AFNI Message Board

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  

|
March 08, 2021 02:42PM
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.

The error is the following:
'/Users/erichoekstra/PycharmProjects/brainnetworks_eric_linda/structural_flirt+tlrc.HEAD' <class 'str'> was specified

It's a FileNotFoundError, this file is indeed not in the folder stated above, but why is this not the case? Shouldn't it be made by Afni?

My code in Python:

```python
autoTLRC = afni.AutoTLRC()
autoTLRC.inputs.in_file = 'structural_flirt.nii.gz'
autoTLRC.inputs.no_ss = True
autoTLRC.inputs.base = "MNI_avg152T1+tlrc"
autoTLRC.cmdline
'@auto_tlrc -base TT_N27+tlrc -input structural.nii -no_ss'
res = autoTLRC.run()
```

Thank you in advance!
Subject Author Posted

Afni autoTLRC FileNotFoundError

ikbeneeneric March 08, 2021 02:42PM

Re: Afni autoTLRC FileNotFoundError

Daniel Glen March 08, 2021 05:27PM

Re: Afni autoTLRC FileNotFoundError

ikbeneeneric March 08, 2021 07:45PM