Hello Bruce, I am still waiting on your response or Lilla's. Thank you.
Best, Paul On Wed, Oct 18, 2017 at 8:20 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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.e >> du/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 > > > 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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