Transforming from TT_N27 to MNI space

[danlittledan]

Dear AFNI experts,

I am attempting to open a functional map of task-related activity on the MNI template. Preprocessing and group analyses were performed based on TT_N27 space.

How to accurately convert TT_N27 space to MNI space?

Thank you for your help,

Dan

[dglen]

If your dataset is specifically in TT_N27 space (you have aligned all your data to the TT_N27+tlrc template, then you can use the exact transformation, the inverse of the 12-piece transformation that brought the N27 dataset to Talairach space. This command applies that inverse transformation:

3dfractionize -input dset+tlrc -warp ~/abin/TT_N27+tlrc -prefix dset_mni -template template_mni+tlrc

[danlittledan]

Thank you so much for your help.

I tried the command :
3dfractionize -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -prefix MNI_FIRST_HOUSEFC_FACEFC_rppa -template MNI152_2009_template+tlrc

But it was warning: Template is not in +orig view (as attached)

I don’t know why this happens…Could you give me some suggestions?

[dglen]

3dfractionize wasn’t made for this exactly. To work around this, you can first copy the dataset to the orig view:

3dcopy MNI152_2009_template+tlrc tempMNI152_2009+orig
3dfractionize -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc
-prefix MNI_FIRST_HOUSEFC_FACEFC_rppa -template MNI152_2009_template+orig

[danlittledan]

Hi, AFNI expert,

I had a problem with “3dfractionize”.

I tried the approaches:

3dfractionize -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -prefix MNI2009c_FIRST_HOUSEFC_FACEFC_rppa
-template …/ffa_ppa/0815/MNI152_T1_2009c+orig

The form of [OverLay] was [abuc] rather than [fbuc], I can’t find the activated brain regions. It was just a pure red area.

Attached is the picture I have of MNI2009c_FIRST_HOUSEFC_FACEFC_rppa+tlrc on the MNI152_T1_2009c template.

Could someone give me some suggestions?

Thanks a lot!

[dglen]

I hadn’t noticed this behavior, but you can use “-preserve” to move the data with something like NN interpolation with this option. I don’t think we have another existing program to warp the 12-piece transformation with other interpolation methods. See if that option works well enough for you. If you want output to be formally in MNI space in the output. You can refit the dataset with

3drefit -space MNI -view tlrc MNI2009c_FIRST_HOUSEFC_FACEFC_rppa+tlrc

[danlittledan]

Hi Daniel,

I’m sorry to reply so late…

I use “-preserve” to move the data with 3dfractionize:
3dfractionize -template …/ffa_ppa/0815/MNI152_T1_2009c+orig -input FIRST_HOUSEFC_FACEFC_rppa+tlrc -warp TT_N27+tlrc -preserve -clip 0.2 -prefix MNI_FIRST_HOUSEFC_FACEFC_rppa.
The warning was: this option requires short- or byte-valued input dataset！New dataset output failed. (attachment)
I did not successfully transfer the data to the MNI space.

I also tried :
3drefit -space MNI -view tlrc MNI2009c_FIRST_HOUSEFC_FACEFC_rppa+tlrc

I found it just changed some of the information inside the dataset’s header, I’m not sure the dataset was in MNI space after 3drefit.

How about “-tta2mni” in 3dWarp? I saw that it can also transform a dataset in tlrc to MNI space.

Could you give me some advice again? I really need the space conversion.

Thanks a lot!

[dglen]

Sorry this is more complicated than expected. Convert your dataset to short with

3dcalc -a mydset+tlrc’[1]’ -prefix func_short -expr a -datum short -gscale

Pick the dataset and subbrick you want, and then use func_short+orig as your input to 3dfractionize. I don’t think any clipping is needed here.

[danlittledan]

Thank you very much.

I have reprocessed my datasets on the MNI space.

Thanks again for your help!

Dan