External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best, Da-Yea
---------------------------------------------------------------------- Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGl LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTUX nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7BDZ5Vmt5nwPIL5NPyilKyo&e=
---------------------------------------------------------------------- Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGl LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTUX nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7BDZ5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Could you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTU X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7BD Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDGdzOEiotN1YAG72S5Dkhs4&e=
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eTU X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7BD Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDGdzOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMP G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHc X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eT U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDGd zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ-UYG8cFkvREz9KpJNo3sE&e=
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMP G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHc X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5eT U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDGd zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ-UYG8cFkvREz9KpJNo3sE&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
I've taken a look at the mri_annotation2label command and it seems like it requires a specific subject to run this command. We were looking to pull out the ROI from the Desikan atlas (rather than from a particular participant). Is there a way to do that?
Thank you so much in advance, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh. h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYM P G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00 s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhH c X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5e T U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7 B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDG d zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ- UYG8cFkvREz9KpJNo3sE&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=QqRaW9fHGmQuja_Y9aFmcbfqWUXEI3Ek-KZv8p3cxQY&s=OiYIjlp3kCD5gIrSycioJETP0Br-YgNBwkzNwX8QCs4&e=
yes, do it on fsaaverage and it will more-or-less be in the common coordinate space.
cheers Bruce
On Mon, 10 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
I've taken a look at the mri_annotation2label command and it seems like it requires a specific subject to run this command. We were looking to pull out the ROI from the Desikan atlas (rather than from a particular participant). Is there a way to do that?
Thank you so much in advance, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh. h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYM P G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00 s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhH c X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5e T U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7 B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDG d zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ- UYG8cFkvREz9KpJNo3sE&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=QqRaW9fHGmQuja_Y9aFmcbfqWUXEI3Ek-KZv8p3cxQY&s=OiYIjlp3kCD5gIrSycioJETP0Br-YgNBwkzNwX8QCs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
Will the mri_annotation2label work on /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot?
Thanks, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh. h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYM P G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00 s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhH c X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5e T U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7 B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDG d zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ- UYG8cFkvREz9KpJNo3sE&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=QqRaW9fHGmQuja_Y9aFmcbfqWUXEI3Ek-KZv8p3cxQY&s=OiYIjlp3kCD5gIrSycioJETP0Br-YgNBwkzNwX8QCs4&e=
yes, it should On Mon, 10 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
Will the mri_annotation2label work on /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot?
Thanks, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI really appreciate the quick reply back Bruce!
I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot
Any suggestions?
Thank you, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
$FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionCould you please direct me on where I could find the fsaverage annot file for the Desikan atlas?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
yes, use the fsaverage annot file. That is essentially what you want
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionHi Bruce,
We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use?
Thank you, Da-Yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases
Hi Da-yea
what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it
cheers Bruce
On Fri, 7 Dec 2018, Song, Da-Yea wrote:
External Email - Use CautionI tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use?
Thank you so much in advance for your help!
Best, Da-yea
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases
You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use
On 12/04/2018 12:51 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats?
Thank you so much in advance for your time.
Best,
Da-Yea
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh. h a r vard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYM P G l LDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00 s 8 & m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhH c X 5 eTUXnQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = j jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw&s=7LTBome-I69Xsk1RhHcX5e T U X nQrBP5am9WANIUlhe4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.h a r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPG l L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& m = tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs&s=umuIN7eRbxiiTsuM6-vQ7 B D Z5Vmt5nwPIL5NPyilKyo&e=
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha r v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGl L D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m = JkKHKrnIv2DSudDyGuqjHRg5e_zIHekjcgw0eABuRPY&s=TBZ7cORD7agx8omWQdfpDG d zOEiotN1YAG72S5Dkhs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlL D GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m= GVFWQY3GS7YHjbojyZZaJGWo84Myr7kN5xfEDoJPpmU&s=uzpUNHyQF7CMDrmq_8uZXQ- UYG8cFkvREz9KpJNo3sE&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIDAw&c=-6Xp7zzYCOuh1vlHYMPGlLD GrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=QqRaW9fHGmQuja_Y9aFmcbfqWUXEI3Ek-KZv8p3cxQY&s=OiYIjlp3kCD5gIrSycioJETP0Br-YgNBwkzNwX8QCs4&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Song, Da-Yea