Hi Sam,
Are your images all in alignment with each other? If not, then it
doesn't make sense to perform cross-subject statistics on them.
What exactly are you doing? You originally mentioned that you have
structural images and lesion masks, but in your later email you appear
to be working with diffusion data.
In either case, before you can perform any sort of cross-subject
statistics, will need to register and transform the data from each
subject to a common space, and then perform the statistics on the
transformed images.
Paul
On 25/07/2019, Sam W. <[log in to unmask]> wrote:
> Thanks Paul, that's what I thought. All of my images have the same voxel
> dimensions and resolution but different voxel-to-world mapping. What is the
> most appropriate way to have them all in the same voxel-to-world affine? I
> thought maybe rigid-body transforming my dwi images to the FMRIB58_FA
> template with the -noresample flag?
>
> flirt -in sub01-dwi.nii.gz -ref $FSLDIR/data/standard/FMRIB58_FA_1mm.nii.gz
> -out sub01-dwi-2.nii.gz -dof 12 -omat reg.mat -noresample -applyxfm
>
> However the sub01-dwi-2 is still being resampled to FMRIB58_FA_1mm. But
> this is probably not the correct approach anyway if I only want to make the
> voxel-to-world mapping identical for all scans, is it? What would you
> suggest?
> Best regards,
> Sam
>
> On Thu, Jul 25, 2019 at 10:00 AM paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Sam,
>>
>> Yes - setup_masks expects all input images to have the same voxel
>> dimensions, resolution, and voxel-to-world affine.
>>
>> Paul
>>
>> On 24/07/2019, Sam W. <[log in to unmask]> wrote:
>> > Hi,
>> >
>> > I inherited some lesion data and the structural scans of the different
>> > subjects show slightly different transformation matrices. Now I tried
>> > to
>> > run setup_masks with lesions masks and got a warning:
>> >
>> > WARNING:: Inconsistent orientations for individual images when
>> > attempting
>> > to merge.
>> > Merge will use voxel-based orientation which is probably
>> > incorrect - *PLEASE CHECK*!
>> >
>> > I tried the setup_masks command with two subjects and the output image
>> > includes only the first lesion mask. I assume this is because the
>> > lesions
>> > also have different transformation matrices?
>> > Do I need to ensure that all subjects have the same transformation
>> > matrix
>> > before running setup_masks?
>> >
>> > Best regards,
>> > Sam
>> >
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