External Email - Use Caution
Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias http://www.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias http://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WU...
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-NyVsc6yKaeyRHfki2X4pgHpg4bU9UdbP5m5dAvgtU_FW_...
Uuumm can you please try adding “-odt float” to the command?
Juan Eugenio Iglesias http://www.jeiglesias.com
On Aug 15, 2022, at 18:23, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WUvCSp05LF1S089h0oP4XCQ3hJcM65zQ0DhzpUOWBOjh1ImMeygYvNzIfrDxmcNE8rtljT6FQireC73u3qNT7_7SDo22lqWjYplhx738o8EFMp9Eh1Eysbxhi-IM6TyFuiqgYRF4v0q3mvcvtDY-CoGcquvDQQcrpDjJ4rsQNxqT05OQ-2KOd4ps1PjTDavvaZqV9-HseiCjsawlq63MBMmiTMtypIw-bHsCJ7v7ogTWw2MX82EsmO4ZI_OFZS5o34I084CVKgSvP_9FY-Z/http%3A%2F%2Fwww.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ 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/1-NyVsc6yKaeyRHfki2X4pgHpg4bU9UdbP5m5dAvgtU_FW_xzL4iiLNUK2kLdzwA6SiScaLe7RcB6AlG_0Do1aKgU8MIayFkserQo0_Q1SYJXdzl2JlDBMMaKxFOFTclLS7fOHjGbmHm8JQ7zvcfmhdV7mgH664jPRjI9Laq3XVMXWPm3KCS9CIherQ4z4Jg3kBj2yolXd4GOfOQQPmHl8zpk3CFRrIIU3IbLpgSS8wzvK2ix40NyVEoV5k85UlnN5EQka2HG9U_gHyZFHDaXHuHUB_-PVkIX1pIcYcv3i7eGx4sonkfB56KTavSCGCB2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
That worked - thank you!
If it's not too difficult, could you please tell me what that command does? (I had a quick google but couldn't find anything).
Thanks again!
Elizabeth ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU Sent: 16 August 2022 08:29 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Uuumm can you please try adding “-odt float” to the command?
Juan Eugenio Iglesias http://secure-web.cisco.com/1hsg0Vr58iFvltKBrv6Oysu4B0G7Ps6JoKRX7D1Cvx_xewAd...
On Aug 15, 2022, at 18:23, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1hsg0Vr58iFvltKBrv6Oysu4B0G7Ps6JoKRX7D1Cvx_xewAd...http://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WUvCSp05LF1S089h0oP4XCQ3hJcM65zQ0DhzpUOWBOjh1ImMeygYvNzIfrDxmcNE8rtljT6FQireC73u3qNT7_7SDo22lqWjYplhx738o8EFMp9Eh1Eysbxhi-IM6TyFuiqgYRF4v0q3mvcvtDY-CoGcquvDQQcrpDjJ4rsQNxqT05OQ-2KOd4ps1PjTDavvaZqV9-HseiCjsawlq63MBMmiTMtypIw-bHsCJ7v7ogTWw2MX82EsmO4ZI_OFZS5o34I084CVKgSvP_9FY-Z/http%3A%2F%2Fwww.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ 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://secure-web.cisco.com/1BHD7jYlXk9GAReOyY2LK2FEt3gUHmKGzCz0N1qTU-E6jgN...https://secure-web.cisco.com/1-NyVsc6yKaeyRHfki2X4pgHpg4bU9UdbP5m5dAvgtU_FW_xzL4iiLNUK2kLdzwA6SiScaLe7RcB6AlG_0Do1aKgU8MIayFkserQo0_Q1SYJXdzl2JlDBMMaKxFOFTclLS7fOHjGbmHm8JQ7zvcfmhdV7mgH664jPRjI9Laq3XVMXWPm3KCS9CIherQ4z4Jg3kBj2yolXd4GOfOQQPmHl8zpk3CFRrIIU3IbLpgSS8wzvK2ix40NyVEoV5k85UlnN5EQka2HG9U_gHyZFHDaXHuHUB_-PVkIX1pIcYcv3i7eGx4sonkfB56KTavSCGCB2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1BHD7jYlXk9GAReOyY2LK2FEt3gUHmKGzCz0N1qTU-E6jgN...
It sets the output type to float and avoids rescaling of the intensities ;-)
Juan Eugenio Iglesias http://www.jeiglesias.com
On Aug 15, 2022, at 18:45, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
That worked - thank you!
If it's not too difficult, could you please tell me what that command does? (I had a quick google but couldn't find anything).
Thanks again!
Elizabeth ________________________________ 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 Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Sent: 16 August 2022 08:29 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Uuumm can you please try adding “-odt float” to the command?
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1hsg0Vr58iFvltKBrv6Oysu4B0G7Ps6JoKRX7D1Cvx_xewAdQezAnPPwf6uj5-c-T9uNhLF3tlIHnH2vrU2UOnVxec0P9ydhf-4jkE8zMR32BrlHqoUN6KayNkecYapfoBFaRxUEUWK2stGEiMuSy4-3kK_75KqdnNjI5Q3aeVCWLphuQa2WIDpEAX-lAUUfEAlMNUC7ZMEhZa0ovo8JY-Nm7g7C8ZH2HnOYizgYlcg6EXYmYwWCwlGaueA2b87wWN1JoNWqIIr1TSvbR-e_IeykdFkiku8qcPgYHz1T2qrSFtIF_33bJk6DD-jXN1Olv/http%3A%2F%2Fwww.jeiglesias.com
On Aug 15, 2022, at 18:23, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WUvCSp05LF1S089h0oP4XCQ3hJcM65zQ0DhzpUOWBOjh1ImMeygYvNzIfrDxmcNE8rtljT6FQireC73u3qNT7_7SDo22lqWjYplhx738o8EFMp9Eh1Eysbxhi-IM6TyFuiqgYRF4v0q3mvcvtDY-CoGcquvDQQcrpDjJ4rsQNxqT05OQ-2KOd4ps1PjTDavvaZqV9-HseiCjsawlq63MBMmiTMtypIw-bHsCJ7v7ogTWw2MX82EsmO4ZI_OFZS5o34I084CVKgSvP_9FY-Z/http%3A%2F%2Fwww.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ 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/1-NyVsc6yKaeyRHfki2X4pgHpg4bU9UdbP5m5dAvgtU_FW_xzL4iiLNUK2kLdzwA6SiScaLe7RcB6AlG_0Do1aKgU8MIayFkserQo0_Q1SYJXdzl2JlDBMMaKxFOFTclLS7fOHjGbmHm8JQ7zvcfmhdV7mgH664jPRjI9Laq3XVMXWPm3KCS9CIherQ4z4Jg3kBj2yolXd4GOfOQQPmHl8zpk3CFRrIIU3IbLpgSS8wzvK2ix40NyVEoV5k85UlnN5EQka2HG9U_gHyZFHDaXHuHUB_-PVkIX1pIcYcv3i7eGx4sonkfB56KTavSCGCB2/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/1BHD7jYlXk9GAReOyY2LK2FEt3gUHmKGzCz0N1qTU-E6jgNhrf5dEK1FYxE6buDYaHENqOwZnpxkFDODK872P00WzRRLwPD218pqpHVEw7HWqS1KaakrI41KZQ5VenY6fTQk1JcpUgfUQ25mHAE8X3H0svqGvmaJM9LbMGzkdkwz4oOQ183WTYBv11oYkAjnb9TMuh_Csj8NS-1YbvikxOYYyHOtPeSmfDHw87s9KlxF7u0UvwqPvgWCUlUkt37DnwX_tvlxuJvk0W4eGCWMOexPTaSnmMsnLIIFuiB4-Ti6YWt8nRLm73livPBjUAPZHW7dtrGhdvUlkGXEP0UGeoA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Ahh, great! Thanks so much! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU Sent: 16 August 2022 08:58 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
It sets the output type to float and avoids rescaling of the intensities ;-)
Juan Eugenio Iglesias http://secure-web.cisco.com/1OD75OtZCnN2W1TE_5dfH2jEp2NfOKJKFj6BNkUA-PebzSrI...
On Aug 15, 2022, at 18:45, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
That worked - thank you!
If it's not too difficult, could you please tell me what that command does? (I had a quick google but couldn't find anything).
Thanks again!
Elizabeth ________________________________ 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 Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Sent: 16 August 2022 08:29 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Uuumm can you please try adding “-odt float” to the command?
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1OD75OtZCnN2W1TE_5dfH2jEp2NfOKJKFj6BNkUA-PebzSrI...http://secure-web.cisco.com/1hsg0Vr58iFvltKBrv6Oysu4B0G7Ps6JoKRX7D1Cvx_xewAdQezAnPPwf6uj5-c-T9uNhLF3tlIHnH2vrU2UOnVxec0P9ydhf-4jkE8zMR32BrlHqoUN6KayNkecYapfoBFaRxUEUWK2stGEiMuSy4-3kK_75KqdnNjI5Q3aeVCWLphuQa2WIDpEAX-lAUUfEAlMNUC7ZMEhZa0ovo8JY-Nm7g7C8ZH2HnOYizgYlcg6EXYmYwWCwlGaueA2b87wWN1JoNWqIIr1TSvbR-e_IeykdFkiku8qcPgYHz1T2qrSFtIF_33bJk6DD-jXN1Olv/http%3A%2F%2Fwww.jeiglesias.com
On Aug 15, 2022, at 18:23, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution
Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1OD75OtZCnN2W1TE_5dfH2jEp2NfOKJKFj6BNkUA-PebzSrI...http://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WUvCSp05LF1S089h0oP4XCQ3hJcM65zQ0DhzpUOWBOjh1ImMeygYvNzIfrDxmcNE8rtljT6FQireC73u3qNT7_7SDo22lqWjYplhx738o8EFMp9Eh1Eysbxhi-IM6TyFuiqgYRF4v0q3mvcvtDY-CoGcquvDQQcrpDjJ4rsQNxqT05OQ-2KOd4ps1PjTDavvaZqV9-HseiCjsawlq63MBMmiTMtypIw-bHsCJ7v7ogTWw2MX82EsmO4ZI_OFZS5o34I084CVKgSvP_9FY-Z/http%3A%2F%2Fwww.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
External Email - Use Caution Hi Freesurfer Developers,
I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
Many thanks, Elizabeth _______________________________________________ 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://secure-web.cisco.com/199DF9Q2nXbitH9ORyh9Zm702w1KEdz1rg56WBlPU7HM7gT...https://secure-web.cisco.com/1-NyVsc6yKaeyRHfki2X4pgHpg4bU9UdbP5m5dAvgtU_FW_xzL4iiLNUK2kLdzwA6SiScaLe7RcB6AlG_0Do1aKgU8MIayFkserQo0_Q1SYJXdzl2JlDBMMaKxFOFTclLS7fOHjGbmHm8JQ7zvcfmhdV7mgH664jPRjI9Laq3XVMXWPm3KCS9CIherQ4z4Jg3kBj2yolXd4GOfOQQPmHl8zpk3CFRrIIU3IbLpgSS8wzvK2ix40NyVEoV5k85UlnN5EQka2HG9U_gHyZFHDaXHuHUB_-PVkIX1pIcYcv3i7eGx4sonkfB56KTavSCGCB2/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://secure-web.cisco.com/199DF9Q2nXbitH9ORyh9Zm702w1KEdz1rg56WBlPU7HM7gT...https://secure-web.cisco.com/1BHD7jYlXk9GAReOyY2LK2FEt3gUHmKGzCz0N1qTU-E6jgNhrf5dEK1FYxE6buDYaHENqOwZnpxkFDODK872P00WzRRLwPD218pqpHVEw7HWqS1KaakrI41KZQ5VenY6fTQk1JcpUgfUQ25mHAE8X3H0svqGvmaJM9LbMGzkdkwz4oOQ183WTYBv11oYkAjnb9TMuh_Csj8NS-1YbvikxOYYyHOtPeSmfDHw87s9KlxF7u0UvwqPvgWCUlUkt37DnwX_tvlxuJvk0W4eGCWMOexPTaSnmMsnLIIFuiB4-Ti6YWt8nRLm73livPBjUAPZHW7dtrGhdvUlkGXEP0UGeoA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/199DF9Q2nXbitH9ORyh9Zm702w1KEdz1rg56WBlPU7HM7gT...
freesurfer@nmr.mgh.harvard.edu
-
Elizabeth Haris -
Iglesias Gonzalez, Juan E.