Hello List,
on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution.
Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or would they possibly decrease accuracy)?
Thanks in advance,
Nicola
Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote:
Hello List,
on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution.
Would you recommend passing these (T2+PD) to the recon-all stream anyway
- would they add value/accuracy to the segmentation/parcellation (or
would they possibly decrease accuracy)?
Thanks in advance,
Nicola
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right now).
If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream.
many thanks, Gari
On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote:
Hello List,
on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution.
Would you recommend passing these (T2+PD) to the recon-all stream anyway
- would they add value/accuracy to the segmentation/parcellation (or
would they possibly decrease accuracy)?
Thanks in advance,
Nicola
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.
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right now).
If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream.
many thanks, Gari
On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > _______________________________________________ > 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.
see:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&am...
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right now).
If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream.
many thanks, Gari
On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurtmore than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), weusually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > _______________________________________________ > 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 towhom 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
and 1mm isotropic On Thu, 7 Mar 2013, Nick Schmansky wrote:
see:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&am...
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right now).
If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream.
many thanks, Gari
On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurtmore than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), weusually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > _______________________________________________ > 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 towhom 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
Many thanks for your answers!
I have another question: Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well. Lüsebrink et al (2013) say that: "FreeSurfer is not designed to process data with a spatial resolution other than 1 mm and was modified to avoid this limitation."
When running 0.7 mm3 T1-s with the recon-all standard stream we observe the following in recon-all.log: "Original Data has (0.35, 0.35, 0.7) mm size and (640, 640, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions"
Will FS 5.2 work with other resolutions different to 1 mm3? With the current limitation, can we expect any gain in cortical thickness
(or other) measurements using lower voxel size-s, if at the end everything is conformed to 1 mm3?
many thanks again for your responses! Gari
On Thu, Mar 7, 2013 at 4:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
and 1mm isotropic
On Thu, 7 Mar 2013, Nick Schmansky wrote:
see:
http://surfer.nmr.mgh.harvard.**edu/fswiki/FreeSurferWiki?** action=AttachFile&do=get&**target=FreeSurfer_Suggested_** Morphometry_Protocols.pdfhttp://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf
Hi Gari
we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details
cheers Bruce
On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce,is there any recommended protocol for T2 acquisition to be used
in the 5.2 recon-all stream?
Should we used the same voxel size as the T1? (we are using 1 mm3 right now).
If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream.
many thanks, Gari
On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurtmore than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), weusually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person towhom 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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Gari
the post-hoc surface deformation will use whatever resolution you have, and works quite nicely with .7mm scans.
cheers Bruce On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Many thanks for your answers!
I have another question: Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well. Lüsebrink et al (2013) say that: "FreeSurfer is not designed to process data with a spatial resolution other than 1 mm and was modified to avoid this limitation."
When running 0.7 mm3 T1-s with the recon-all standard stream we observe the following in recon-all.log: "Original Data has (0.35, 0.35, 0.7) mm size and (640, 640, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions"
Will FS 5.2 work with other resolutions different to 1 mm3? With the current limitation, can we expect any gain in cortical thickness (or other) measurements using lower voxel
size-s, if at the end everything is conformed to 1 mm3?
many thanks again for your responses! Gari
On Thu, Mar 7, 2013 at 4:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: and 1mm isotropic On Thu, 7 Mar 2013, Nick Schmansky wrote:
see:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&am... _Protocols.pdf
Hi Gari we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE with a FLAIR inversion pulse. Andre (ccd) can give you the details cheers Bruce On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote: Hi Bruce,is there any recommended protocol for T2 acquisition to be used in the 5.2 recon-all stream? Should we used the same voxel size as the T1? (we are using 1 mm3 right now). If it is going to improve the skull striping and pial surface creation, we might acquire specific T2 images just to be used in the recon-all stream. many thanks, Gari On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Nicola the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
I have a similar question: My T2 scans are similar to Nicola's - approximately .86 x .86 x 4.5mm. However, about 60/168 subjects don't have T2 scans. Would you recommend including the T2's for the subjects who have them, or excluding the T2 scans altogether?
Thank you in advance for your help!
On Wed, Feb 27, 2013 at 5:44 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out
cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote:
Hello List,
on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution.
Would you recommend passing these (T2+PD) to the recon-all stream anyway
- would they add value/accuracy to the segmentation/parcellation (or
would they possibly decrease accuracy)?
Thanks in advance,
Nicola
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.
Hi Ashley
I think including them would potentially bias your results if for example more of your scans with T2s were controls or some such.
cheers Bruce On Mon, 18 Mar 2013, Ashley Shurick wrote:
Hi all, I have a similar question: My T2 scans are similar to Nicola's - approximately .86 x .86 x 4.5mm. However, about 60/168 subjects don't have T2 scans. Would you recommend including the T2's for the subjects who have them, or excluding the T2 scans altogether?
Thank you in advance for your help!
On Wed, Feb 27, 2013 at 5:44 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicola
the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually > acquire T2 and PD images - however they are at 1x1x5 mm resolution. > > Would you recommend passing these (T2+PD) to the recon-all stream anyway > - would they add value/accuracy to the segmentation/parcellation (or > would they possibly decrease accuracy)? > > Thanks in advance, > > Nicola > > _______________________________________________ > 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.-- Ashley A. ShurickGraduate Student, Psychology Stanford University
freesurfer@nmr.mgh.harvard.edu
-
Ashley Shurick -
Bruce Fischl -
Garikoitz Lerma-Usabiaga -
Nick Schmansky -
Nicola Toschi