Hello Bruce, Thank you very much for the update.
Best Paul Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Wednesday, October 18, 2017 8:20 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis Hi Paul I was waiting for Lilla to respond :) Bruce On Wed, 18 Oct 2017, miracle ozzoude wrote: > Hello Bruce, > > I wasn't sure if you answered my previous message hence, I'm sending it > again. Thank you. > > Best, > Paul > > ---------- Forwarded message ---------- > From: miracle ozzoude <miracoo...@gmail.com> > Date: Sat, Oct 14, 2017 at 3:32 PM > Subject: Re: [Freesurfer] cortical/subcortical volume based analysis > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > > Hello Bruce, > Thank you for the response. I was able to look into CVS command and I wrote a > command on how to > register each subjects to cvs_avg35_inMNI152 template using the following: > mri_cvs_register --mov > subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz > --step1 --step2 --step3 > --outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i > need to use the T1 in > the mri folder or mri.2mm folder when performing mri_cvs_register? > > My next goals are to: > 1) sample the volumes created using mri_cvs_register to the > cvs_avg35_inMNI152 template using > mri_vol2vol -reg . > -which of the outputs from mri_cvs_register should i use > to > achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or > final_CVSmorphed_toTEMPLATE_aseg.mgz > 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the > output from mri_vol2vol. > - How can I create the cortical mask from the > cvs_avg35_inMNI152/mri.2mm folder? This is > because the folder already has a subcortical mask and I want to create a > cortical mask, combine both > (using mri_merge) and use it to smooth with 8mm. > > 3) Lastly, use mri_concat to combine the smoothened maps in order to perform > group level analysis on > them. > - when performing mri_glmfit on the combined maps, i don't need to > specify the --surf > fsaverage and lh/rh flags because it is a volume based analysis and it was > done on MNI template not > fsaverage? > > Thank you very much > > Best, > Paul > > > On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > Hi Paul > > I guess you could use CVS for this. > > cheers > Bruce > On Sat, 14 Oct 2017, miracle ozzoude wrote: > > Hello Bruce, > > Thank you very much. Can I still general cortical and subcortical maps with > the Spherical warp of r/lh.white surface? If yes, please what are the steps > to achieve this? can I still analyze it with mri_glm? > > Best, > Paul > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Bruce Fischl > Sent: Saturday, October 14, 2017 11:27 AM > To: Freesurfer support list > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] cortical/subcortical volume based analysis > > Hi Paul > > if you use a property (like gm) to drive intersubject registration it then > becomes difficult to also analyze it. If your warp was truly perfect you > could just analyze the properties of the warp, but even then it is hard to > localize effects (e.g. if you changed the smoothness of the warp field > would the effect move somewhere else?). If the warp is not perfect then > some of the effect is in your warp and some in the residual anatomical > differences. There are lots of caveats like this you have to worry about. > It's the reason we drive our spherical warp with the ?h.white surface. It > is invariant to gm atrophy and so can be used to assess it without worrying > about this kind of thing > > cheers > Bruce > > > > On Fri, 13 Oct 2017, miracle ozzoude wrote: > > Hello Bruce, > > Thank you for the response. I meant the latter ( making maps > etc). I want to do something similar to the subcortical volume > based analysis on PETSurfer page however, on freesurfer T1. > Freesurfer doesn't perform VBM hence, why should there be a > problem with interpretation? > > Best, > Miracle > > Sent from my BlackBerry 10 smartphone. > Original Message > From: Bruce Fischl > Sent: Friday, October 13, 2017 6:53 PM > To: Freesurfer support list > Reply To: Freesurfer support list > Subject: Re: [Freesurfer] cortical/subcortical volume based > analysis > > Hi Paul > > we typically do this type of analysis by looking at scatter > plots of > structure volumes (e.g. hippocampus). Alternatively, you can > make maps, > but that opens up all the problems/difficulties of > interpretation of VBM. > Which did you mean? > cheers > Bruce > > On Fri, 13 Oct 2017, miracle ozzoude wrote: > > Hello FreeSurfer experts, > I want to perform a whole brain volume based group > analysis for cortical and subcortical regions. > That's something very similar to surface based group > analysis for cortical thickness however, for > volume. Is there a tutorial on how to do it? if yes, > please can i get the link. If not, please can > someone direct me how to go about doing it? My goal > is to perform a group comparison between control > and PD patients based on volume. Thank you very > much. > > Best, > Paul > > > > _______________________________________________ > 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 > > > > _______________________________________________ > 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
