Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > > Hi Sal, yes you can. Use bbregister to register the lowb image to the > anatomical. This creates a registration matrix. Use mri_vol2vol and the > registration to map the ADC map to the anatomical, then use mri_segstats to > extract the values > doug > > ps. Please post questions to the FS list instead of us directly so that > others can benefit and it gets archived. thanks! > > > > On 5/25/13 1:03 PM, Salil Soman wrote: > >> Dear Dr. Greve, >> >> Is it possible to register a nonstructural MR sequences (e.g. an ADC map) >> with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the >> segmentation from the aseg (or aparc+aseg) file to output a mean ADC value >> for each anatomic area segmented? >> >> Thank you for your time and consideration. >> >> Best wishes, >> >> Sal >> >> Salil Soman, MD, MS >> > > > > 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<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.
