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help > RE: Preprocessing error, functional normalization
Nov 15, 2016 07:11 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Preprocessing error, functional normalization
Hi Eshel,
It is possible that in the latest Conn release, the explicit naming of the files has been changed and made clearer. Also, it explains why the appending is happening as postfix rather than prefix (for some of the steps which Conn does outside of SPM). So far so good (I have not yet had the opportunity to get going with the latest Conn release!).
Now, as far as subject 004 goes (as in your previous post), there is clearly something going wrong. As you can see, "dn_p004_tp1_meanesting_state.nii" does not match any pattern at all! Your file name should be "dana_p004_tp1_resting_state.nii" and not "dn*_meanesting*.nii'. This looks like a bug (unless there was a problem in the name of the file itself).
The mean functional file (which Conn was unable to find in your previous post) should (most likely) have been named "meanaudana_p004_tp1_resting_state.nii". This would reflect the fact that the functional volume was subjected to "realign and unwarp" and "slice timing correction" (in that order), subsequent to which the mean functional image was created.
I think you might have to wait for Dr. Alfonoso to have a look at what's going wrong. In the meantime, you can try working with an older version (I assume you are using release 17?) to explore the features of Conn.
Best
Pravesh
Originally posted by Neir Eshel:
It is possible that in the latest Conn release, the explicit naming of the files has been changed and made clearer. Also, it explains why the appending is happening as postfix rather than prefix (for some of the steps which Conn does outside of SPM). So far so good (I have not yet had the opportunity to get going with the latest Conn release!).
Now, as far as subject 004 goes (as in your previous post), there is clearly something going wrong. As you can see, "dn_p004_tp1_meanesting_state.nii" does not match any pattern at all! Your file name should be "dana_p004_tp1_resting_state.nii" and not "dn*_meanesting*.nii'. This looks like a bug (unless there was a problem in the name of the file itself).
The mean functional file (which Conn was unable to find in your previous post) should (most likely) have been named "meanaudana_p004_tp1_resting_state.nii". This would reflect the fact that the functional volume was subjected to "realign and unwarp" and "slice timing correction" (in that order), subsequent to which the mean functional image was created.
I think you might have to wait for Dr. Alfonoso to have a look at what's going wrong. In the meantime, you can try working with an older version (I assume you are using release 17?) to explore the features of Conn.
Best
Pravesh
Originally posted by Neir Eshel:
> Thanks for such a quick response! I'm
running the Conn default
> preprocessing pipeline. The functional input files are all named
> "dana_pXXX_tp1_resting_state.nii.gz", where the XXX is a number from 001
> to 999. I'm actually selecting the files directly using the Conn gui. I
> just downloaded Conn, so I wanted to try everything manually first, before
> writing scripts. It seems like the program is occasionally getting confused
> about the prefixes. I just ran it again for one of the same subjects that
> failed before and now it was able to complete the full preprocessing
> pipeline, creating "...resting_state_uw" and then "centering_meanu...",
> then "meanu...", then "u...", then "au...", then "y_meanu", then
> "wmeanu...", then "wau", then "swau..."
>
Is there something with the names? Thank you!
> preprocessing pipeline. The functional input files are all named
> "dana_pXXX_tp1_resting_state.nii.gz", where the XXX is a number from 001
> to 999. I'm actually selecting the files directly using the Conn gui. I
> just downloaded Conn, so I wanted to try everything manually first, before
> writing scripts. It seems like the program is occasionally getting confused
> about the prefixes. I just ran it again for one of the same subjects that
> failed before and now it was able to complete the full preprocessing
> pipeline, creating "...resting_state_uw" and then "centering_meanu...",
> then "meanu...", then "u...", then "au...", then "y_meanu", then
> "wmeanu...", then "wau", then "swau..."
>
Is there something with the names? Thank you!
Threaded View
Title | Author | Date |
---|---|---|
Neir Eshel | Nov 15, 2016 | |
Pravesh Parekh | Nov 15, 2016 | |
Neir Eshel | Nov 15, 2016 | |
Pravesh Parekh | Nov 15, 2016 | |
Alfonso Nieto-Castanon | Nov 16, 2016 | |
Neir Eshel | Nov 19, 2016 | |
Gunes Sevinc | Aug 7, 2018 | |
Pravesh Parekh | Nov 15, 2016 | |