External Email - Use Caution

Dear Douglas,

My image is in the correct orientation. The reason is that am using a software to detect brain lesions that only works in left hemisphere and my subject have the lesion in the right hemisphere. I tried it with the following command and it works

mri_convert --in_orientation PIL t1.nii t1_flip.nii

Now I would like to come back to the original orientation, which command should I use?

Thanks in advance.

Best regards,

El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

Is the image in the wrong orientation (ie, is it not truly in PIR) or do you want to change the orientation? doing a left-right swap is more than changing the orientation

On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:

    External Email - Use Caution

Dear Freesurfer experts,

Which command should I use to flip the left-right orientation of a T1 image?. Actually my image is in PIR orientation, I used the following command

mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'

*PIR*

Thanks in advance,

Best regards,

-- *Miguel Ángel Rivas Fernández*

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Yes, it works!.

Thank you so much.

El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

You can try, mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii but I'm not promising anything

On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:

    External Email - Use Caution

Dear Douglas,

My image is in the correct orientation. The reason is that am using a software to detect brain lesions that only works in left hemisphere and my subject have the lesion in the right hemisphere. I tried it with the following command and it works

mri_convert --in_orientation PIL t1.nii t1_flip.nii

Now I would like to come back to the original orientation, which command should I use?

Thanks in advance.

Best regards,

El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:

...

Is the image in the wrong orientation (ie, is it not truly in PIR) or do you want to change the orientation? doing a left-right swap is more than changing the orientation

On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:

    External Email - Use Caution

Dear Freesurfer experts,

Which command should I use to flip the left-right orientation of a T1 image?. Actually my image is in PIR orientation, I used the following command

mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'

*PIR*

Thanks in advance,

Best regards,

-- *Miguel Ángel Rivas Fernández*

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- *Miguel Ángel Rivas Fernández*

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Have you tried using LAS ?

On 3/19/2020 12:48 PM, Miguel Ángel Rivas Fernández wrote:

External Email - Use Caution

Dear Douglas,

In these emails I asked to you how to flip the left-right orientation of an image in PIL orientation and you recommend to me this command

mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii

All have worked fine but now I am in the same situation with an image in RAS orientation. *Which command should I use to flip the left/right orientation of an image in RAS orientation?*. As I explained in my previous emails, the orientation is fine. The reason is that am using a software to detect brain lesions that only works in left hemisphere and my subject have the lesion in the right hemisphere. After the lesion estimation I need to flip the left-right orientation.

Thank you very much for your time and attention.

Best regards,

El vie., 14 feb. 2020 a las 17:34, Miguel Ángel Rivas Fernández (<miguelrivasfdez@gmail.com mailto:miguelrivasfdez@gmail.com>) escribió:

Yes, it works!.

Thank you so much.

El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve
(<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió:

    You can try,
    mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
    but I'm not promising anything

    On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:

...

            External Email - Use Caution

    Dear Douglas,

    My image is in the correct orientation. The reason is that am
    using a software to detect brain lesions that only works in
    left hemisphere and my subject have the lesion in the right
    hemisphere. I tried it with the following command and it works

    mri_convert --in_orientation PIL t1.nii t1_flip.nii

    Now I would like to come back to the original orientation,
    which command should I use?

    Thanks in advance.

    Best regards,

    El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve
    (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>)
    escribió:

        Is the image in the wrong orientation (ie, is it not
        truly in PIR) or do you want to change the orientation?
        doing a left-right swap is more than changing the orientation

        On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:

...

                External Email - Use Caution

        Dear Freesurfer experts,

        Which command should I use to flip the left-right
        orientation of a T1 image?. Actually my image is in PIR
        orientation, I used the following command

        mri_info --orientation
        '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'

        *PIR*


        Thanks in advance,

        Best regards,

        -- 
        *Miguel Ángel Rivas Fernández*

        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



    -- 
    *Miguel Ángel Rivas Fernández*

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
*Miguel Ángel Rivas Fernández*

-- *Miguel Ángel Rivas Fernández*

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer