Re: [Freesurfer] T2pial shrinks pial surface
Thanks Bruce, Doing the bias correct and -odt float fixed the issue. Adding -odt short did not. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 11:46 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface it might, but you will need to make some fixes that are in 6.0 (soon) but not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it resamples it to be in register with the T1. You should change that line to have -odt short or -odt float so that it doesn't saturate at 255, which is what caused the original problem. On Tue, 8 Mar 2016, Chris Adamson wrote: > I see it now. I will try to perform a bias correction on the image prior to > importing and see if that helps. Thanks Bruce. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Tuesday, 8 March 2016 4:23 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] T2pial shrinks pial surface > > Hi Chris > > I took a look, and the problem is that there are big changes in contrast > between occipital and frontal lobes. If we normalize both posterior and > frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray > gets >255. This kind of thing can be caused by a transmit "bias" > field, or by dielectric effects. I'm not sure why this is a problem > with this dataset and not others > > cheers > Bruce > > On Mon, 7 Mar 2016, Chris Adamson wrote: > >> Thanks Bruce. >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris >> Adamson >> Sent: Monday, 7 March 2016 1:54 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] T2pial shrinks pial surface >> >> It is checkT2pial.zip >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Monday, 7 March 2016 1:35 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] T2pial shrinks pial surface >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >> On Mon, 7 Mar >> 2016, Chris Adamson wrote: >> >>> How can I upload it to you? >>> >>> -Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >>> Fischl >>> Sent: Monday, 7 March 2016 1:25 PM >>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] T2pial shrinks pial surface >>> >>> Hi Chris >>> >>> if you upload that dataset I'll try to take a look soon >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 7 Mar 2016, Chris Adamson wrote: >>> >>>> >>>> The T2pial option mostly works beautifully. I have a few cases >>>> where the pial surface just shrinks globally and wraps over the >>>> white surface (see attached). I have checked the T2.mgz and the >>>> registration with the T1 is fine. This happens sometimes in one hemisphere >>>> only. >>>> >>>> Any ideas? >>>> >>>> >>>> >>>> [IMAGE] >>>> >>>> Chris Adamson >>>> Senior Research Officer >>>> Developmental Imaging >>>> Murdoch Childrens Research Institute The Royal Children’s Hospital >>>> Flemington Rd Parkville, Victoria 3052 AUS >>>> T: (03) 9936 6780 >>>> E: chris.adam...@mcri.edu.au >>>> www.mcri.edu.au >>>> >>>> >>>> >>>> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] >>>> >>>> >>>> >>>> This e-mail and any attachments to it (the "Communication") are, >>>> unless otherwise stated, confidential, may contain copyright >>>> material and is for the use only of the intended recipient. If you >>>> receive the Communication in error, please notify the sender >>>> immediately by return e-mail, delete the Communication and the >>>> return e-mai
Re: [Freesurfer] T2pial shrinks pial surface
it might, but you will need to make some fixes that are in 6.0 (soon) but not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it resamples it to be in register with the T1. You should change that line to have -odt short or -odt float so that it doesn't saturate at 255, which is what caused the original problem. On Tue, 8 Mar 2016, Chris Adamson wrote: I see it now. I will try to perform a bias correction on the image prior to importing and see if that helps. Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit "bias" field, or by dielectric effects. I'm not sure why this is a problem with this dataset and not others cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface It is checkT2pial.zip -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [IMAGE] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au www.mcri.edu.au [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email _ _ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _ _ _ _ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. _ _ _ _ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _ _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht
Re: [Freesurfer] T2pial shrinks pial surface
I see it now. I will try to perform a bias correction on the image prior to importing and see if that helps. Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, 8 March 2016 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit "bias" field, or by dielectric effects. I'm not sure why this is a problem with this dataset and not others cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: > Thanks Bruce. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris > Adamson > Sent: Monday, 7 March 2016 1:54 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] T2pial shrinks pial surface > > It is checkT2pial.zip > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, 7 March 2016 1:35 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] T2pial shrinks pial surface > > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > On Mon, 7 Mar > 2016, Chris Adamson wrote: > >> How can I upload it to you? >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Monday, 7 March 2016 1:25 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] T2pial shrinks pial surface >> >> Hi Chris >> >> if you upload that dataset I'll try to take a look soon >> >> cheers >> Bruce >> >> >> On Mon, 7 Mar 2016, Chris Adamson wrote: >> >>> >>> The T2pial option mostly works beautifully. I have a few cases where >>> the pial surface just shrinks globally and wraps over the white >>> surface (see attached). I have checked the T2.mgz and the >>> registration with the T1 is fine. This happens sometimes in one hemisphere >>> only. >>> >>> Any ideas? >>> >>> >>> >>> [IMAGE] >>> >>> Chris Adamson >>> Senior Research Officer >>> Developmental Imaging >>> Murdoch Childrens Research Institute The Royal Children’s Hospital >>> Flemington Rd Parkville, Victoria 3052 AUS >>> T: (03) 9936 6780 >>> E: chris.adam...@mcri.edu.au >>> www.mcri.edu.au >>> >>> >>> >>> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] >>> >>> >>> >>> This e-mail and any attachments to it (the "Communication") are, >>> unless otherwise stated, confidential, may contain copyright >>> material and is for the use only of the intended recipient. If you >>> receive the Communication in error, please notify the sender >>> immediately by return e-mail, delete the Communication and the >>> return e-mail, and do not read, copy, retransmit or otherwise deal >>> with it. Any views expressed in the Communication are those of the >>> individual sender only, unless expressly stated to be those of >>> Murdoch Childrens Research Institute >>> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does >>> not accept liability in connection with the integrity of or errors >>> in the Communication, computer virus, data corruption, interference >>> or delay arising from or in respect of the Communication. >>> >>> >>> >>> P Please consider the environment before printing this email >>> >>> >>> >>> >>> >>> _ _ This email has been scanned by the Symantec Email Security.cloud >>> service. >>> For more information please visit http://www.symanteccloud.com >>> >>> _ >>> _ >>> >>> >> >> ___
Re: [Freesurfer] T2pial shrinks pial surface
Hi Chris I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit "bias" field, or by dielectric effects. I'm not sure why this is a problem with this dataset and not others cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface It is checkT2pial.zip -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [IMAGE] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au www.mcri.edu.au [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email _ _ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _ _ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.har
Re: [Freesurfer] T2pial shrinks pial surface
Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface It is checkT2pial.zip -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: > How can I upload it to you? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, 7 March 2016 1:25 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] T2pial shrinks pial surface > > Hi Chris > > if you upload that dataset I'll try to take a look soon > > cheers > Bruce > > > On Mon, 7 Mar 2016, Chris Adamson wrote: > >> >> The T2pial option mostly works beautifully. I have a few cases where >> the pial surface just shrinks globally and wraps over the white >> surface (see attached). I have checked the T2.mgz and the >> registration with the T1 is fine. This happens sometimes in one hemisphere >> only. >> >> Any ideas? >> >> >> >> [IMAGE] >> >> Chris Adamson >> Senior Research Officer >> Developmental Imaging >> Murdoch Childrens Research Institute >> The Royal Children’s Hospital >> Flemington Rd Parkville, Victoria 3052 AUS >> T: (03) 9936 6780 >> E: chris.adam...@mcri.edu.au >> www.mcri.edu.au >> >> >> >> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] >> >> >> >> This e-mail and any attachments to it (the "Communication") are, >> unless otherwise stated, confidential, may contain copyright material >> and is for the use only of the intended recipient. If you receive the >> Communication in error, please notify the sender immediately by >> return e-mail, delete the Communication and the return e-mail, and do >> not read, copy, retransmit or otherwise deal with it. Any views >> expressed in the Communication are those of the individual sender >> only, unless expressly stated to be those of Murdoch Childrens >> Research Institute >> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does >> not accept liability in connection with the integrity of or errors in >> the Communication, computer virus, data corruption, interference or >> delay arising from or in respect of the Communication. >> >> >> >> P Please consider the environment before printing this email >> >> >> >> >> _ >> _ This email has been scanned by the Symantec Email Security.cloud >> service. >> For more information please visit http://www.symanteccloud.com >> _ >> _ >> >> > > __ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > If you have any questions, please contact MCRI IT Servicedesk for further > assistance. > __ > > __ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > __ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud servi
Re: [Freesurfer] T2pial shrinks pial surface
It is checkT2pial.zip -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:35 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: > How can I upload it to you? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, 7 March 2016 1:25 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] T2pial shrinks pial surface > > Hi Chris > > if you upload that dataset I'll try to take a look soon > > cheers > Bruce > > > On Mon, 7 Mar 2016, Chris Adamson wrote: > >> >> The T2pial option mostly works beautifully. I have a few cases where >> the pial surface just shrinks globally and wraps over the white >> surface (see attached). I have checked the T2.mgz and the >> registration with the T1 is fine. This happens sometimes in one hemisphere >> only. >> >> Any ideas? >> >> >> >> [IMAGE] >> >> Chris Adamson >> Senior Research Officer >> Developmental Imaging >> Murdoch Childrens Research Institute >> The Royal Children’s Hospital >> Flemington Rd Parkville, Victoria 3052 AUS >> T: (03) 9936 6780 >> E: chris.adam...@mcri.edu.au >> www.mcri.edu.au >> >> >> >> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] >> >> >> >> This e-mail and any attachments to it (the "Communication") are, >> unless otherwise stated, confidential, may contain copyright material >> and is for the use only of the intended recipient. If you receive the >> Communication in error, please notify the sender immediately by >> return e-mail, delete the Communication and the return e-mail, and do >> not read, copy, retransmit or otherwise deal with it. Any views >> expressed in the Communication are those of the individual sender >> only, unless expressly stated to be those of Murdoch Childrens >> Research Institute >> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does >> not accept liability in connection with the integrity of or errors in >> the Communication, computer virus, data corruption, interference or >> delay arising from or in respect of the Communication. >> >> >> >> P Please consider the environment before printing this email >> >> >> >> >> _ >> _ This email has been scanned by the Symantec Email Security.cloud >> service. >> For more information please visit http://www.symanteccloud.com >> _ >> _ >> >> > > __ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > If you have any questions, please contact MCRI IT Servicedesk for further > assistance. > __ > > __ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > __ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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] T2pial shrinks pial surface
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [IMAGE] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au www.mcri.edu.au [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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] T2pial shrinks pial surface
How can I upload it to you? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, 7 March 2016 1:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: > > The T2pial option mostly works beautifully. I have a few cases where > the pial surface just shrinks globally and wraps over the white > surface (see attached). I have checked the T2.mgz and the registration > with the T1 is fine. This happens sometimes in one hemisphere only. > > Any ideas? > > > > [IMAGE] > > Chris Adamson > Senior Research Officer > Developmental Imaging > Murdoch Childrens Research Institute > The Royal Children’s Hospital > Flemington Rd Parkville, Victoria 3052 AUS > T: (03) 9936 6780 > E: chris.adam...@mcri.edu.au > www.mcri.edu.au > > > > [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] > > > > This e-mail and any attachments to it (the "Communication") are, > unless otherwise stated, confidential, may contain copyright material > and is for the use only of the intended recipient. If you receive the > Communication in error, please notify the sender immediately by return > e-mail, delete the Communication and the return e-mail, and do not > read, copy, retransmit or otherwise deal with it. Any views expressed > in the Communication are those of the individual sender only, unless > expressly stated to be those of Murdoch Childrens Research Institute > (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does > not accept liability in connection with the integrity of or errors in > the Communication, computer virus, data corruption, interference or > delay arising from or in respect of the Communication. > > > > P Please consider the environment before printing this email > > > > > __ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > __ > > __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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] T2pial shrinks pial surface
Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [IMAGE] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au www.mcri.edu.au [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE] This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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] T2pial shrinks pial surface
5.3.0 stable From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Monday, 7 March 2016 11:50 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Chris Adamson <chris.adam...@mcri.edu.au<mailto:chris.adam...@mcri.edu.au>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, March 6, 2016 at 6:14 PM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] T2pial shrinks pial surface The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [cid:image001.jpg@01D17868.5965F100] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au<mailto:chris.adam...@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> [cid:image002.png@01D17868.5965F100]<https://www.facebook.com/MurdochChildrensResearchInstitute>[cid:image003.png@01D17868.5965F100]<https://twitter.com/MCRI_for_kids>[cid:image004.png@01D17868.5965F100]<http://instagram.com/murdoch_childrens>[cid:image005.png@01D17868.5965F100]<http://www.youtube.com/user/MurdochChildrens/videos>[cid:image006.jpg@01D17868.5965F100]<https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. PPlease consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any questions, please contact MCRI IT Servicedesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _ 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 cont
Re: [Freesurfer] T2pial shrinks pial surface
What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Chris Adamson <chris.adam...@mcri.edu.au> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Sunday, March 6, 2016 at 6:14 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] T2pial shrinks pial surface The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children¹s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adam...@mcri.edu.au www.mcri.edu.au <http://www.mcri.edu.au/> <https://www.facebook.com/MurdochChildrensResearchInstitute> <https://twitter.com/MCRI_for_kids> <http://instagram.com/murdoch_childrens> <http://www.youtube.com/user/MurdochChildrens/videos> <https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. PPlease consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ 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.
