Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences

When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does it overlay correctly on the T1.mgz? doug

On 09/14/2014 11:40 PM, Salil Soman wrote:

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 mailto: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 <mailto: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
    <mailto: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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-- 
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences
Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health
Care System

-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System