Dear Mark,
Thanks very much for your reply - your help is much appreciated! We have
since changed our protocol so we don't run into the same problem, but
thanks again for the confirmation that it is ok to fix in this way if
needed.
Kind regards,
Kristin
On 17/01/2014 12:39, "Mark Jenkinson" <[log in to unmask]> wrote:
>Dear Kristin and Vincent,
>
>This process does require trial and error like you are describing. The
>first time you deal with data of a particular protocol from a scanner
>then you often need to go through this process. However, once you've
>done it for one dataset then the same change should apply to all other
>datasets that use this protocol on that scanner.
>
>All the best,
>Mark
>
>
>On 14 Jan 2014, at 07:24, Kristin Koller <[log in to unmask]> wrote:
>
>> Hi Vincent,
>>
>> I had the same problem before and would really appreciate advice from
>>an FSL expert on whether there is a correct/better way to fix this
>>problem.
>>
>> This is what I did to fix the orientation:
>>
>> I swapped around the rows that represent the x, y and z coordinates in
>>the bvecs file before running DTIfit.
>> (It is easier to see when you transpose the bvecs file from rows to
>>columns in Matlab. When in directory containing my bvecs file I just
>>typed load bvecs, and then typed
>> bvecs').
>>
>> In my data the initial colour orientation in FSL was:
>> X(anterior-posterior; red) y (inferior-superior, green) z (left-right,
>> blue). I made a new bvecs matrix in Matlab representing the same
>> columns of bvecs but in the order z x y - this gave the right
>> orientation; (L-R red, A-P green, I-S blue). I used the command line
>> bvecs = [bvecs(:,3), bvecs(:,1), bvecs(:,2)]. I copied this matrix
>> into a new txt file and saved it as the new bvecs file
>> ready for bedposting/DTI fit.
>>
>> Also, after doing this, the red left-right
>> fibres were going the wrong direction, which meant that the
>> inferior-superior fibres were flipped (ie. the positive and negative
>> directions were the other way around). I swapped the plus and minus
>>signs in front of each value of the third
>> bvec column (z-direction), which fixed the problem.
>>
>> It might take a few times of checking all options (ie swapping columns
>>in different ways and using +/- in front of
>> each column) to see what works for your data.
>>
>> I'm not sure if this is the way to go but it seemed to work for my data.
>>
>> Hope this helps!
>>
>> Kristin
>> ________________________________________
>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>>Vincent Koppelmans <[log in to unmask]>
>> Sent: 13 January 2014 22:48
>> To: [log in to unmask]
>> Subject: [FSL] DTIFIT: orientation issue
>>
>> Dear FSL experts,
>>
>> I have DWI data that was (unintentionally) acquired from left to right.
>>
>> When I use dtifit for tensor fitting and modulate the resulting FA
>>image with the V1 image, the corpus callosum appears green.
>>
>> What should do to fix this?
>>
>> Thanks,
>>
>> Vincent
>>
>>
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Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.
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