Re: [Freesurfer] correction for field dishomogeneity
Hi Clelia, I think the reviewer might refer to the -3T flag of recon-all which enables 3T-specific NU intensity correction parameters and usage of a special atlas for Talairach alignment. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von clelia pellicano Gesendet: Freitag, 3. Juli 2015 18:55 An: Freesurfer support list Betreff: Re: [Freesurfer] correction for field dishomogeneity I did it. Thank you very much. C Il giorno 03/lug/2015 18:51, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu ha scritto: not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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] correction for field dishomogeneity
Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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] correction for field dishomogeneity
Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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 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] correction for field dishomogeneity
I did it. Thank you very much. C Il giorno 03/lug/2015 18:51, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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] correction for field dishomogeneity
not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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] correction for field dishomogeneity
Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MD PhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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.
