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Dear Christian,
thank you again!
I already knew about the possibility to change the voxel size!
However I have one last question for you:
I've resliced the TPMs (all 6) and the Templates and I didn't get any error or warning, but the images with the mw prefix, (both segmentated and not) were incorrect.(see the file attached)
Can you tell me what went wrong?
Thank you so much for your availability!
Elena

2016-07-28 11:08 GMT+02:00 Elena Bassanelli <[log in to unmask]>:
Dear Christian,
thank you again!
I already knew about the possibility to change the voxel size!
However I have one last question for you:
I've resliced the TPMs (all 6) and the Templates and I didn't get any error or warning, but the images with the mw prefix, (both segmentated and not) were incorrect.(see the file attached)
Can you tell me what went wrong?
Thank you so much for your availability!
Elena

2016-07-20 17:28 GMT+02:00 Christian Gaser <[log in to unmask]>:
Dear Elena,

I have forgotten to mention that you can change the voxel size of the written segmentations in the GUI ("Voxel size for normalized images"). However, if you have small lesions in your data this will be difficult anyway because lesions are not very well handled with standard segmentation tools. Lesions are simply not covered by the model. Furthermore, the location of the lesions might largely vary and thus the resulting overlap in a sample might be rather small. You should keep this in mind if you find nothing...

Best,

Christian


On Wed, 20 Jul 2016 13:13:20 +0200, Elena Bassanelli <[log in to unmask]> wrote:

>Thank you for your answer!
>However it's important to me to maintain the original resolution because
>what i'm trying to do is to compare a template of healty subjects with one
>hill subject to find very small lesions (I'm styding cortical dysplasias).
>So there is my follow question: how can i mantain the same resolution even
>in the spatial registration and smoothing?
>My idea was to reslice also the template used in the cat 12 segmentation
>(Template_1_|X|555_MNI152.nii), but i get some errors during the
>segmentation. Is this the right way or is there another solution?
>thank you again
>Elena
>
>2016-07-18 14:52 GMT+02:00 Christian Gaser <[log in to unmask]>:
>
>> Dear Elena,
>>
>> the TPM.nii is a 4D image with the tissue classes as fourth dimension.
>> Thus, the reslicing might only use the first (GM) image and does not
>> considers the remaining tissue classes. However, this is just a guess.
>>
>> Anyway, although I understand your motivation to keep the original spatial
>> resolution of your images you have to keep in mind that after spatial
>> registration and smoothing (usually with 8mm FWHM) your high spatial
>> resolution might not be be used in a group study and the 1.5mm voxel-size
>> after writing spatially registered images is a good tradeoff. Segmentation
>> will internally always use your original resolution (in fact images are
>> segmented in native space) but will be saved using the voxel size of your
>> TPM image...
>>
>> Best,
>>
>> Christian
>>
>> On Tue, 5 Jul 2016 12:18:28 +0200, Elena Bassanelli <
>> [log in to unmask]> wrote:
>>
>> >Dear spm users,
>> >I'm doing a segmentation on children's brains so I use Tpms made with
>> TOM8,
>> >but my intent is to maintain the same resolution from the beginning to the
>> >end.
>> >The TPMs made with Tom8 have different resolution from the images that i
>> >want to segment (the images have higher resolution), therefore I've
>> >resliced the tpms to my images to have the same resolution.
>> >But during the segmentation whit cat12 I get the follow error:
>> >
>> >-<error>
>> >
>> ><item>MATLAB:badsubscript</item>
>> >
>> ><item>Index exceeds matrix dimensions.</item>
>> >
>> ><item>2441 - clean_gwc</item>
>> >
>> ><item>292 - cat_main</item>
>> >
>> ><item>552 - cat_run_job</item>
>> >
>> ><item>13 - cat_run_newcatch</item>
>> >
>> ><item>246 - run_job</item>
>> >
>> ><item>154 - cat_run</item>
>> >
>> >Can anyone tell me why I get this error?
>> >thanks
>> >Elena
>> >
>>
>>
>>
>