yetianmed / subcortex

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Unable to open/load the S*_3T_2009cAsym.nii.gz #5

Closed albertleemon closed 8 months ago

albertleemon commented 2 years ago

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 commented 2 years ago

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

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albertleemon commented 2 years ago

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