Unable to open/load the S*_3T_2009cAsym.nii.gz

[albertleemon]

Hi!
Thanks for your great work.

I'm writing to confirm is there an issue to open/load the 'subcortex/Group-Parcellation/3T/Subcortex-Only/S*_3T_2009cAsym.nii.gz'. These images could not be loaded or opened properly as followings. I am not sure is this only happen on my side or not?

$ fslinfo 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz'
Error: file does not appear to be a valid NIFTI or ANALYZE image

$ fslview_deprecated 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz'
** ERROR: nifti_convert_nhdr2nim: bad dim[0]
** ERROR (nifti_image_read): cannot create nifti image from header 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz'

Best Regards
Meng

[yetianmed]

Hi Meng, These NIFTI images are in compressed format (*.gz). You can run gunzip to get rid of the *.gz and fslinfo should be able to recognise the file. Best, Ye From: Meng ***@***.***> Reply to: yetianmed/subcortex ***@***.***> Date: Wednesday, 10 November 2021 at 11:58 pm To: yetianmed/subcortex ***@***.***> Cc: Subscribed ***@***.***> Subject: [yetianmed/subcortex] Unable to open/load the S*_3T_2009cAsym.nii.gz (Issue #5) Hi! Thanks for your great work. I'm writing to confirm is there an issue to open/load the 'subcortex/Group-Parcellation/3T/Subcortex-Only/S*_3T_2009cAsym.nii.gz'. These images could not be loaded or opened properly as followings. I am not sure is this only happen on my side or not? $ fslinfo 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz' Error: file does not appear to be a valid NIFTI or ANALYZE image $ fslview_deprecated 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz' ** ERROR: nifti_convert_nhdr2nim: bad dim[0] ** ERROR (nifti_image_read): cannot create nifti image from header 'Tian_Subcortex_S2_3T_2009cAsym.nii.gz' Best Regards Meng — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#5>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ANJ3HLY4FK2PBGTQDEG2EOTULJUAJANCNFSM5HX2UVBQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[albertleemon]

Hi Ye,

Thanks for your rapid reply. It does not work in that way. (I think FSL can handle the nii.gz on default.)

$ gunzip Tian_Subcortex_S2_3T_2009cAsym.nii.gz

$ fslinfo 'Tian_Subcortex_S2_3T_2009cAsym.nii'
Error: file does not appear to be a valid NIFTI or ANALYZE image

$mricron 'Tian_Subcortex_S2_3T_2009cAsym.nii'
Warning: the header file is not in NIfTi format [the first 4 bytes do not have the value 348]. Assuming big-endian data.

Does you the NIFIT file at hand? Would be possible to have a second look? Thanks a lot.

Best regards
Meng