Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you force it to report hundreds (or thousands) of ROIs which are not represented in the aparc+aseg.mgz. Also, try removing --seg-erode.

On 09/18/2014 04:43 PM, Salil Soman wrote:

Dear Doug,

Thank you for your email.

The registration overlap looks reasonable. Thank you for considering this question.

Best wishes,

Sal

On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    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>

        <mailto: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>
            <mailto: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>

                        <mailto: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


    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center

    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/





--
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

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/