Hi Mark,
still nothing..! I tried using the applyXFM GUI, and set voxel size
3x3x3.9900000095 and FOV 64x64x33, both taken straight off avwhd.
Yet when I then apply the transf matrix to my lowres I still get it off to
the side, as before..
I 'm a bit puzzled at this point..
Do you have other suggestions? Or, is there a way I can upload the images
and get you to try it?
cheers
Martin
----- Original Message -----
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, April 21, 2006 10:21 AM
Subject: Re: [FSL] FLIRT problem..
> Hi,
>
> Glad that this has helped.
>
> One thing to note still is that if the FOV of BH_sample_EPI is smaller
> than the FOV of BH_anat_bet then you will end up with off centre or
> truncated images like you had before. If this is the case and you still
> want the low res then I suggest using the ApplyXFM gui and selecting
> the voxel size and number of voxels (and hence FOV) manually.
>
> All the best,
> Mark
>
>
> On 21 Apr 2006, at 15:15, Martin M Monti ([log in to unmask]) wrote:
>
>> Mark, Steve,
>>
>> thanks, it hadn't occurred to me that the default is 12dof! (doh!)
>>
>> Re Mark's point though, I actually want the registered image (the
>> output) to have the same low resolution as my sample_EPI (which is the
>> same as the initial resolution of BH_EPI), can I then just use
>> sample_EPI as the reference in the second step (i.e. when I apply the
>> matrix created by registering sample_EPI to the anatomical)?
>> So like this:
>>
>> flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat -dof 7
>> flirt -in BH_EPI -ref BH_sample_EPI -applyxfm -init BH_mat2anat -out
>> BH_EPI_reg2
>>
>> Thanks for the help!
>>
>> Martin
>>
>> ----- Original Message -----
>> From: Mark Jenkinson <[log in to unmask]>
>> Date: Friday, April 21, 2006 3:10 am
>> Subject: Re: [FSL] FLIRT problem..
>> To: [log in to unmask]
>>
>>> Dear Martin,
>>>
>>> Using the first flirt command will only generate a single output
>>> volumeas that is our normal usage. I thought that it would do the
>>> same as
>>> the -applyxfm option and generate a 4D output, but it doesn't. I
>>> guessthat we don't use it in this mode so we've never noticed.
>>>
>>> Using the -applyxfm option will generate a 4D output though, so the
>>> second form is what you want, but you need a different reference
>>> volumeif you want it to have the same output size as an
>>> anatomical. So the
>>> commands you want are:
>>>
>>> flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat -dof 7
>>> flirt -in BH_EPI -ref BH_anat_bet -applyxfm -init BH_mat2anat -out
>>>
>>> BH_EPI_reg2
>>>
>>> Note that in the first line you use the -dof 7 option, as in your
>>> first form,
>>> and in the second line you use the image BH_anat_bet as your
>>> reference,since this controls the output voxel resolution and FOV.
>>>
>>> This works fine for me, but if you have a lot of timepoints in
>>> BH_EPI
>>> then the
>>> output image will be *huge* and this might be why it is hanging
>>> for you.
>>> In this case you should check how big you expect the output to be and
>>> see if that is causing problems with the available RAM/swap.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 21 Apr 2006, at 01:26, Martin M. Monti wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to simply register an EPI to an anatomical. Very
>>> easy
>>>> you'd say, yet..
>>>>
>>>> I used the sample code on the website, but I get either of 2
>>> problems:> Either only one volume is in the output image (if I do
>>> the
>>>> registration directly, as in the First Method), or the image
>>> looks
>>>> awefully off (if I use method two - also straight from the website).
>>>>
>>>> First method:
>>>> 1) flirt -in BH_EPI -ref BH_anat_bet -out BH_EPI_reg -omat
>>>> BH_mat2anat -dof 7 -v
>>>> This gives me as output a SINGLE volume, resampled at the
>>>> resolution of the anatomical, although (according to slices)
>>> well
>>>> aligned.
>>>>
>>>> Second method:
>>>> 1) flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat
>>> [Get
>>>> the matrix by transforming a ONE volume EPI image (the
>>> sample_EPI)
>>>> to the Anatomical]
>>>> 2) flirt -v -in BH_EPI -ref BH_sample_EPI -applyxfm -init
>>>> BH_mat_F1toAnat -out BH_EPI_reg2 [Apply the matrix]
>>>>
>>>> This one gives the correct voxel size, correct number of
>>>> timepoints, but when I open it with FSLView it's off to the side
>>>
>>>> (seehttp://webmartin.altervista.org/flirt.htm for a picture
>>>> comparison of before and after using FLIRT - although no obvious
>>>
>>>> diffwrence when I look into avwhd for the pre and post FLIRT
>>>> images), with the right (left) side being cut off slightly, and
>>> the
>>>> top slice being in fact still several slices away (in the Z
>>>> direction) from the top of the brain. Unfortunately I can't open
>>> it
>>>> with slices and overlay it to the anatomical given that they are
>>> of
>>>> different sizes.
>>>>
>>>> I tried using the high_res image as the -ref, in step (2) of the
>>>
>>>> second method but it hangs on me..
>>>>
>>>> Can I get a little help please?
>>>>
>>>> Cheers
>>>>
>>>> Martin
>>>>
>>>> PS: should you think it's relevant this is how I obtained the
>>>> BH_EPI image:
>>>>
>>>> avwroi subjectEPI_bet subjectEPI_del 4 83
>>>> slicetimer -i subjectEPI_del -o subjectEPI_slct -r 2 --
>>> ocustom=../
>>>> Slice_Order.txt -v
>>>> mcflirt -in subjectEPI_slct -out BH_EPI -dof 6 -verbose 1 -
>>> stages 4
>>>> -report
>>>>
>>>> --------------------------
>>>> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>>>>
>>>> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>>>>
>>>> Would you tell me, please, which way I ought to go from here?
>>>> ''That depends a good deal on where you want to get to.'' Said
>>> the
>>>> Cat. I don't much care where -- Said Alice. Then it doesn't
>>> matter
>>>> which way you go, said the Cat. [Lewis Carroll]
>>>>
>>>> Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu,
>>> a
>>>> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto
>>>> Vecchioni]
>>>>
>>>> --------------------------------------------
>>>> Martin M. Monti
>>>> Princeton University
>>>> Department of Psychology
>>>> Green Hall 3-S-8
>>>> (609) 258-5679
>>>> www.webmartin.net
>>>> --------------------------------------------
>>>>
>>>
>
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