Re: [Freesurfer] Major problems with T2-based pial removal
Hi, quick question I'm just going to rerun these without the -T2 stuff for now so I can get going on analysis. What stages of recon-all do I have to run to fix everything the -T2pial mishap broke? The process flow tables on the website seem a bit out of date. mw On Sat, Sep 28, 2013 at 3:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: hmmm, maybe Nick or Doug can investigate, although we are crazy busy at the moment On Sat, 28 Sep 2013, Michael Waskom wrote: On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm. That would be strange and would result in complete failure I agree, but $ grep bbregister recon_log_withT2.txt $ grep fslregister recon_log_withT2.txt both turn up empty 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/**compliancelinehttp://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] Major problems with T2-based pial removal
hmmm. That would be strange and would result in complete failure (which I guess is what you have seen). For what it's worth, Matt is right and we haven't tested the code on many datasets, but at least so far it has been independent of contrast (that is, it works on both T2 and FLAIR) cheers Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hmm, Ok. Thanks Matt. I still think it's weird that the T2 didn't seem to ever get registered to the FS volume, but it's not a huge loss if we can't use them. With that said, it might help to clarify the docs on this point a bit, as it sort of sounded like any reasonably-sized T2-weighted image would be useful, and I would have tried to collect a different image if I had known! On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote: So the T2-SPACE is a variable flip angle sequence that actually has a fair amount of T1 and MT contrast in it and relatively less T2 contrast. As a result, you can clearly see the difference between grey and white matter, and CSF is not massively brighter than grey and white matter. If you are using a different kind of T2w sequence where the distance between CSF intensity and grey matter intensity is much greater, some of the internal settings to the -T2pial flag will likely not be optimal. I don't know if recon-all allows you to modify those with expert options or not. Bruce, is it possible for the user to modify the –nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic
Re: [Freesurfer] Major problems with T2-based pial removal
On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: hmmm. That would be strange and would result in complete failure I agree, but $ grep bbregister recon_log_withT2.txt $ grep fslregister recon_log_withT2.txt both turn up empty ___ 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] Major problems with T2-based pial removal
hmmm, maybe Nick or Doug can investigate, although we are crazy busy at the moment On Sat, 28 Sep 2013, Michael Waskom wrote: On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm. That would be strange and would result in complete failure I agree, but $ grep bbregister recon_log_withT2.txt $ grep fslregister recon_log_withT2.txt both turn up empty ___ 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] Major problems with T2-based pial removal
Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.eduwrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
So the T2-SPACE is a variable flip angle sequence that actually has a fair amount of T1 and MT contrast in it and relatively less T2 contrast. As a result, you can clearly see the difference between grey and white matter, and CSF is not massively brighter than grey and white matter. If you are using a different kind of T2w sequence where the distance between CSF intensity and grey matter intensity is much greater, some of the internal settings to the -T2pial flag will likely not be optimal. I don't know if recon-all allows you to modify those with expert options or not. Bruce, is it possible for the user to modify the nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
Hmm, Ok. Thanks Matt. I still think it's weird that the T2 didn't seem to ever get registered to the FS volume, but it's not a huge loss if we can't use them. With that said, it might help to clarify the docs on this point a bit, as it sort of sounded like any reasonably-sized T2-weighted image would be useful, and I would have tried to collect a different image if I had known! On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote: So the T2-SPACE is a variable flip angle sequence that actually has a fair amount of T1 and MT contrast in it and relatively less T2 contrast. As a result, you can clearly see the difference between grey and white matter, and CSF is not massively brighter than grey and white matter. If you are using a different kind of T2w sequence where the distance between CSF intensity and grey matter intensity is much greater, some of the internal settings to the -T2pial flag will likely not be optimal. I don't know if recon-all allows you to modify those with expert options or not. Bruce, is it possible for the user to modify the –nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael ___ 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] Major problems with T2-based pial removal
I'm sure it was registered to the T1w with BBR, though I don't know the internals of that in recon-all. Given that you might only be the second person to try this with non T2-SPACE T2w images (and I unfortunately had not told Bruce about my bad experience with this), you can forgive the FreeSurfer docs for not mentioning it yet. :) That being said, it isn't guaranteed not to work, you just might have to do some fiddling with the nsigma parameters to get it to work, as the defaults for T2-SPACE are probably not good for your images. Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 10:06 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hmm, Ok. Thanks Matt. I still think it's weird that the T2 didn't seem to ever get registered to the FS volume, but it's not a huge loss if we can't use them. With that said, it might help to clarify the docs on this point a bit, as it sort of sounded like any reasonably-sized T2-weighted image would be useful, and I would have tried to collect a different image if I had known! On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote: So the T2-SPACE is a variable flip angle sequence that actually has a fair amount of T1 and MT contrast in it and relatively less T2 contrast. As a result, you can clearly see the difference between grey and white matter, and CSF is not massively brighter than grey and white matter. If you are using a different kind of T2w sequence where the distance between CSF intensity and grey matter intensity is much greater, some of the internal settings to the -T2pial flag will likely not be optimal. I don't know if recon-all allows you to modify those with expert options or not. Bruce, is it possible for the user to modify the nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic
