Yes, but you need to set the number of erodes. Each erode will be 1mm, and you just need to erode enough to avoid partial voluming, so 2 is probably fine. The more you erode, the smaller your ROI gets (and it can disappear).
On 11/14/2014 02:05 PM, Bruce Fischl wrote: > I think so, but I defer to Doug > Bruce > On Fri, 14 Nov 2014, Alshikho, Mohamad J. > wrote: > >> Doug an Bruce thanks a lot!! >> I will do the following as I understood from your orientations and kindly >> correct me if I am wrong: >> >> first of all I will resample my FA map into the anatomical space as the >> following command line : >> mri_vol2vol --mov fa.nii --lta dti-analysis register.lta --fstarg --o >> fa.anat.mgh >> >> Then I will generate the statistics by using: >> >> mri_segstats --seg $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh --erode --sum >> fa.stats >> >> Is it correct? >> >> Mohamad >> >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Friday, November 14, 2014 12:41 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Prefrontal white matter >> >> yes, sorry. That is what I meant >> Bruce >> On Fri, 14 Nov 2014, Douglas N Greve wrote: >> >>> I think Bruce is referring to the wmparc.mgz. Map the FA into the >>> anatomical space. Then use it with mri_segstats, probably with the erode >>> option. >>> >>> doug >>> >>> On 11/14/2014 11:41 AM, Bruce Fischl wrote: >>>> Hi Mohamad >>>> >>>> I would think you are better off using the wmseg for this. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> >>>> >>>> cheers >>>> Bruce >>>> On Fri, 14 Nov >>>> 2014, Alshikho, Mohamad J. wrote: >>>> >>>>> Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and >>>>> right >>>>> prefrontal white matter areas. My plan is to derive a mask for that area >>>>> from >>>>> aseg.mgz then I will register this mask to the FA map to calculate the FA >>>>> value. Is >>>>> it possible to derive like this mask from aseg.mgz and can I control the >>>>> dimensions >>>>> of that mask? >>>>> >>>>> thanks a lot >>>>> Mohamad >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
