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  March 2009

FSL March 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Better spatial normalization of subcortial regions with FSL FIRST?

From:

Brian Patenaude <[log in to unmask]>

Reply-To:

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

Date:

Fri, 20 Mar 2009 20:48:41 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (246 lines)

Hi,

> Can someone tell if I need to use a MNI template or the same individual's
> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, in
> the following script)?
>

Use it for what, specifically ?

Cheers,

Brian



>
>  Hi FSL users,
>
> I am trying to normalize PET images with FSL FIRST hoping to get better
> registration.
>
> Although I posted the same question several days ago, but I didn't get any
> reply ( I guess it is too simple question).
> I am not sure which reference image I need to use to generate final
> normalized PET image (the last step of the following script '# generate
> the normalized image w${flirt_in}.nii').
>
> Can someone tell if I need to use a MNI template or the same individual's
> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, in
> the following script)?
>
>
>
>
>
>
> I adapted the detailed instruction that Mark replied a while ago (see the
> end of email if you want see it).
>
>
>
> #!/bin/sh
> # Use direction: xfm_ff image1.nii (or img) image2.nii (or img)
>
> # image1: input image for flirt: BP image.
>
> # image2: reference image for flirt: structural MRI.
>
>
>
> # Extract the basename of the input images and give them to the
> corresponding variables.
> flirt_in=$($FSLDIR/bin/remove_ext $1)
>
> flirt_ref=$($FSLDIR/bin/remove_ext $2)
>
>
>
> #run flirt (BP image to sMRI)
>
> flirt -in $flirt_in -ref $flirt_ref -omat ${flirt_in}1.mat -bins 256 -cost
> mutualinfo -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6
>
>
>
> #run first_flirt of FSL First.
>
> echo "starting first_flirt ${flirt_ref}"
>
> first_flirt $flirt_ref x${flirt_ref}_to_std_sub
>
>
>
> # generate ${flirt_in}_final.mat - combined transformation matrix
> f4=x${flirt_ref}_to_std_sub
>
> convert_xfm -omat ${flirt_in}_final.mat -concat $f4.mat ${flirt_in}1.mat
>
>
>
> # generate the normalized image w${flirt_in}.nii"
>
> flirt -in $flirt_in -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain
> -applyxfm -init ${flirt_in}_final.mat -out w${flirt_in}.nii -paddingsize
> 0.0 -interp sinc -sincwidth 7 -sincwindow hanning -v
>
>
>
> Thank you,
>
>
>
> Buyean
>
>
>
> ** email from Mark
>
> Hi,?
>
> ?
>
>
> I *think* I know what you want to do, but part of the problem is?
>
>
> the term "normalize" as we call both co-registration and normalization?
>
>
> just "registration" because that's what they are, just with different?
>
>
> reference images.?
>
> ?
>
>
> So I think you want the following:?
>
>
> ?- get the transformation matrix relating Image_A to Image_B but do not?
>
>
> ?  resample (reslice) anything?
>
>
> ?- get the transformation (warp field or matrix) relating Image_A to the?
>
>
> ?  MNI template but do not resample?
>
>
> ?- apply the combined transformations to Image_B to resample it into?
>
>
> ?  MNI space?
>
> ?
>
>
> What I'm still unsure about is whether you want a linear or non-linear?
>
>
> registration (transformation) from Image_A to the template.?
>
> ?
>
>
> I will describe the linear case here as it is easier (and your subject?
>
>
> is "Flirt question"):?
>
>
> ?- run flirt between Image_B and Image_A with the -omat option to?
>
>
> ?  save the matrix, but not the -out option (which resamples):?
>
> ?
>
>
> ?  flirt -in Image_B -ref Image_A -dof 6 -omat TransB2A.mat -cost
> mutualinfo?
>
> ?
>
>
> ?- run flirt between Image_A and the MNI template, again with -omat?
>
>
> ?  but not with -out:?
>
> ?
>
>
> ?  flirt -in Image_A -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -omat
> TransA2MNI.mat?
>
> ?
>
>
> ?- run convert_xfm to combine the two matrices that you obtained?
>
>
> ?  above:?
>
> ?
>
>
> ?  convert_xfm -omat TransB2MNI.mat -concat TransA2MNI.mat TransB2A.mat?
>
> ?
>
>
> ?- run flirt with -applyxfm to resample Image_B into the MNI space:?
>
> ?
>
>
> ?  flirt -in Image_B -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain
> -applyxfm -init TransB2A.mat?
>
> ?
>
>
> That should do what I described, which I hope is what you want.?
>
>
> Note that I'm assuming that you've run brain extraction on Image_A (and?
>
>
> Image_B if it makes sense).?
>
> ?
>
>
> If you want to do the same but with a non-linear transformation to?
>
>
> the MNI template, then you'll need to use fnirt and applywarp instead.?
>
> ?
>
>
> All the best,?
>
>
> ?  Mark
>
>
>
>
>
>
>
>
>
> Great Deals on Dell 15" Laptops - Starting at $479
>
>
>
>
>
>

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