Thanks Mark.
I inherited this structural image. It's sized at 1x1x1, 182x182x218 and bounding box -90 -09 -91/91 108 90 so I'm guessing its in standard space (ICBM-152). I have flat files accompanying it of 'voxel' and 'MNI' coordinates. What has been lost in translation is whether these "MNI" coordinates are in mm, and that is what I am trying to check. After some googling it seemed img2stdcoord might do this job.
I don't use FLIRT for coreg, so I'm not super familiar with which parts of the command relate to the flirt matrix and what the structural template names are in FSL
If my image is already in standard space what is the exact command?
I guess I could also go ahead and coregister (possibly redundantly) the image I have of uncertain provenance using FLIRT? If its already in standard space I assume this wouldn't hurt
Nina
On Thu, 9 Mar 2017, Mark Jenkinson wrote:
> Hi Nina,
>
> That's not quite right.
> You need to do:
>
> cat myvoxelcoords.txt | img2stdcoord -img mysrcimage.nii.gz -xfm myimage2std.mat -std $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz -vox - > standardspace.txt
>
> The input (myvoxelcoords.txt) and output (standardspace.txt) need to be space separated values, not comma separated values, and you need to specific the image that the coordinates relate to as well as the standard space image and the flirt matrix from the registration of the image to standard space. If the image is already in standard space then you can skip the "-xfm myimage2std.mat" part.
>
> I hope this helps.
> All the best,
> Mark
>
>
>> On 9 Mar 2017, at 04:20, Nina de Lacy <[log in to unmask]> wrote:
>>
>> Hi there:
>>
>> I have a flat file with (essentially) a list x,y,z coordinates in voxel space. I would like to convert them to mm (MNI space). The man page seems to suggest I can do this with a flat file using img2stdcoord (I think)
>>
>> Something like this work?
>>
>> cat coordfile.txt | img2stdcoord -src myvoxelcoords.csv -dest standardspace.csv
>>
>> Thanks
>> Nina
>>
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