Apologies, please ignore the other email response. I believe this should be tagged to the right thread (hopefully!) -----
Many thanks for the information, Doug! I will give it a go.
Actually, I would like to carry out the following analyses:
Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to that cluster in terms of WM paths. Is it possible to do that in Freesurfer environment?
How can I do PVC for perfusion in ROIs? Will the -pv ppvol flag be crucial during the mri_segstats stage?
Thanks again for help.
Best Wishes, Elijah
Re: [Freesurfer] ASL processing in Freesurfer? http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+ASL+processing+in+Freesurfer%5C%3F%22&o=newest
Douglas Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22 Mon, 21 Nov 2016 12:31:41 -0800 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161121
No, not really. If you're not doing anything fancy (eg, just computing mean of tag-control) and mapping to the surface, it is easy enough to do (mri_concat --paired-diff --sum, then bbregister to register to the anat, then mri_vol2surf or mris_preproc to map to fsaverage, then mri_glmfit and mri_glmfti-sim. If you're trying to correct for decay, intensity gradients, etc, then no.
On 11/21/16 1:40 PM, Foo Keat Mak wrote:
Hi Freesurfer Team,
Is there an ASL-friendly processing pipeline embedded in Freesurfer? Something like an equivalent to that of PetSurfer? Thanks.
Best Wishes, Elijah
Sent from my iPad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 athttp://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.
On 11/21/2016 08:59 PM, Elijah Mak wrote:
Apologies, please ignore the other email response. I believe this should be tagged to the right thread (hopefully!)
Many thanks for the information, Doug! I will give it a go.
Actually, I would like to carry out the following analyses:
Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to that cluster in terms of WM paths. Is it possible to do that in Freesurfer environment?
Yes. You can sample the ASL to the surface, then use mri_segstats specifying the ocn output of mri_glmfit-sim as the segmentation (--seg) and either --sum as output (if input only has one frame) or --avgwf as output (if multiple frames)
How can I do PVC for perfusion in ROIs? Will the -pv ppvol flag be crucial during the mri_segstats stage?
You would use mri_gtmpvc for this specifying --fwhm 0 (so that it just corrects for the voxel fraction effect).
Thanks again for help.
Best Wishes, Elijah
Re: [Freesurfer] ASL processing in Freesurfer? http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+ASL+processing+in+Freesurfer%5C%3F%22&o=newest
Douglas Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22 Mon, 21 Nov 2016 12:31:41 -0800 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161121
No, not really. If you're not doing anything fancy (eg, just computing mean of tag-control) and mapping to the surface, it is easy enough to do (mri_concat --paired-diff --sum, then bbregister to register to the anat, then mri_vol2surf or mris_preproc to map to fsaverage, then mri_glmfit and mri_glmfti-sim. If you're trying to correct for decay, intensity gradients, etc, then no. On 11/21/16 1:40 PM, Foo Keat Mak wrote:
Hi Freesurfer Team,
Is there an ASL-friendly processing pipeline embedded in Freesurfer? Something like an equivalent to that of PetSurfer? Thanks.
Best Wishes, Elijah
Sent from my iPad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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