Incomplete ACT image

Hello folks
I searched the forum for this error but couldn’t find anything,
I ran 5ttgen command to generate an ACT image. but resultant image is incomplete. while there is no problem with my actual co-registered image.

what could be possible reason for this.
My data has b0=1000 and is of 64 dir. and AP acquisition.

Dear Nayan,
In my experience this is usually related to skull stripping of the input anatomical (T1w) image that you gave as input to 5ttgen.

If the input is already skull-stripped, let 5ttgen know this by adding the -premasked flag.
If the input was not skull-stripped, I suggest that you create a brain mask yourself (for example, using FSL’s command bet, trying different values for -f. Then, you can give this mask as another input using the -mask option.

Hope this helps!


1 Like

@Roey_Schurr thanks for the suggestion…
It actually solved my problem …
Thanks a lot for the solution…