Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer. It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer. It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi!
Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal commands such as tkregister it works , but if I try PETsurfer commands I have errors such as "mri_gtmpvc: Command not found”. Any idea?
Thank you, Ludovica
On Nov 3, 2021, at 10:05, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer. It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here: https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCf...
I'd suggest downloading the newest release which will have the most updated code.
You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+ (gtmseg, mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often recommended for reproducibility sake to use the same version of FS if you can spare the compute time).
On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica < LBRUSAFERRI@mgh.harvard.edu> wrote:
Hi!
Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal commands such as tkregister it works , but if I try PETsurfer commands I have errors such as "mri_gtmpvc: Command not found”. Any idea?
Thank you, Ludovica
On Nov 3, 2021, at 10:05, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://secure-web.cisco.com/1BqgJn5GtD8lBmMhFIdkypD8JUZh4G9z6XnAbXLEtWVfk5a.... It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VG8NHQjMyXjfVA8Q-aZJAk1M3VKcrsLhnr6tz1fijn045v...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VG8NHQjMyXjfVA8Q-aZJAk1M3VKcrsLhnr6tz1fijn045v... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1yXinNOw9p6nBoYxDqYaL5BmR01Tx_cuqA7BLBxWoX22UWc1... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Great!
Thanks SO much.
Kindly, Ludovica
On Nov 3, 2021, at 20:43, Adam Martersteck acmarter@gmail.com wrote:
External Email - Use Caution
PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCft8AUJ0fOq2tnIi9H-neObzRYbNnzQ_f-6Te5NpdO_gdoIcUF7wBpGrIgl62EZEaig2VymVFjCNARkni1wUTJ13czIyMTklgwK4iZYXxPXCi62hXdypysMt1AovGhIBjCBbxwxARFiBo7UK4yxCu_DkX3qIclp985He7UPMP41zXb2euSPBiCtR_UvI2e1n30GWDH8BltpJ7syxjN2U7Gvsjo_ROof_krSJUUDh2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
I'd suggest downloading the newest release which will have the most updated code.
You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+ (gtmseg, mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often recommended for reproducibility sake to use the same version of FS if you can spare the compute time).
On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica <LBRUSAFERRI@mgh.harvard.edumailto:LBRUSAFERRI@mgh.harvard.edu> wrote: Hi!
Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal commands such as tkregister it works , but if I try PETsurfer commands I have errors such as "mri_gtmpvc: Command not found”. Any idea?
Thank you, Ludovica
On Nov 3, 2021, at 10:05, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote: Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurferhttps://secure-web.cisco.com/1BqgJn5GtD8lBmMhFIdkypD8JUZh4G9z6XnAbXLEtWVfk5ajdnK2tMbsx-SPWVIKjr-pvrXHZkfmuy822Z5VxuFrJPxx1uk4mN5QrGBjkWDzSIIb2mqQM8GVyIgapEgf8nTKrJooRayERS_AT_qr18crszq0A-mVtb3-oyYRRpGnUWMHEYJ0c9HDY4jv0xzEi3hUz7v4hsPpfk4MreO51RBUg69F_vA1eLD3NJOnCWDMFQBWsa9ugagsp6DyfQmNDEP2oIcThnq9fsmkqvQt6zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer. It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1VG8NHQjMyXjfVA8Q-aZJAk1M3VKcrsLhnr6tz1fijn045vf7JE7X7VMS57DnqE3RAipSxtQy_nCO4-3KiIgRlEa-ED2_oSVJJsu5wrGWE2gnQn83El9b0LCXKW3DW8rdKFFKdYvBrAU1sHqT_6YJ8eiNKy9JWroqOwKdgdh1pzePIv8UuSeRrj8spCnpFgJHXbGPGvJh9ZT_hE5umA_jNpy1qqvm_V11QS-YxZxnS8QygaqWrrNvO81SbjPWdfv-Hmoshw9nchDgbUphWgp9lQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1VG8NHQjMyXjfVA8Q-aZJAk1M3VKcrsLhnr6tz1fijn045vf7JE7X7VMS57DnqE3RAipSxtQy_nCO4-3KiIgRlEa-ED2_oSVJJsu5wrGWE2gnQn83El9b0LCXKW3DW8rdKFFKdYvBrAU1sHqT_6YJ8eiNKy9JWroqOwKdgdh1pzePIv8UuSeRrj8spCnpFgJHXbGPGvJh9ZT_hE5umA_jNpy1qqvm_V11QS-YxZxnS8QygaqWrrNvO81SbjPWdfv-Hmoshw9nchDgbUphWgp9lQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1VG8NHQjMyXjfVA8Q-aZJAk1M3VKcrsLhnr6tz1fijn045vf7JE7X7VMS57DnqE3RAipSxtQy_nCO4-3KiIgRlEa-ED2_oSVJJsu5wrGWE2gnQn83El9b0LCXKW3DW8rdKFFKdYvBrAU1sHqT_6YJ8eiNKy9JWroqOwKdgdh1pzePIv8UuSeRrj8spCnpFgJHXbGPGvJh9ZT_hE5umA_jNpy1qqvm_V11QS-YxZxnS8QygaqWrrNvO81SbjPWdfv-Hmoshw9nchDgbUphWgp9lQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1yXinNOw9p6nBoYxDqYaL5BmR01Tx_cuqA7BLBxWoX22UWc1cWTnlCXAfv0UQZYGMZKzgwadWUOuUeAI9dS2xoc0aAv1oDRk9TS-eDNQHgv--stgHLGbhs-DQyfZ9MZ_SLUei-h6vX8y5b0d6ba8zPjlq-oeiSuInsHI0nUVAmvCJiU-XqdcAeoFrJNeyW1_8qdB4yP7bEd18MlWkN1SaiMtq_L_rC3v94mvsT3bn-Mc9BERa-oSNHPn8MunQJZ7Fz5o2XedkpslcHv4vsYTbTA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Adam Martersteck -
Brusaferri, Ludovica -
Douglas N. Greve