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  August 2009

FSL August 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: padding volume in y direction

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Tue, 4 Aug 2009 08:10:57 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (97 lines)

Hi,

The -noresample flag does not stop using the reference volume
to determine the output size and resolution.  It just stops internal
calculations doing resampling which, given the -applyxfm flag, is
totally irrelevant.

Using your new reference image is the right thing to do.
However, the qform has nothing to do with how flirt will resample
the intensities.  So if the image *looks* wrong after this then there
is a bigger problem.  Getting the right qform for your output will
then be a second problem.  I'm not sure if "data in the wrong
place" means that just the coordinates are wrong (incorrect qform)
or that the image looks wrong (wrong intensities, and hence a bigger
problem).

What I think you should do is the following:
  - run fslorient with -deleteorient on your new reference volume,
	to remove its qform info (which would otherwise taken precedence)
  - run: flirt -in inplane -ref newref -applyxfm -init yshift.mat -out  
inplane_paddedFOV

Hopefully this will make an image which looks correct (the
intensities are where they should be in the image) and has the
transformed qform from the input image (as the newref will have
had no info to override this).

Let us know if you have any problems with this.
All the best,
	Mark



On 4 Aug 2009, at 00:22, Ed Vessel wrote:

> Ping ... Got no response on this, just doublechecking to see if there
> are any recommendations or if I'm missing something obvious.
>
> Thanks,
> Ed
>
> On Thu, Jul 30, 2009 at 10:17 AM, Ed Vessel<[log in to unmask]> wrote:
>> Hi there -
>>
>> I have some EPI and 2D T1 ("inplane") data that were collected with
>> the same slice prescription but different fields of view in the image
>> plane, and I'm trying to pad my inplane to have the same FOV (without
>> changing the NIFTI qform location info).
>>
>> The EPI scan is 3x3x3mm, 64x80 voxels (192x240 FOV).
>>
>> The 2D T1 inplane is 1.5x1.5x3mm, 128x128 voxels (192x192 FOV).
>>
>> I've tried using some flirt commands to do this but can't get it to  
>> work right.
>>
>> flirt -in inplane -ref EPI -noresample -applyxfm -init yshift.mat - 
>> out
>> inplane_paddedFOV
>>
>> ... does the right thing but the "noresample" tag seems to not have  
>> an
>> effect and I get 3x3x3 voxels (not 1.5x1.5x3).
>> (note, my yshift.mat file is there just to re-center the data in the
>> middle of the slice, adding the padding on both sides rather than  
>> just
>> one side.  It contains a 24mm shift in y).
>>
>> flirt -in dino_inplane_090729+03+t12Dmprage26sl -ref
>> ../04+Online/dino_inplane_090729+04+Online -applyisoxfm 1.5 -init
>> yshift.mat -out inplane_paddedFOV2
>>
>> ... this resamples in all directions, giving me 1.5x1.5x1.5mm voxels,
>> which is no good because now I can't use it as an "inplane" ... it
>> doesn't have the same slices as the EPI.
>>
>> I've also tried creating a _new_ reference file with the right image
>> dimensions (1.5x1.5x3, 128x160 voxels), but have been unsuccessful at
>> getting the qform of this new file set correctly, so that it places
>> the data in the wrong place in the file when I then use this as the
>> -ref.
>>
>> Any suggestions on how to do this?
>>
>> Ed
>
>
> -- 
> Ed Vessel
> Center for Brain Imaging
> New York University
> [log in to unmask]
> 4 Washington Place, Rm. 156
> New York, NY 10003                           http://www.cns.nyu.edu/~vessel
> (212) 998-8217
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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