Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
You can run this command to incorporate the T2 image: recon-all -i /path/to/MEMPRAGE -T2 /path/to/T2 -T2pial -s subject_name -all After completing, this will produce ?h.pial which use the T2 image, and ?h.woT2.pial which are the same pial surfaces as recon-all without T2 input. Best, Lee On Tue, 18 Aug 2015, Bruce Fischl wrote: no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or something. Sorry, I don't remember, maybe someone else can fill in the details Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information,
Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or something. Sorry, I don't remember, maybe someone else can fill in the details Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
