01/09/2018 at 12:21 PM #3978RafDMParticipant
Hello to LeadDBS community,
I´d like to add to my templates the pediatric MNI NIHPD by Fonov et al.
Is it possible to do this?
Thanks in advance for your help01/09/2018 at 2:23 PM #3979andreashornKeymaster
sure, just make a new folder in the /templates/space directory and feed in the templates (e.g. t1.nii, t2.nii). Then you can copy/paste the file ea_space_def.mat file from the MNI_ICBM_2009b_NLIN_ASYM folder and adjust it accordingly.
Important is whether there is an FA template or not (hasfa=1 or 0), which anat_*.nii file will be mapped to which template (normmapping) and which is the default template (will be used for anat_*.nii files that are not explicitly assigned.
Best, Andy01/10/2018 at 9:15 AM #3987RafDMParticipant
Many Thanks for your answer.
FA template is not contained in the package (only T1, T2 and PD).
However, I renamed these nifti files accordingly with those present in default template but I cannot check normalization in detail and pre-reconstruction gave me this error:
Running job #4
Running ‘Image Calculator’
SPM12: spm_imcalc (v6961) 16:47:16 – 09/01/2018
Failed ‘Image Calculator’
Error using spm_vol>spm_vol_hdr (line 80)
File “/_/_/LeadDBS/templates/space/MNI_NIHPD/bb.nii” does not exist.
In file “/home/_/spm12/spm_vol.m” (v5958), function “spm_vol_hdr” at line 80.
In file “/home/_/spm12/spm_vol.m” (v5958), function “spm_vol” at line 61.
In file “/home/_/spm12/spm_imcalc.m” (v6961), function “spm_imcalc” at line 101.
In file “/home/_/spm12/config/spm_cfg_imcalc.m” (v7216), function “my_spm_imcalc” at line 232.
The following modules did not run:
Failed: Image Calculator
Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the
exact #job as displayed in this error message)
Running job #4
Error while evaluating UIControl Callback
Then I have tried to copy/paste bb.nii in the folder of this new template.
Could this create a bias? (in the MNI_NIHPD package are contained only t1w, t2w, pdw, wm, gm, csf)
At this point I obtained different images of CT artifact: correct for left electrode and completely wrong for the right one.
I have encountered the same problem when I tried in the default template.
The weird thing is that it happened when I normalized with ANTs (both SyN or BsplineSyN) but not with three-steps affine normalization (coregistration with ANTs, they are preoperative T1 and postoperative CT)
Do you know what is the problem?
Thank you for your help and availability
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