Hi
Thanks so much...the solution was in not using MSWord to create text
files...when the values were entered upon prompt as per your suggestion,
results were appropriate.
Appreciate the suggestion,
Steve
> Hi,
>
> Firstly, I would not recommend using MS Word to create text files as
> it often inserts unwanted characters, which might result in numbers
> being interpretted as zeros (the default for unreadable values).
> Try TextEdit or similar programs instead. You can double check if
> this is a problem by using the manual input option instead: i.e.
> std2imgcoord -std avg152T1_brain.hdr -img bT1.hdr -xfm native2MNI.mat
> -
> which will wait for you to type three values (space separated)
> on each line.
>
> Secondly, are you after voxel coordinates? If so, then you
> should use the -vox, otherwise you are likely to get the fsl
> "scaled mm" coordinates - that is, the voxel coordinates multiplied
> by the voxel dimensions. So I would advise using the voxel
> coordinates as there is less ambiguity with them. Also note
> that you will get coordinates with the same conventions as
> FSLView shows, where they start at 0.
>
> Apart from that everything looks fine.
>
> All the best,
> Mark
>
>
>
> On 22 Sep 2006, at 01:10, Steve Cramer wrote:
>
>> Hi
>>
>> I am trying to determine the xyz coordinates for native space images
>> on WinXP.
>>
>> I start with a specific MNI space xyz coordinate. I wish to know the
>> corresponding coordinates on a subject's native space T1-weighted
>> volumetric
>> brain MRI.
>>
>> I skull stripped the native space MRI using BET (let's call the product
>> bT1.hdr), looks great, then registerd the result to the
>> avg152T1brain.hdr
>> using FLIRT. The result looks just fine, and the .mat transformation
>> file
>> (let's call it native2MNI.mat) seems healthy (size, name, location).
>>
>> I then used MS Word to create a txt file that has the MNI xyz
>> coordinates of
>> interest (let's call it COORD.txt).
>>
>> I then open cygwin.bat and with all img/hdr in the pwd, type
>> std2imgcoord -std avg152T1_brain.hdr -img bT1.hdr -xfm
>> native2MNI.mat
>> COORD.txt
>>
>> In a flash 3 coordinates appear but these values specify the middle of
>> nowhere...yes they are in the brain but they are miles from where they
>> should be. I tried varying image dimensions and origins but the
>> transform
>> has already taken this into consideration and so it has no effect. I
>> tried
>> using img2imgcoord instead but arrive at same place.
>>
>> What else could be wrong here? The goal is relatively simple: to
>> take an
>> MNI xyz and learn, in each of several subject's native space images,
>> the
>> precise xyz coordinates.
>>
>> Many thanks,
>>
>> Steve Cramer
>> [log in to unmask]
>
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