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 2010

FSL September 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: field map for Philips 3T

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Tue, 28 Sep 2010 17:01:14 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (112 lines)

Hi,

It is difficult to answer this precisely without seeing the actual
images but I suspect the following:

The phase image (256x256x56 image) looks correct, although
there is really no need to get such high-resolution, 1mm, data
as 3mm resolution would be fine and really speed up your acquisition!

The magnitude image (256x256x32x2) seems incorrectly
reconstructed (i.e. probably wrongly converted from DICOM to NIfTI)
as the z field-of-view is much smaller than that of the phase,
and it should be matched to the phase image.

The other two images clearly are incorrectly reconstructed as
they have ridiculous sizes (1087 or 953 slices!)

So I think you probably need to try another method of
conversion to NIfTI.  You can also considerably speed
up your sequence by increasing the voxel size, assuming
that these voxel sizes are the same as was in your original
DICOM.

All the best,
	Mark




On 28 Sep 2010, at 16:43, Jenifer Juranek wrote:

> Thanks, Matt.
> Your comments on what I do have (see fslinfo below) would be very  
> helpful (since I'm not sure what I need vs what I received). I've  
> looked at the following for some guidance, but the data I received  
> does not seem to fit. http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html
> Any ideas what I have here?
>
> 1) 2040 dicom files
> 2) dcm2nii -->16 phase and magnitude image pairs
> 3) 2 unpaired image files (see fslinfo below)
> 4) partial FOV (inferior  portion of the brain only...mainly  
> subcallosal along the entire A-P axis...z=31 in each pair)
>
> magnitude image (#7 out of 16)
> fslinfo 20100914_153118IM_0007B0mapSENSEPPSF002s801a6008A.nii
> data_type      INT16
> dim1           256
> dim2           256
> dim3           32
> dim4           2
> datatype       4
> pixdim1        1.0000000000
> pixdim2        1.0000000000
> pixdim3        2.0000000000
> pixdim4        0.0500000007
> cal_max        0.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>
> phase image (#7 out of 16)
> fslinfo 20100914_153118IM_0007B0mapSENSEPPSF002s801a6008.nii
> data_type      INT16
> dim1           256
> dim2           256
> dim3           56
> dim4           1
> datatype       4
> pixdim1        1.0000000000
> pixdim2        1.0000000000
> pixdim3        2.0000000000
> pixdim4        0.0500000007
> cal_max        0.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>
> Unpaired image file with combination of phase info (in X,Y planes of  
> FSLview window) and a magnitude image (whole brain) in the Z plane  
> FSLview window
> fslinfo 20100914_153118IM_0017B0mapSENSEPPSF002s801a008.nii
> data_type      INT16
> dim1           256
> dim2           256
> dim3           1087
> dim4           1
> datatype       4
> pixdim1        1.0000000000
> pixdim2        1.0000000000
> pixdim3        2.0000000000
> pixdim4        0.0500000007
> cal_max        0.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>
> Unpaired image file all 3 planes of FSLview window contain complex  
> data
> fslinfo 20100914_153118IM_0001B0mapSENSEPPSF002s801a008.nii
> data_type      INT16
> dim1           256
> dim2           256
> dim3           953
> dim4           1
> datatype       4
> pixdim1        1.0000000000
> pixdim2        1.0000000000
> pixdim3        2.0000000000
> pixdim4        0.0500000007
> cal_max        0.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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