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  October 2018

FSL October 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: dtifit error - all white fa map

From:

Josh Robinson <[log in to unmask]>

Reply-To:

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

Date:

Wed, 10 Oct 2018 15:47:41 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (228 lines)

Hi Fidel & Saad,

Thank you both for the help! Yes, there are two b0s total, both of which are in the concatenated data as the 31st and 62nd volume (they were acquired last for each run), and this is accurately reflected in the bvals and bvecs. Per Fidel's advice, I rewrote both files to use only tabs and again to use only spaces, but still the same problem either way, and both files also had accurate dimensions (3x62 & 1x62). Visually inspecting the data, it looks as expected, with the b0s in the correct place and contrast from volume to volume.

At this point I am thinking it must be an issue with the bvals/bvecs. Could this be an error in initially generating these files? I used dcm2niix, but I have found that using that to convert par/rec files can sometimes be problematic. I then used the linux function to paste those values into one file

paste file1.bvec file2.bvec --delimiters="" | tr -d '\r' > concatenated.bvec

Alternatively, would it perhaps be better to run the two runs I have through eddy separately and concatenate them & align them to each other later? It would be ideal to concatenate them first, but it is looking more and more like this may not be a feasible approach...

Your assistance is much appreciated!

Josh





On Tue, 9 Oct 2018 20:46:39 +0100, Fidel Alfaro Almagro <[log in to unmask]> wrote:

>Hi Josh,
>
>Your bvals/bvecs file does not have a b0 at the beginning. I am not sure if
>that is a problem (probably not), but it wouldn't hurt if you can confirm
>that is really the case (as far as I can see from your bvals, you have 2
>b0s, right?).
>
>More problems: Your bvecs file has 5 lines (it should have 3). Your bvals
>file has 3 lines (it should have one).
>
>More problems: Your bvals file has BOTH tabs and spaces to separate values.
>Not sure if that is a problem, but better be consistent.
>
>One last note: Even though it would be logical to presume that eddy and
>dtifit are consistent in the way that they read bvals and bvecs files, I
>would not make that assumption. Those 2 tools were written by different
>people, so it may not be the case that the same bvals/bvecs are accepted by
>both.
>
>Please, check all these issues and try dtifit again.
>
>Cheers
>
>Also, opening the
>
>El mar., 9 oct. 2018 a las 18:41, Josh Robinson (<
>[log in to unmask]>) escribió:
>
>> Hi Paul,
>>
>> Thanks for the suggestions! I played around withe display thresholds and
>> still looks like a binary mask no matter what.
>>
>> I had suspected that my bvecs were the most likely culprit, but I don't
>> see how. I did manually manipulate these files (from a windows computer) to
>> be in the correct order in the 3x62 matrix, so the only thing I can think
>> of is Windows adding its wonderful carriages, but I thought I took steps to
>> avoid this (ending files in a new line, per the advice of the FAQ page on
>> the fsl website). Plus, I figured that if the bvecs were bad, eddy would
>> have failed but it finished and looks like it did a good job on visual
>> inspection. I suppose I will go back and try concatenating them in a
>> different way than before.
>>
>> Thank you for your input!
>>
>> Josh
>>
>>
>>
>>
>> On Tue, 9 Oct 2018 17:06:43 +0100, paul mccarthy <[log in to unmask]>
>> wrote:
>>
>> >Hi Josh,
>> >
>> >I'm guessing that it's not simply a matter of a strange display range
>> >in your image viewer, but it's worth checking that.
>> >
>> >Otherwise, my guess is that the order in the bvecs/bvals files do not
>> >match the volume order  of the data.
>> >
>> >Cheers,
>> >
>> >Paul
>> >
>> >On 09/10/2018, Josh Robinson <[log in to unmask]> wrote:
>> >> Yes of course!
>> >>
>> >> dtifit --data=data.nii.gz --out=dtifit --mask=nodif_brain_mask.nii.gz
>> >> --bvecs=bvecs --bvals=bvals --save_tensor
>> >>
>> >> I have also attached copies of the bvals and bvecs files as well as
>> >> screenshots as the inputted nodif_brain_mask and the resulting fa map.
>> >> ***I know the brain mask looks a little funky,  we were unable to run
>> topup
>> >> thanks to the acquisition so there is still some distortion in the eddy
>> >> corrected data, but this is not yet for the purposes of data analysis so
>> >> much as it is an attempt at seeing how we can implement the FSL toolbox
>> to
>> >> our data.
>> >>
>> >> Thank you in advance,
>> >>
>> >> Josh
>> >>
>> >>
>> >>
>> >> On Tue, 9 Oct 2018 09:51:16 +0100, paul mccarthy <
>> [log in to unmask]>
>> >> wrote:
>> >>
>> >>>Hi Josh,
>> >>>
>> >>>Can you share the dtifit command you used, and some screenshots of the
>> >>>inputs and the resulting FA map?
>> >>>
>> >>>Cheers,
>> >>>Paul
>> >>>
>> >>>On 08/10/2018, Josh Robinson <[log in to unmask]> wrote:
>> >>>> Hello FSL experts,
>> >>>>
>> >>>> I am trying to run dtifit on my data, and it runs through with no
>> >>>> errors,
>> >>>> but when I open the FA map, it looks like it just returned my brain
>> mask.
>> >>>> I
>> >>>> have seen that others have run into this problem before, but none of
>> the
>> >>>> solutions for them seem to be working here.
>> >>>>
>> >>>> Our acquisition is a little old, and includes getting to two identical
>> >>>> DTI
>> >>>> acquisitions with one b0 and 30 directions each. These scans were
>> >>>> concatenated and run through eddy. The bvals and bvecs files were also
>> >>>> concatenated (in the same order), in a 3x62 matrix, with the 0s
>> >>>> corresponding to the b0s in the data (the last volume of each scan). I
>> >>>> have
>> >>>> made sure these files end with the appropriate carriage, I have
>> checked
>> >>>> my
>> >>>> output data from eddy as well as the brain mask and both look normal,
>> >>>> and
>> >>>> running the data through bedpostx_datacheck returns the following:
>> >>>>
>> >>>> bedpost/data
>> >>>> data_type      FLOAT32
>> >>>> dim1           256
>> >>>> dim2           256
>> >>>> dim3           60
>> >>>> dim4           62
>> >>>> datatype       16
>> >>>> pixdim1        0.828000
>> >>>> pixdim2        0.828000
>> >>>> pixdim3        2.200000
>> >>>> pixdim4        1.000000
>> >>>> cal_max        0.0000
>> >>>> cal_min        0.0000
>> >>>> file_type      NIFTI-1+
>> >>>>
>> >>>> bedpost/nodif_brain_mask
>> >>>> data_type      INT16
>> >>>> dim1           256
>> >>>> dim2           256
>> >>>> dim3           60
>> >>>> dim4           1
>> >>>> datatype       4
>> >>>> pixdim1        0.828000
>> >>>> pixdim2        0.828000
>> >>>> pixdim3        2.200000
>> >>>> pixdim4        1.000000
>> >>>> cal_max        1.0000
>> >>>> cal_min        0.0000
>> >>>> file_type      NIFTI-1+
>> >>>>
>> >>>>  num lines in bedpost/bvals
>> >>>> 1
>> >>>>  num words in bedpost/bvals
>> >>>> 62
>> >>>>  num lines in bedpost/bvecs
>> >>>> 3
>> >>>>  num words in bedpost/bvecs
>> >>>> 186
>> >>>>
>> >>>> I am wondering if using two scans with the same acquisition is
>> >>>> introducing
>> >>>> this issue? Otherwise my money is on an error being in the bvecs file,
>> >>>> however after running through eddy successfully I don't know what. Any
>> >>>> help
>> >>>> is much appreciated!
>> >>>>
>> >>>> Josh Robinson
>> >>>>
>> >>>>
>> ########################################################################
>> >>>>
>> >>>> To unsubscribe from the FSL list, click the following link:
>> >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >>>>
>> >>>
>> >>>########################################################################
>> >>>
>> >>>To unsubscribe from the FSL list, click the following link:
>> >>>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >>
>> >>
>> >
>> >########################################################################
>> >
>> >To unsubscribe from the FSL list, click the following link:
>> >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>> ########################################################################
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>
>########################################################################
>
>To unsubscribe from the FSL list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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