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 <greve@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

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