Dear Doug, dear freesurfers,

thank you very much! If I'd like to change the orientation (from PSR to LAS), is there a way in Freesurfer to do it? Thanks again!

Best, Brigitte

2013/6/20 Douglas Greve greve@nmr.mgh.harvard.edu

If you just want to check the orientation, then you can run mri_info. It will not tell you whether the orientation is correct or not, but neither will fslhd doug

On 6/19/13 11:18 AM, Bruce Fischl wrote:

Hi Brigette,

not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet)

cheers Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)?

Thank you very much! Brigitte

---

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how do you know which is the left hemisphere? The rest is ok Bruce On Thu, 20 Jun 2013, Ray, Siddharth wrote:

Hey,

Sorry to interrupt in between. But just want to confirm on this.

Bruce, I am having same problem with orientation and the one way i inspect whether its a L/R flip or not is by opening the image in freeview in 2x2 window and then i try moving those green,red and blue slides on my 4 image and see how the marker moves on axial, coronal and sagittal view. Now since i know which is left hemisphere on 4th image, i easily check whether its a flip or not.

Please let me know, if this way is not correct.

and i think one can easily see for A/P though.

Thanks, -Siddharth ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brigitte Dahmen [biggida@googlemail.com] Sent: Thursday, June 20, 2013 7:30 AM To: Douglas Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] check orientation

Dear Doug, dear freesurfers,

thank you very much! If I'd like to change the orientation (from PSR to LAS), is there a way in Freesurfer to do it? Thanks again!

Best, Brigitte

2013/6/20 Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>

If you just want to check the orientation, then you can run mri_info. It will not tell you whether the orientation is correct or not, but neither will fslhd doug

On 6/19/13 11:18 AM, Bruce Fischl wrote: Hi Brigette,

not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet)

cheers Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)?

Thank you very much! Brigitte

---

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

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Brigitte Dahmen - Benedikt-Schmittmann-Str. 22 - 40479 Düsseldorf / Mariabrunnstr. 42 - 52064 Aachen - 0160-3774566 - mailto: biggida@gmail.commailto:biggida@gmail.com

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How do you know that the left side of the brain is indeed what is shown on the right side of the display? The only way to know for sure if there are questions regarding the L/R axis is if a marker of some sort was attached to one side of the head at the time of acquisition.

cheers, -MH -- Michael Harms, Ph.D.

----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu

On 6/21/13 9:51 AM, "Ray, Siddharth" Siddharth.Ray@uth.tmc.edu wrote:

Well , I am not sure about the way I am doing, but if you look on brain (not skull stripped) in freeview in a 2x2 window and try to move those rgb bars on the whole volume you can see the corresponding change in position of cursor on Axial, coronal and sagittal. So if look at 4th image with nose pointing towards you (out of the screen), you know the left side of brain is in your right and then if you move the red bar towards your right on that volume you can see where cursor is moving on the axial surface and thus can tell about left-right of brain.

Please let me know if I am missing something.

-Siddharth

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Friday, June 21, 2013 8:48 AM To: Ray, Siddharth Cc: Brigitte Dahmen; Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] check orientation

how do you know which is the left hemisphere? The rest is ok Bruce On Thu, 20 Jun 2013, Ray, Siddharth wrote:

...

Hey,

Sorry to interrupt in between. But just want to confirm on this.

Bruce, I am having same problem with orientation and the one way i inspect whether its a L/R flip or not is by opening the image in freeview in 2x2 window and then i try moving those green,red and blue slides on my 4 image and see how the marker moves on axial, coronal and sagittal view. Now since i know which is left hemisphere on 4th image, i easily check whether its a flip or not.

Please let me know, if this way is not correct.

and i think one can easily see for A/P though.

Thanks, -Siddharth ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brigitte Dahmen [biggida@googlemail.com] Sent: Thursday, June 20, 2013 7:30 AM To: Douglas Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] check orientation

Dear Doug, dear freesurfers,

thank you very much! If I'd like to change the orientation (from PSR to LAS), is there a way in Freesurfer to do it? Thanks again!

Best, Brigitte

2013/6/20 Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>

If you just want to check the orientation, then you can run mri_info. It will not tell you whether the orientation is correct or not, but neither will fslhd doug

On 6/19/13 11:18 AM, Bruce Fischl wrote: Hi Brigette,

not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet)

cheers Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)?

Thank you very much! Brigitte

---

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

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-- Brigitte Dahmen - Benedikt-Schmittmann-Str. 22 - 40479 Düsseldorf / Mariabrunnstr. 42 - 52064 Aachen - 0160-3774566 - mailto: biggida@gmail.commailto:biggida@gmail.com

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Thank you, seems to work well! Best, Brigitte

2013/6/21 Douglas Greve greve@nmr.mgh.harvard.edu

Try

mri_convert file.nii --out_orientation LAS file2.nii

doug

On 6/20/13 5:30 AM, Brigitte Dahmen wrote:

Dear Doug, dear freesurfers,

thank you very much! If I'd like to change the orientation (from PSR to LAS), is there a way in Freesurfer to do it? Thanks again!

Best, Brigitte

2013/6/20 Douglas Greve greve@nmr.mgh.harvard.edu

...

If you just want to check the orientation, then you can run mri_info. It will not tell you whether the orientation is correct or not, but neither will fslhd doug

On 6/19/13 11:18 AM, Bruce Fischl wrote:

Hi Brigette,

not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet)

cheers Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)?

Thank you very much! Brigitte

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Brigitte Dahmen - Benedikt-Schmittmann-Str. 22 - 40479 Düsseldorf / Mariabrunnstr. 42 - 52064 Aachen - 0160-3774566 - mailto: biggida@gmail.com