Unary Operator error

[nmskhan]

Hi
I tried running my data set on the second script, and the following error was encountered.

./preproc_script_mouse2.sh: line 250: [: -eq: unary operator expected

Parse error: bad expression
:1

Is this something to worry about or does it change the final results? Is this bash-specific?
Please let me know
Thanks
Ned

[imnanxu]

Hi, please strictly follow the manual to specify the parameters to avoid such errors.Sent from my iPhoneOn Aug 27, 2023, at 12:11 PM, nmskhan ***@***.***> wrote: Hi I tried running my data set on the second script, and the following error was encountered. ./preproc_script_mouse2.sh: line 250: [: -eq: unary operator expected Parse error: bad expression :1 Is this something to worry about or does it change the final results? Is this bash-specific? Please let me know Thanks Ned —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[nmskhan]

Hi Thank you for your quick reply. I am strictly following the manual. Only issue I have, I am using my own atlas. This could be the reason for the error. The script does not give any errors for the sample data you provided. Thanks Ned

…

On Aug 27, 2023, at 12:35 PM, Nan Xu ***@***.***> wrote: Hi, please strictly follow the manual to specify the parameters to avoid such errors.Sent from my iPhoneOn Aug 27, 2023, at 12:11 PM, nmskhan ***@***.***> wrote: Hi I tried running my data set on the second script, and the following error was encountered. ./preproc_script_mouse2.sh: line 250: [: -eq: unary operator expected Parse error: bad expression :1 Is this something to worry about or does it change the final results? Is this bash-specific? Please let me know Thanks Ned —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <https://github.com/imnanxu/rodent-whole-brain-preprocessing-recipe/issues/14#issuecomment-1694709601>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI3HO4C5HIRRNRQCDONJH4TXXNZMJANCNFSM6AAAAAA4AM6IR4>. You are receiving this because you authored the thread.

[imnanxu]

Could you please inform which step this error occurs?
Another thing you might wanna check: If you use your own atlas, you will need to build your own template as well. Does your atlas match the template you built?

[nmskhan]

Thanks for your reply. I was able to figure it out (it was because of some alignment issue). I am running this on hamster brain, I do have hamster atlas and t2 image files and I am generating EPI hamster template from t2 file.

One quick question, I get these warnings when I run script 2, (I think this is because of type of data I used and orientation)
Is there anything to worry about, I simply just ignore them.

WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - PLEASE CHECK!

*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /Volumes/2TBSSD/EmoryPairWiseAnalysis/Hamsters_RAS/data_hamster1/EPI_n4_mask.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique

*+ WARNING: Input dataset ./data_hamster1/EPI_nuisance_brain.nii.gz grid mismatch from mask.

** WARNING: NIfTI file /Volumes/2TBSSD/EmoryPairWiseAnalysis/Hamsters_RAS/lib/tmp_hamster_128/hamsterEPIatlas.nii dimensions altered since AFNI extension was added

[imnanxu]

Glad that you figured that out!

The orientation issue is alarming. I would check the alignment/orientation of the atlas&template&t2 on fsleyes to make sure they have the same orientation. I think the following warnings might be all due to this misorientation issue:

• WARNING:: Inconsistent orientations for individual images in pipeline!
  *+ WARNING: Input dataset ./data_hamster1/EPI_nuisance_brain.nii.gz grid mismatch from mask.

You could ignore this for now:
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /Volumes/2TBSSD/EmoryPairWiseAnalysis/Hamsters_RAS/data_hamster1/EPI_n4_mask.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique

This warning means your atlas and EPI template don't have the same resolution/dimension. For this, you need to double-check with your t2 and atlas files.
** WARNING: NIfTI file /Volumes/2TBSSD/EmoryPairWiseAnalysis/Hamsters_RAS/lib/tmp_hamster_128/hamsterEPIatlas.nii dimensions altered since AFNI extension was added

[nmskhan]

Yes, I did check both atlas, t2 and my func data and aligned them manually as well as in RAS orientation.

Only issue could be, my atlas was in high resolution and I downsampled it to match your rat atlas file. However, I was able to get a decent seed correlation matrix. Thanks for your suggestions.