FATCAT and T1 images question

PS. It seems to work for version FreeSurfer 6.0 and the final version of 5.3 (I’d been using 5.3 beta for some prior work)…

However, now I have a different question. I am using FATCAT and mappng my T1 images and freesurfer brain.mgz images to DTI space. How do I map files like lh.smoothwm.gii to DTI space? This would allow me to examine the tracts generated in FATCAT on the surfaces that are in DTI space.

I don’t see an option in fat_proc_map_to_dti to handle surface-related data.



I split this question off and gave it a meaningful title because it is on a very different topic than what had previously been being discussed.

You are right, there isn’t something in fat_proc_map_to_dti to handle surfaces. However, I asked the wise Daniel Glen about what function could apply a (affine, 12 DOF) transform made with fat_proc_map_to_dti, and he said ConvertSurface is the function in question. Now, I haven’t used this yet, but you could:

  1. use fat_proc_map_to_dti to align the T1w volume from FS to the DTI space, and then
  2. take the transform made from that and apply it to the *.gii file surfaces with ConvertSurface.

This would be a really useful thing to include within fat_proc_map_to_dti, so I will probably aim to do that this week. If you want to try out the above, please let me know how it goes; if you want to wait until I have tried it myself and added it, then that’s fine, too. I have just gotten up to this point in the online tutorial help for the fat_proc* functions, so this is excellent timing for this question-- thanks!


Also, note that using “fat_proc_align_anats” before running FreeSurfer should mean that your T1w volume overlays the T2w volume well; and if you are processing your DWI data, I will hope/assume that you are using TORTOISE, whereby your T2w space should also be where what your DTI space is. Therefore, your FreeSurfer output could already pretty much be in the DTI space, if processing went well at the various stages.


Thanks, and also thanks for creating a new subject for the post. I will give this all a try.


fat_proc_map_to_dti has been updated now to be able to map surface files, as well as supplementary *.niml.dset and *.spec files from the @SUMA_Make_Spec_FS output of FS’s recon-all.

This capability is effective from:
Aug 9 2017 (Version AFNI_17.2.07)

There is an example in the function’s help file about adding those other types of files as followers to the 3dAllineate-create transform from FS space to the DWI space. Also, there is some documentation now for the function on the following page:
(NB: this is still early stages of documenting and likely to change over time, but it should give an intro to the function, in addition to reading the help file)

Please let me know how that works out for you.