JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  November 2010

FSL November 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: FSL orientation/swap query

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 20 Nov 2010 21:19:05 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (220 lines)

Hi,

I'm glad that helped.

If you are confident that your labels are correct then you
can continue to use the same commands as before.  Neither
fslswapdim nor fslorient have changed significantly for some
time.  FSL always interprets the images in the same way that
FSLView shows them.  So as long as FSLView is fine (and
hence the reason I keep talking about checking the labels)
then everything inside FSL will be fine.

All the best,
	Mark

On 19 Nov 2010, at 21:00, Woodman, Sandra wrote:

> Mark,
> 
> Thanks for your thorough response!  It has been a bit confusing, but this has
> helped clarify.
> 
> One additional question.. currently we are working in a freesurfer environment,
> which doesn't recognize fslreorient2std as a command.  In this case is it okay
> if we continue with our current protocol, ie using fslswapdim and fslorient?  We
> have looked over some of our old data (images with hemispheric adnormalities) in
> fslview against tkmedit (freesurfer viewer) where we know the orientation is
> correct and it appears that all our images are in correct orientation with the
> correct labels (L/R).  Has there been any changes in FSL recently (past year)
> that would have effected the way FSL unpacks and orients, ie does FSL
> automatically swap/reorient images at any stage?
> 
> Thank you for your help!
> 
> Sandra 
> 
> 
> 
> Sandra Woodman
> Mood and Motor Control Laboratory
> Athinoula Martinos Center for Biomedical Imaging
> Massachusetts General Hospital 
> 120 6th St.
> Charlestown, MA 02129
> Tel: 617-643-6245
> Fax: 617-726-1351
> Email: [log in to unmask]
> 
> 
> 
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Fri 11/19/2010 5:21 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FSL orientation/swap query
> 
> Dear Sandra,
> 
> Once upon a time the nifti fairy gave us a new data format.
> Unlike the nasty old Analyze format, this new format allowed
> us to store information about orientation in the image itself
> and so the analysis programs no longer had to guess which
> way around the images were stored (or, as was more common,
> assume a given default and let the users make sure that their
> images adhered to that ordering).
> 
> So this was the situation in 2004 when FSL 3.2beta was
> released.  We put in nifti support, but although most of our
> tools could cope with different orientations, not 100% of
> them were able to do this, so we stuck with the convention
> that people needed to make sure that their images adhered
> to the "old" style FSL convention - which was to be "like" the
> MNI152 template images. By "like" we mean that you could
> rotate your image to make it match this template (that is,
> no reflections were needed).  This is related to left-right
> ordering but a little more complicated.  I decided (in one
> of the worst decisions I've ever made in FSL) to call this
> convention "radiological ordering".  This terminology, and
> the intrinsic complicated nature of storage vs voxel coordinates
> vs "world" coordinates, has caused a lot of confusion.  However,
> this was a *temporary* situation (that is, requiring things be
> stored in the "old" FSL convention) and was resolved fully in 
> the FSL4.0 (2007).  Unfortunately, the belief that FSL *needed*
> things in the old convention (radiologically-ordered) persisted
> well past the point that this was actually true.  It has been
> happy for quite a long time now with data in *any* ordering.
> So there is *no* need to convert anything between different
> orderings (i.e. between "radiological" and "neurological").
> 
> As I said though, people still wanted to swap between these
> and so fslswapdim and fslorient were regularly used and
> these are *dangerous* operations as it is really very, very
> easy to get the left and right parts of the images mislabeled
> as a result of using these tools incorrectly.  Partly to help
> avoid these problems I introduced a label-based syntax
> for fslswapdim a while ago, and more recently have introduced
> a new tool, fslreorient2std.  This new tool is there for a different
> reason - not to convert between orderings ("radiological" and
> "neurological") but, instead, to reorient the image so that it 
> appears, in FSLView, with the same slicings as the standard
> template brains (MNI152).  This therefore changes the 
> *orientation* but not the *ordering*.  It seems that a lot of
> people confuse these two issues, and a lot of people are 
> unhappy if their images are not in the same orientation as
> the MNI152 template images.  However, for the analysis
> it doesn't matter if they are in the same orientation or not,
> which is why we'd never worried about it much in the past.
> It is purely an issue of display (although there can be minor
> benefits in the registration).
> 
> The other important issue to bring up here is labels in FSLView.
> These are *THE MOST IMPORTANT* aspect of data orientation
> and need to be checked.  It is absolutely crucial that these
> labels are correct (as seen in FSLView) when you look at your data.
> If the labels are not correct then *DO NOT* do any processing until
> they are fixed.  To fix these labels, if they are incorrect, requires the
> use of fslswapdim and fslorient, and this is really one of the few
> instances where people need to interact with these tools.  If the
> labels are fine, then I *strongly* advise people not to use fslswapdim 
> or fslorient.  In the early days of nifti it was quite common that images
> were incorrectly labeled when they were converted to the nifti format
> from their native scanner format, but these days it is rare.  However,
> be vigilant and always check the labels.  Obviously it is extremely
> difficult/impossible to tell left from right in the brain by visual inspection
> (at least for most healthy brains) and so it is a *really good idea* to
> attach something like a vitamin/oil capsule to the subject when 
> scanning so that you can tell left from right in the actual MR images.
> 
> As different centres have different scanners, protocols, conversion
> routines and so forth, we cannot recommend a general workflow
> beyond inspecting your data and fixing problems if they arise.
> If there is no *problem* with the labels, but you just want your
> images to look like the MNI152 images, in terms of orientation,
> then use fslreorient2std.  There is no need in FSL (and hasn't
> been for some time) to convert anything between "radiological"
> and "neurological" ordering.  Just forget about this in the way
> that you can forget about the datatype that the image is stored
> in.  It is a technical detail and is currently dealt with fine within
> the software.  The only instance I can imagine that it might 
> play a role is when you are using data across several different
> packages and some of them are not fully compliant with 
> both orderings (as the very old versions of FSL used to be).
> 
> There is more information on the tools and some technical
> details about orientations and orderings on the webpage
> for FSLUTILS.  Look at the "Orientation-related Utilities"
> section of:  http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html
> 
> I really strongly recommend that people do not use fslswapdim
> or fslorient unless they absolutely have to because their
> labels are *incorrect*.  I know I said this above, but I would
> really like to emphasize this point, as I've seen far too much
> incorrect, and unnecessary, use of these tools causing problems.
> 
> If you are worried about old data then just *check the labels*
> in FSLView.  As long as these are correct then everything is fine.
> The labels are the only crucial thing.  Then, if you like, you can
> apply fslreorient2std to put the images in the same orientation
> as the MNI152 brains, but this is not necessary, it is only if that
> is what you like to see in the viewer.  It will not affect the analysis.
> Once again, it is *only the labels* which are important.  OK, I
> think I've probably emphasized that enough now.
> 
> I hope this has answered all your questions.  It is a pity that
> there is so much confusion about these issues, and I hope
> that this has helped.
> 
> All the best,
> 	Mark
> 
> 
> On 18 Nov 2010, at 22:34, Woodman, Sandra wrote:
> 
>> Hi,
>> 
>> We recently spoke with someone doing fMRI analysis with FSL and they ran 
>> into some issues with finding that using fslswapdim and fslorient was 
>> actually flipping their data such that right was left and left was right 
>> (the functional header said it was in neurologic orientation and the 
>> structural said radiologic; when he swapped only the functional images, 
>> the functional and structural became mirror images of each other). I 
>> believe he heard from someone on the FSL list who mentioned that the 
>> procedures for dealing with orientation have changed recently, and that he 
>> no longer needs to use fslswapdim (and maybe fslorient, too?).
>> 
>> So here are our questions: Was there really a change in how orientation 
>> is dealt with, and if so, does it affect all types of images (fMRI, 
>> structural, DTI, etc.)? Do we need to still run fslorient or is it just 
>> fslswap that should not be used? If orientation procedures have indeed 
>> changed, when did this change take effect? And finally, at what stage do 
>> the changes apply, i.e. was there a change at the stage of unpacking or 
>> is the change further downstream (I'm asking this because we did some 
>> recent processing of images that were unpacked awhile ago, so they may 
>> not be affected by this change and would still need to be swapped--I 
>> think).
>> 
>> Our current questions are specifically about DTI analysis, but we will 
>> also be using FSL for fMRI in the near future. We are currently using both 
>> bedpostx/probtrackx and randomise for the DTI analyses. Also, we are using 
>> unpacksdcmdir to unpack our images.  We are using NIFTI format images.
>> 
>> Thank you!
>> 
>> Sandra Woodman
>> 
>> 
>> 
>> 
>> 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.
>> 
> 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager