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  September 2011

FSL September 2011

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Registration problem

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Thu, 1 Sep 2011 22:46:06 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (113 lines)

Dear Fernanda,

The arrows in the top panel point to areas where the brain
extraction in the highres image is imperfect.  However, it has
not affected the alignment of any of the real brain structures
and so you can ignore it.

The arrows in the bottom panel point to parts of the brain
that are not covered in your functional images (they must 
have limited FOV) and so these too can be ignored as
the parts of the brain that are imaged are aligned well.

You will find that in any situation where the functional
images do not cover the entire brain that you will have
these areas of blank areas.  There is nothing else that
can be done as there is no image data to cover these
areas.

So, in summary, I still think you have great registration results!  :)

All the best,
	Mark


On 1 Sep 2011, at 22:21, Fernanda Palhano wrote:

> Hi Mark,
> I'm very happy that you think my results are good. =)
> But I'm still worried about the red lines. I'm sending the same image but now
> with arrows pointing to where I think that there is a problem.
> http://imago.neuro.ufrn.br/imagens/
> 
> Maybe it's just a visualization problem. Can you please look again this image? Sorry to bother you with this, but I want
> to be sure that my registration is good enough.
> 
> Thank you very very much!
> Fernanda
> 
> On Thu, Sep 1, 2011 at 5:37 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Fernanda,
> 
> Thank you for sending the links to the images.
> The results to me look very, very close to *perfect*!!
> 
> What are you unhappy about?
> 
> Your functional images have a limited Field Of View (FOV)
> and so do not cover some parts of the superior and
> inferior parts of the brain.  This is why you see blank
> patches in the overlays and sharp, angled lines.
> However, the structures within the brain look like they
> align very, very well.
> 
> So I don't think you need to do anything else.
> I think the results are great.
> 
> All the best,
>        Mark
> 
> 
> 
> On 1 Sep 2011, at 18:39, Fernanda Palhano wrote:
> 
> > Hi Mark,
> >
> > Thank you for your quick reply. I just realize that my attachment didn't go.
> > You can see the images accessing the follow address: http://imago.neuro.ufrn.br/imagens/
> >
> > I don't know if this have some relation with my problem but I used fslswapdim (with the option RL PA IS) to reorientate all my structural T1 images before doing the registration.
> > I never tried the Full Search option, but if I want to try it, should I use it in both registrations (Main Structural Image and Standard Space)?
> > And, unfortunatelly I don't have fieldmaps.
> >
> > I'm now running a new data set (from another scanner) and I'm having the same registrations problems. Although this, my statistical results seem fine. I was wondering if it's not only a misplace of the red lines...
> > Do you think this is possible?
> >
> > Thanks again,
> > Fernanda
> >
> > On Thu, Sep 1, 2011 at 2:08 PM, Mark Jenkinson <[log in to unmask]> wrote:
> > Dear Fernanda,
> >
> > There was no attachment (as the list does not allow anything except very,
> > very small attachments) so I couldn't really be sure of what you are seeing.
> > Do your images start in very different alignments (i.e. 90 or 180 degrees
> > different)?  If so then you might find that running fslreorient2std on your
> > data might help - do this on either the functional or the structural or both -
> > depending on which are in different orientations compared to the template
> > MNI152 images.  You can also try "Full Search" if you have not tried that.
> >
> > If you have fieldmaps then we strongly advise using those as they can
> > really help the functional to structural (example_func2highres) registration
> > hugely.  Often these "failures" of registration relate to uncorrected distortion
> > in the functional EPI images.
> >
> > All the best,
> >        Mark
> >
> >
> >
> >
> > On 1 Sep 2011, at 14:46, Fernanda Palhano wrote:
> >
> > > Hi,
> > >
> > > I used FEAT GUI, first-level analysis to run the data, but I noticed a registration problem when I checked the registration report, the alignment (in red) didn't fit,  please refer to  the photos attached, the problem is quite clear according to the photos. The alignment for the images on the top seems fit the image on the bottom, and the alignment lines (red lines) for the images on the bottom seems fit the images on the top.
> > > I'm registering my functional image (EPI) to the MNI template. For this, I used a T1 structural image as Main structural image, 6 DOF, and MNI152_T1_2mm_brain, linear 12 DOF, as standard space.
> > >
> > > Thanks in advance.
> > >
> > > Fernanda
> >
> 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2024
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