I am trying to use the @AddEdge program to check the alignment result (aligning functional to anatomical dataset).
I would like AddEdge to show me an overlay of the edges of the final anatomical image and of the edges of the functional image (before alignment). And then the same with the Edges of the functional (after alignment).
The overlays that I get in the AddEdge display don t make sense because I see only the light blue and dark red color, but no purple.
After running the proc.py script, I ran @AddEdge alone.
the first file is the final anatomical image, the second is the functional volume before alignment and the third is the functional volume after alignment resampled to the final_epi_vr_base_min_outlier+orig.
Once I ran the above command, afni recommends the command @AddEdge in the terminal, so I simply type @AddEdge. Afni then opens up the GUI and the first overlay I see is final_epi_vr_base_min_outlier_ec+orig & anat_final_final_epi_vr_base_min_outlier_ec+orig.The images are lacking the purple color and therefore I can not make sense out of them.
The issue here is that @AddEdge was originally made to take a single EPI dataset first and then the anatomicals after that (“@AddEdge epi0+orig anat1+orig anat2+orig anat3+orig …”). Your order is reversed. I put in a couple new changes to allow for resampling to the grid of your choice with “-master mymasterdset+orig” or let the script find the dataset with the smallest voxels among all the datasets provided (slightly changing its previous behavior). I just checked this in, so look for binary updates following this posting.
Also consider @snapshot_volreg for a single image picture of the EPI and anatomical volumes with edge images.
I tried to use @AddEdge on one EPI data set (the min_outlier volume) and two anatomical data sets. I still have the same problem that the displayed overlap image has only light blue and dark red color (the purple color is missing) and that AddEdge seems to overlap the wrong images.
I used: @AddEdge final_epi_vr_base_min_outlier+orig. anat_final.103+orig. anat_final_2.103+orig.
after this is run in the terminal and creates all those files:
_ae.ExamineList.log anat_final_2.103_rs_ec+orig.BRIK
anat_final.103+orig.BRIK anat_final_2.103_rs_ec+orig.HEAD
anat_final.103+orig.HEAD final_epi_vr_base_min_outlier+orig.BRIK
anat_final.103_e3+orig.BRIK final_epi_vr_base_min_outlier+orig.HEAD
anat_final.103_e3+orig.HEAD final_epi_vr_base_min_outlier_anat_final.103_ec+orig.BRIK
anat_final.103_ec+orig.BRIK final_epi_vr_base_min_outlier_anat_final.103_ec+orig.HEAD
anat_final.103_ec+orig.HEAD final_epi_vr_base_min_outlier_anat_final_2.103_rs_ec+orig.BRIK
anat_final_2.103+orig.BRIK final_epi_vr_base_min_outlier_anat_final_2.103_rs_ec+orig.HEAD
anat_final_2.103+orig.HEAD final_epi_vr_base_min_outlier_e3+orig.BRIK
anat_final_2.103_rs+orig.BRIK final_epi_vr_base_min_outlier_e3+orig.HEAD
anat_final_2.103_rs+orig.HEAD final_epi_vr_base_min_outlier_ec+orig.BRIK
anat_final_2.103_rs_e3+orig.BRIK final_epi_vr_base_min_outlier_ec+orig.HEAD
anat_final_2.103_rs_e3+orig.HEAD
it tells me that it recommends the command @AddEdge. So I run @AddEdge
The image that is opened after I run @AddEdge is: anat_final.103_ec & final_epi_vr_base_min_outlier_anat_final.103_ec
What am I doing wrong? I would be very happy when I could receive some help to get it work. Thanks a lot in advance!
Carolin
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