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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
History of AFNI updates
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I found out what I did wrong, I accidentally gave the wrong input. After that I only had to add -epi2anat instead of -anat2epi. Thanks for the help!
by
ikbeneeneric
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AFNI Message Board
Yeah, my output is something like anatal_junk+orig.HEAD/BRIK. And this is a 3D file, it only contains one image. I would like to have a 4D file with the same amount of volumes as the input functional .nii.gz (98 volumes). Should I try to run this coregistration for each volume separately or can I somehow run it on each one of them with only 1 run and also get an output with 98 volumes?
by
ikbeneeneric
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AFNI Message Board
Hi there,
Thanks again for your response.
I did copy and paste the command from my python script incorrectly, that's why the amount of double-quotes is odd.
We're using the -epi, I pasted the entire line of code from the Python script down below.
os.system("align_epi_anat.py -anat2epi -anat " + functional_dir + " -save_skullstrip -suffix "
by
ikbeneeneric
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AFNI Message Board
Hi there,
Thanks for your response.
The command we're running is:
align_epi_anat.py -anat2epi -anat " + functional_dir + " -save_skullstrip -suffix "
"al_junk -epi " + input_name_coregistration + " -epi_base 0 -epi_strip 3dAutomask -giant_move -volreg off -tshift off"
Where the functional_dir is a .nii.gz with more than one volume
by
ikbeneeneric
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AFNI Message Board
We're using align_epi_anat.py to perform coregistration on resting state MRI data. The script does work but it doesn't give us the desired output. As input we're giving a .nii.gz anatomical file and a functional .nii.gz file with about 98 volumes. Align_epi_anat.py gives us a 1D file as output, which makes sense when looking at the docs, but we're wondering if it's possib
by
ikbeneeneric
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AFNI Message Board
That is true, but when I change that the same error occures.
The output of the function I'm running should be:
out_file (a pathlike object or string representing an existing file) – Output file.
And the full error states:
traits.trait_errors.TraitError: The 'out_file' trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing
by
ikbeneeneric
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AFNI Message Board
Hello everyone, I'm a Bio-Informatics student from The Netherlands and for a school project I'm using the Nipype afni interface. I'm trying to perform normalization on structural coregistrated images using the autoTLRC function in nipype based on the @auto_tlrc from Afni. Now I'm running into an error while running it, I'm very new to the neurology preprocessing field.
by
ikbeneeneric
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AFNI Message Board