[Freesurfer] check orientation

[Brigitte Dahmen]

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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Re: [Freesurfer] check orientation

[Bruce Fischl]

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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Re: [Freesurfer] check orientation

[Bruce Fischl]

Hi Brigitte,

could you cc the list so that others can answer? I'm not sure what 
qualifies as "turned around" in FSL. They may have some preferred 
oreintation.  In general we don't, and as long as the direction cosines are 
preserved (i.e. avoid analyze format!) you should be fine

Bruce


On Wed, 19 Jun 2013, Brigitte Dahmen wrote:


Dear Bruce,
thank you very much! 
Please excuse a (potentially naive) follow-up question (as we didn't use
external markers): So if in FSL some raw T1 data are found to be "turned
around", is it something that Freesurfer "takes care of" at a certain point
in the analysis or would you suggest to swap/correct the data after checking
w/ FSL and then analyze them with Freesurfer?

Thanks again and kind regards!
Brigitte


2013/6/19 Bruce Fischl 
  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




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
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Re: [Freesurfer] check orientation

[Brigitte Dahmen]

Hi Bruce,

thank you very much!

Brigitte


2013/6/19 Bruce Fischl 

> Hi Brigitte,
>
> could you cc the list so that others can answer? I'm not sure what
> qualifies as "turned around" in FSL. They may have some preferred
> oreintation.  In general we don't, and as long as the direction cosines are
> preserved (i.e. avoid analyze format!) you should be fine
>
> Bruce
>
>
> On Wed, 19 Jun 2013, Brigitte Dahmen wrote:
>
>  Dear Bruce,
>> thank you very much!
>> Please excuse a (potentially naive) follow-up question (as we didn't use
>> external markers): So if in FSL some raw T1 data are found to be "turned
>> around", is it something that Freesurfer "takes care of" at a certain
>> point
>> in the analysis or would you suggest to swap/correct the data after
>> checking
>> w/ FSL and then analyze them with Freesurfer?
>>
>> Thanks again and kind regards!
>> Brigitte
>>
>>
>> 2013/6/19 Bruce Fischl 
>>   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
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
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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: bigg...@gmail.com
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Re: [Freesurfer] check orientation

[Douglas Greve]

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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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] check orientation

[Brigitte Dahmen]

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 

>
> 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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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> 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: bigg...@gmail.com
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Re: [Freesurfer] check orientation

[Douglas Greve]

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 >



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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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
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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: 
bigg...@gmail.com  


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Re: [Freesurfer] check orientation

[Bruce Fischl]

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-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Brigitte Dahmen 
[bigg...@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 
mailto:gr...@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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--
Brigitte Dahmen - Benedikt-Schmittmann-Str. 22 - 40479 Düsseldorf / Mariabrunnstr. 42 
- 52064 Aachen - 0160-3774566 - mailto: 
bigg...@gmail.com<mailto:bigg...@gmail.com>

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Re: [Freesurfer] check orientation

[Brigitte Dahmen]

Thank you, seems to work well!
Best,
Brigitte


2013/6/21 Douglas Greve 

>
> 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 
>
>>
>> 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 
>> listfreesur...@nmr.mgh.harvard.eduhttps://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:
> bigg...@gmail.com
>
>
>


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