Hi Vasudev,

On the surface, your commands seem correct, although you are using the same name (Amygdala_L.nii.gz) for your MNI-space input as for your functional-space output - is there a chance you have overwritten the original input?

Would you be able to upload the files listed below to this url so I can take a look: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=771963AC5AF6AD77F1

T1w.nii.gz
highres2standard.mat
highres2standard_warp.nii.gz
highres2standard_warp_inv.nii.gz
Amygdala_L.nii.gz
Amygdala_L_Hres.nii.gz
highres2example_func.mat
example_func.nii.gz

Cheers,

Paul

On Wed, 21 Aug 2019 at 22:37, Dev vasu <[log in to unmask]> wrote:

Dear all,

I am trying to transform the Label file ( In this case Amygdala_Left hemisphere ) into functional space and i am encountering problems

Following are the steps i have followed

 # Nonlinear transform highres to standard-where T1w.nii.gz is structural image

1. fnirt --in= T1w.nii.gz' --aff=reg/highres2standard.mat --cout=reg/highres2standard_warp --config=/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_2mm

# Inverse of Non linear transform

2. inwarp --ref=T1w.nii.gz' --warp=reg/highres2standard_warp --out=reg/highres2standard_warp_inv

# Now i am warping ROI ( Amygdala_L) to subject T1w.nii.gz space

3.applywarp --ref=T1w.nii.gz'  --in=Amygdala_L.nii.gz --warp=reg/highres2standard_warp_inv --out=reg/Amygdala_L_Hres.nii.gz --interp=nn

# Applying affine transform to move warped ROI (Amygdala_L_Hres.nii.gz) into functional space

flirt -in reg/Amygdala_L_Hres.nii.gz -applyxfm -init reg/highres2example_func.mat -out Amygdala_L.nii.gz -datatype float -paddingsize 0.0 -interp nearestneighbour -ref reg/example_func.nii.gz

and the result of this transformation is attached for your reference

Could you please let me know why the ROI is completely misplaced here, and where i am doing wrong.

Thanks

Vasudev

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

---

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1