Dear Freesurfers,
Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology.
Sincerely,
Joshua - Joshua
Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is.
cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote:
Dear Freesurfers,
Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology.
Sincerely,
Joshua
Joshua
I'd be interested to hear how this goes too.
Thanks,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 14, 2012 4:09 PM To: Joshua Lee Cc: FreeSurfer Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is.
cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote:
Dear Freesurfers,
Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I
understand
that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used
to
improve the accuracy of sub-cortical and cortical segmentation. My
question
is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that
can
help researchers make the most of your technology.
Sincerely,
Joshua
Joshua
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Hi all
I have some longitudinal data ready for the group analysis but I have a doubt:
Can I simply use the following command to resample all left hemisphere thickness maps onto the fsaverage surface (as in traditional cross-sectional analyses)?
mris_preproc --fsgd fsgd.txt --target fsaverage --hemi lh --meas thickness --out lh.fsgd_subj.mgh
Is there any change because of the data being longitudinal?
Thanks -Jorge
That will be fine. We are working on tools to perform mixed effects analysis on longitudinal, but they are not ready yet. I think Martin has some tools to exploit the fact that they are longitudinal (eg, computing a slope normalizing by the first time point or the average of the time points). But what you have is also fine too. doug
On 05/14/2012 11:10 PM, jorge luis wrote:
Hi all
I have some longitudinal data ready for the group analysis but I have a doubt:
Can I simply use the following command to resample all left hemisphere thickness maps onto the fsaverage surface (as in traditional cross-sectional analyses)?
mris_preproc --fsgd fsgd.txt --target fsaverage --hemi lh --meas thickness --out lh.fsgd_subj.mgh
Is there any change because of the data being longitudinal?
Thanks -Jorge
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jorge,
in the longitudinal stream all thickness files within each subject are in correspondence, so it would be sufficient to map all of them simultaneously (e.g. using the surfaces of the base) to fsaverage. Should save time and reduce variability.
Also (and this is true for both cross and longitudinal processing), it makes sense to intersect the cortex labels (first on a subject basis) map them to fsaverage and intersect again. Then use the intersected label for smoothing and ananlysis. This way you make sure you don't pollute your results with information from outside the cortex.
Best, Martin
On Tue, 2012-05-15 at 04:10 +0100, jorge luis wrote:
Hi all
I have some longitudinal data ready for the group analysis but I have a doubt:
Can I simply use the following command to resample all left hemisphere thickness maps onto the fsaverage surface (as in traditional cross-sectional analyses)?
mris_preproc --fsgd fsgd.txt --target fsaverage --hemi lh --meas thickness --out lh.fsgd_subj.mgh
Is there any change because of the data being longitudinal?
Thanks -Jorge
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly?
Best, Michael
On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is.
cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote:
Dear Freesurfers,
Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise
characteristics.
For example, our lab uses 0.7mm isotropic structural MR images. I
understand
that the Freesurfer pipeline will up-sample these to 1mm isotropic, but
it
seems a shame that so much information is left unused which could be
used to
improve the accuracy of sub-cortical and cortical segmentation. My
question
is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that
can
help researchers make the most of your technology.
Sincerely,
Joshua
Joshua
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.
you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has)
On Mon, 14 May 2012, Michael Waskom wrote:
Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly?
Best, Michael
On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: > Dear Freesurfers, > > Over the last years, MR imaging technology hasimproved such that sub 1-mm > isotropic scans can be obtained with good signal to noise characteristics. > For example, our lab uses 0.7mm isotropic structural MR images. I understand > that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it > seems a shame that so much information is left unused which could be used to > improve the accuracy of sub-cortical and cortical segmentation. My question > is whether there are any plans at Freesurfer to change the reference > standard resolution from 1mm isotropic, or provide another solution that can > help researchers make the most of your technology. > > Sincerely, > > > Joshua > - > Joshua > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes, I have a modified script working. For the white surface, the essentials are the same as Bruce's script but it has some additional stuff (e.g register T2w to T1w), and I call it in the middle of the recon-all rather than at the end. For the pial surface, I have done some more complicated stuff, which I'd love to talk to Bruce about some more some time. :)
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, May 15, 2012 7:29 AM To: Michael Waskom Cc: FreeSurfer Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has)
On Mon, 14 May 2012, Michael Waskom wrote:
Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly?
Best, Michael
On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: > Dear Freesurfers, > > Over the last years, MR imaging technology hasimproved such that sub 1-mm > isotropic scans can be obtained with good signal to noise characteristics. > For example, our lab uses 0.7mm isotropic structural MR images. I understand > that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it > seems a shame that so much information is left unused which could be used to > improve the accuracy of sub-cortical and cortical segmentation. My question > is whether there are any plans at Freesurfer to change the reference > standard resolution from 1mm isotropic, or provide another solution that can > help researchers make the most of your technology. > > Sincerely, > > > Joshua > - > Joshua > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce and Michael,
That would be very nice. Do I just email you the hi-res *whole-brain*mprages, or is their another way to get the images to you?
On the other hand, I'm a fair hand at scripting. I'd be willing to experiment with any scripts that you might provide.
Last, and on an unrelated note. Is that programming position at Freesurfer still open? I know someone looking for an interesting and challenging position like that.
Best,
Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, May 15, 2012 at 6:00 AM, Matt Glasser matt@ma-tea.com wrote:
Yes, I have a modified script working. For the white surface, the essentials are the same as Bruce's script but it has some additional stuff (e.g register T2w to T1w), and I call it in the middle of the recon-all rather than at the end. For the pial surface, I have done some more complicated stuff, which I'd love to talk to Bruce about some more some time. :)
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, May 15, 2012 7:29 AM To: Michael Waskom Cc: FreeSurfer Subject: Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has)
On Mon, 14 May 2012, Michael Waskom wrote:
Hi Bruce, Is there a flag for this on recon-all? Or do you need to use mri_make_surfaces directly?
Best, Michael
On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote: Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data and refine the surfaces with it. Haven't tried it on the aseg yet, but if you upload a sample dataset I could see how hard it is. cheers Bruce On Mon, 14 May 2012, Joshua Lee wrote: > Dear Freesurfers, > > Over the last years, MR imaging technology hasimproved such that sub 1-mm > isotropic scans can be obtained with good signal to noise characteristics. > For example, our lab uses 0.7mm isotropic structural MR images. I understand > that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it > seems a shame that so much information is left unused which could be used to > improve the accuracy of sub-cortical and cortical segmentation. My question > is whether there are any plans at Freesurfer to change the reference > standard resolution from 1mm isotropic, or provide another solution that can > help researchers make the most of your technology. > > Sincerely, > > > Joshua > - > Joshua > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Douglas N Greve -
jorge luis -
Joshua Lee -
Martin Reuter -
Matt Glasser -
Michael Waskom