6XFHe9lQtFme_fAuRrj0ZW1uWAwijaVi_ubyQg30iZiWg66Q3h14wGQqifIl_jx-_CJB-D58bmrvuheHE9J_6WPQS3ldlhtVcKrFswbBBIEZDhZ1_86txfkjKcL8FFbs3lp0g8t3_B2D8qDmnFu6RSrrITG8qRDxlvkSm43wDYbxmooE0ANh98GxudoQpQWNct0O0C25cOVhpN-78iiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Hi Doug,
That's exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView? On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution Hi Doug,
That's exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best, Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView? On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I'm a bit confused - what flags did you use with this command to create a probability per vertex map?
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 23, 2021 8:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution Hi Doug,
That's exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best, Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView? On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
_______________________________________________
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Sorry, it doesn’t have the greatest help 😊
mris_spherical_average usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output> where which is one of coords label vals curv area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best, Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best, Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView? On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 25, 2021 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output> where which is one of coords label vals curv area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution
External Email - Use Caution Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best, Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best, Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView? On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best, Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution Good afternoon,
I hope this email finds you well. I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi
Kristi Drudik Ph.D. Student, Clinical Psychology
Montreal Neurological Institute McGill University Montreal, Canada
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fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
cheers Bruce
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kristi Drudik kristina.drudik@mail.mcgill.ca Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution
Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 25, 2021 11:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help ??
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
External Email - Use Caution
External Email - Use Caution
Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution
Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 12:14 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
cheers Bruce ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kristi Drudik kristina.drudik@mail.mcgill.ca Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 12:14 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help ??
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 12:28 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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Can you load the label onto that subject also?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution
Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
_______________________________________________
Freesurfer mailing list
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It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 2:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
External Email - Use Caution
Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
External Email - Use Caution
Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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Oh yes, that is your problem. mris_spherical_average assumes they are in subject space
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Friday, February 26, 2021 2:52 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
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 Sent: February 26, 2021 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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My apologies, Bruce, now I’m more confused. We paint the sulci on the native surfaces in Freeview. Then we register them to fsaverage. We want to register them to fsaverage because we are interested in creating an average map that would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
In brief, we can do this by converting the label registered to fsaverage to a volume (mri_label2vol) then to surface (mri_vol2surf) and adding the subjects together with mri_concat.
What I am wondering: Is there a more direct way to create probability per vertex maps using labels that have been registered to fsaverage?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 3:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
Oh yes, that is your problem. mris_spherical_average assumes they are in subject space
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 Kristi Drudik Sent: Friday, February 26, 2021 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
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 Sent: February 26, 2021 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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mris_spherical_average will use the surface-based registration (?h.sphere.reg) to map the labels to whatever your output subject is and do the averaging in that space. You can specify fsaverage by -o fsaverage on the mris_spherical_average command line. You shouldn’t need to do anything other than draw the labels on the natives surface prior to running it
cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Friday, February 26, 2021 4:20 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution My apologies, Bruce, now I’m more confused. We paint the sulci on the native surfaces in Freeview. Then we register them to fsaverage. We want to register them to fsaverage because we are interested in creating an average map that would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
In brief, we can do this by converting the label registered to fsaverage to a volume (mri_label2vol) then to surface (mri_vol2surf) and adding the subjects together with mri_concat.
What I am wondering: Is there a more direct way to create probability per vertex maps using labels that have been registered to fsaverage?
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 Sent: February 26, 2021 3:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Oh yes, that is your problem. mris_spherical_average assumes they are in subject space
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 Kristi Drudik Sent: Friday, February 26, 2021 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
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 Sent: February 26, 2021 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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Hi Bruce,
Thanks to you help I was able to create surface probability maps of the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%) (see attachment).
I have a quick question. Is there a way to represent this average .label file using a heat colour scale (as when you configure an overlay), where the least likely vertices are drawn in blue and the most likely vertices are drawn in red?
Thank you very much for your help!
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 4:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
mris_spherical_average will use the surface-based registration (?h.sphere.reg) to map the labels to whatever your output subject is and do the averaging in that space. You can specify fsaverage by -o fsaverage on the mris_spherical_average command line. You shouldn’t need to do anything other than draw the labels on the natives surface prior to running it
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 Kristi Drudik Sent: Friday, February 26, 2021 4:20 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution My apologies, Bruce, now I’m more confused. We paint the sulci on the native surfaces in Freeview. Then we register them to fsaverage. We want to register them to fsaverage because we are interested in creating an average map that would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
In brief, we can do this by converting the label registered to fsaverage to a volume (mri_label2vol) then to surface (mri_vol2surf) and adding the subjects together with mri_concat.
What I am wondering: Is there a more direct way to create probability per vertex maps using labels that have been registered to fsaverage?
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 Sent: February 26, 2021 3:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Oh yes, that is your problem. mris_spherical_average assumes they are in subject space
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 Kristi Drudik Sent: Friday, February 26, 2021 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
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 Sent: February 26, 2021 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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Yes, if you store the pvals in the label file you can do this in freeview. Ruopeng: can you provide some instructions on this? Thanks Bruce
On May 12, 2021, at 7:28 PM, Kristi Drudik kristina.drudik@mail.mcgill.ca wrote:
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External Email - Use Caution Hi Bruce,
Thanks to you help I was able to create surface probability maps of the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%) (see attachment).
I have a quick question. Is there a way to represent this average .label file using a heat colour scale (as when you configure an overlay), where the least likely vertices are drawn in blue and the most likely vertices are drawn in red?
Thank you very much for your help!
Best, Kristi
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: February 26, 2021 4:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
mris_spherical_average will use the surface-based registration (?h.sphere.reg) to map the labels to whatever your output subject is and do the averaging in that space. You can specify fsaverage by -o fsaverage on the mris_spherical_average command line. You shouldn’t need to do anything other than draw the labels on the natives surface prior to running it
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 Kristi Drudik Sent: Friday, February 26, 2021 4:20 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution My apologies, Bruce, now I’m more confused. We paint the sulci on the native surfaces in Freeview. Then we register them to fsaverage. We want to register them to fsaverage because we are interested in creating an average map that would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
In brief, we can do this by converting the label registered to fsaverage to a volume (mri_label2vol) then to surface (mri_vol2surf) and adding the subjects together with mri_concat.
What I am wondering: Is there a more direct way to create probability per vertex maps using labels that have been registered to fsaverage?
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 Sent: February 26, 2021 3:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Oh yes, that is your problem. mris_spherical_average assumes they are in subject space
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 Kristi Drudik Sent: Friday, February 26, 2021 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution It does not work when I load to the subject (see attachment). I might add that the .label files that I am using originally have already been registered to fsaverage. Does that make a difference?
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 Sent: February 26, 2021 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
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 Kristi Drudik Sent: Friday, February 26, 2021 2:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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External Email - Use Caution Hi Bruce,
I tried the command on one subject. The output does look like the input, however there vertices being picked up that shouldn’t be.
I’m working the Human Connectome Project data so I did not run recon-all myself.
Best, Kristi
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 Sent: February 26, 2021 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
can you send the full screen output as text? Also, try it on 1 subject first. The output should look like the input. Generally this error means some of your surfaces are out of date (that is, you reran recon-all and didn't regenerate everything, like the label files)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 12:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you again for all your help. I managed to get the command running but the output is not adequate at all (please see screenshot). Do you have any advice about where I might be going wrong? Thank you!!
Best,
Kristi
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 Sent: February 26, 2021 12:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label file name in your case). Subject 1 is the FS id of the first subject you want to load (followed by subject 2, ...)
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 Kristi Drudik <kristina.drudik@mail.mcgill.camailto:kristina.drudik@mail.mcgill.ca> Sent: Friday, February 26, 2021 11:02 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! What is the difference between <fname> and <subject1>. I’m having some trouble running this command.
Best,
Kristi
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 Sent: February 25, 2021 11:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help 😊
mris_spherical_average
usage: mris_spherical_average [option] <which> <fname> <hemi> <spherical surf> <subject 1> ... <output>
where which is one of
coords
label
vals
curv
area
so something like
mris_spherical_average label <label file name> lh sphere.reg <subject list> <output label file name>
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 Kristi Drudik Sent: Thursday, February 25, 2021 9:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Bruce,
Thank you for your reply! I have saved the sulcal labels as a .label file. I’m a bit confused – what flags did you use with this command to create a probability per vertex map?
Best,
Kristi
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 Sent: February 23, 2021 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among other things). I assume you saved the sulcal labels to a .label file?
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 Kristi Drudik Sent: Tuesday, February 23, 2021 2:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Sulcal probability maps
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Hi Doug,
That’s exactly what I mean. We are drawing them directly on FreeView by creating a closed path on the white surface and filling it (see attachment for reference).
Best,
Kristi
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 Douglas N. Greve Sent: February 23, 2021 9:02 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:
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Hi Doug,
The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1.
Best,
Kristi
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 Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal probability maps
What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:
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Good afternoon,
I hope this email finds you well.
I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:
1. Painted the sulcus of interest on the surface by creating a .label file. 2. Registered this .label file to fsaverage (mri_label2label) 3. Converted the .label file to vol (mri_label2vol) 4. Converted it to a surface file (mri_vol2surf) 5. Concatenated the data to create an average (mri_concat --mean) 6. Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage?
Thank you very much for your time and help. Please let me know if you have any questions.
Best, Kristi
Kristi Drudik
Ph.D. Student, Clinical Psychology
Montreal Neurological Institute
McGill University
Montreal, Canada
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<LH-pial.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1toBHpxqM-t_QYcnuz5okeiVk_WoiFY8YV9B98fFZtWsheX...
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fischl, Bruce -
Kristi Drudik