Re: [Freesurfer] Flip left-right orientation command

[Douglas N. Greve]

Have you tried using LAS ?

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


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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 
(mailto:miguelrivasf...@gmail.com>>) escribió:


Yes, it works!.

Thank you so much.

El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve
(mailto:dgr...@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:


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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
(mailto:dgr...@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:


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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*


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-- 
*Miguel Ángel Rivas Fernández*


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-- 
*Miguel Ángel Rivas Fernández*




--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Flip left-right orientation command

[Miguel Ángel Rivas Fernández]

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 (<
miguelrivasf...@gmail.com>) escribió:

> Yes, it works!.
>
> Thank you so much.
>
> El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve (<
> dgr...@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 (<
>> dgr...@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 
>>> listfreesur...@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 
>> listfreesur...@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*
>


-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Flip left-right orientation command

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Yes, it works!.

Thank you so much.

El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve ()
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 (<
> dgr...@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 
>> listfreesur...@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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Flip left-right orientation command

[Douglas N. Greve]

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 
(mailto:dgr...@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*


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--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Flip left-right orientation command

[Miguel Ángel Rivas Fernández]

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 ()
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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Flip left-right orientation command

[Douglas N. Greve]

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*

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