Thank you Doug. I am having trouble with extracting statistics using this method.

I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values.

The command I ran is:

mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1

where SUBJECT_ID_CBF_reg.nii.gz was generated by running:

mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg

(and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder).

for which SUBJECT_ID.dat was generated by running the code:

bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl

Thank you for your consideration of this question.

Best wishes,

Salil Soman, MD, MS

On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

yep, you can use it for anything.
doug
On 9/14/14 12:52 PM, Salil Soman wrote:
Dear Doug,

Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options?

Best wishes,

Salil Soman, MD, MS
On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
On 5/25/13 1:39 PM, Salil Soman wrote:

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

That is right, but add --t2 (since it is t2 weighted).

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

Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff).

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

The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add "--seg-erode 1" to erode the segmentations by a voxel. This helps to prevent partial voluming.

doug

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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