Primary slice direction and image origin?

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falk.luesebrink＠med.ovgu.de

2 May 2019 2 May '19

7:16 a.m.

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Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best, Falk

...............................................

[klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de http://www.kneu.ovgu.de/kneu.html

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Greve, Douglas N.,Ph.D.

2 May 2 May

11:33 a.m.

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...

External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

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

falk.luesebrink＠med.ovgu.de

3 May 3 May

3:01 a.m.

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Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as there is no DICOM tag directly related to it, it has to be determined from some information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general: voxel to ras transform: 0.9367 0.0327 0.0240 -111.2289 -0.0206 0.8545 -0.4108 -82.6730 -0.0339 0.3843 0.9114 -121.5813 0.0000 0.0000 0.0000 1.0000

In that transform the last column indicates the image's origin. However, I was unable to find the relation between the information available in the DICOM header and this transform.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 2. Mai 2019 17:33 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...

External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

Greve, Douglas N.,Ph.D.

11:30 a.m.

You can get the image position from tag 20 32. It might not match what you see in mri_info because we use RAS and dicom uses something else (LPS maybe), so the "first voxel" might not be the same.

On 5/3/2019 3:01 AM, falk.luesebrink@med.ovgu.de wrote:

...

     External Email - Use Caution
Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as there is no DICOM tag directly related to it, it has to be determined from some information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general: voxel to ras transform: 0.9367 0.0327 0.0240 -111.2289 -0.0206 0.8545 -0.4108 -82.6730 -0.0339 0.3843 0.9114 -121.5813 0.0000 0.0000 0.0000 1.0000

In that transform the last column indicates the image's origin. However, I was unable to find the relation between the information available in the DICOM header and this transform.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 2. Mai 2019 17:33 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...
External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

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

falk.luesebrink＠med.ovgu.de

9 May 9 May

5:52 a.m.

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Thanks Doug, I think I may have resolved my orientation / transformation issue.

Do you happen to know how the primary slice direction is determined?

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Freitag, 3. Mai 2019 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can get the image position from tag 20 32. It might not match what you see in mri_info because we use RAS and dicom uses something else (LPS maybe), so the "first voxel" might not be the same.

On 5/3/2019 3:01 AM, falk.luesebrink@med.ovgu.de wrote:

...

     External Email - Use Caution
Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as there is no DICOM tag directly related to it, it has to be determined from some information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general: voxel to ras transform: 0.9367 0.0327 0.0240 -111.2289 -0.0206 0.8545 -0.4108 -82.6730 -0.0339 0.3843 0.9114 -121.5813 0.0000 0.0000 0.0000 1.0000

In that transform the last column indicates the image's origin. However, I was unable to find the relation between the information available in the DICOM header and this transform.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 2. Mai 2019 17:33 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...
External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

Greve, Douglas N.,Ph.D.

4:19 p.m.

It looks at the RAS of the direction cosines for the direction going from one slice to the next. If the absolute value of the R component is the max of the three, then it is assigned to be sagittal. If the A component is max, then it's coronal. If S, then axial

On 5/9/19 5:52 AM, falk.luesebrink@med.ovgu.de wrote:

...

     External Email - Use Caution
Thanks Doug, I think I may have resolved my orientation / transformation issue.

Do you happen to know how the primary slice direction is determined?

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Freitag, 3. Mai 2019 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can get the image position from tag 20 32. It might not match what you see in mri_info because we use RAS and dicom uses something else (LPS maybe), so the "first voxel" might not be the same.

On 5/3/2019 3:01 AM, falk.luesebrink@med.ovgu.de wrote:

...
      External Email - Use Caution
Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as there is no DICOM tag directly related to it, it has to be determined from some information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general: voxel to ras transform: 0.9367 0.0327 0.0240 -111.2289 -0.0206 0.8545 -0.4108 -82.6730 -0.0339 0.3843 0.9114 -121.5813 0.0000 0.0000 0.0000 1.0000

In that transform the last column indicates the image's origin. However, I was unable to find the relation between the information available in the DICOM header and this transform.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 2. Mai 2019 17:33 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...
External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

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falk.luesebrink＠med.ovgu.de

10 May 10 May

2:24 a.m.

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Exellent! Thank you!

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 9. Mai 2019 22:19 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

On 5/9/19 5:52 AM, falk.luesebrink@med.ovgu.de wrote:

...

     External Email - Use Caution
Thanks Doug, I think I may have resolved my orientation / transformation issue.

Do you happen to know how the primary slice direction is determined?

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Freitag, 3. Mai 2019 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can get the image position from tag 20 32. It might not match what you see in mri_info because we use RAS and dicom uses something else (LPS maybe), so the "first voxel" might not be the same.

On 5/3/2019 3:01 AM, falk.luesebrink@med.ovgu.de wrote:

...
      External Email - Use Caution
Hi Doug,

thanks for your answer. I know how to print the slice direction, however, as there is no DICOM tag directly related to it, it has to be determined from some information of the DICOM header. I was wondering which these are.

Same for the image origin or the voxel to ras transform in general: voxel to ras transform: 0.9367 0.0327 0.0240 -111.2289 -0.0206 0.8545 -0.4108 -82.6730 -0.0339 0.3843 0.9114 -121.5813 0.0000 0.0000 0.0000 1.0000

In that transform the last column indicates the image's origin. However, I was unable to find the relation between the information available in the DICOM header and this transform.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Greve, Douglas N.,Ph.D. Gesendet: Donnerstag, 2. Mai 2019 17:33 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can use --slicedirection to get the slice direction (it will also get printed out by just running mri_info on a file). What do you mean by the image origin?

On 5/2/19 7:16 AM, falk.luesebrink@med.ovgu.de wrote:

...
External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the primary slice direction and image origin is determined from the DICOM header as displayed for example using mri_info?

Best,

Falk

...............................................

klinikum_logo_schmal_e-mail_blau

*Universitätsklinik für Neurologie*

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

*Telefon: *+49-391-6117-512

*falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de* *http://www.kneu.ovgu.de/kneu.html*

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

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falk.luesebrink＠med.ovgu.de
Greve, Douglas N.,Ph.D.