search

grandjeanlab / MultiRat

A Rat fMRI multi-center study
Other
32 stars 6 forks source link

There is an inconsistency between the template and altas? #1

Closed doulemint closed 2 years ago

doulemint commented 2 years ago

When I ran preprocessing script, I ran into this error from rabies images:

The file /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/SIGMA_Anatomical_Brain_Atlas.nii does not appear to overlap with provided template /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii

they seemly have different size and aligned to different spaces?

3dinfo /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii
++ 3dinfo: AFNI version=AFNI_20.3.03 (Dec  7 2020) [64-bit]

Dataset File:    /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii
Identifier Code: NII_n31pxrqN0SUbpM1S9tWqDg  Creation Date: Sat May 21 21:55:35 2022
Template Space:  TLRC
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   7,143,424 (7.1 million) bytes
Geometry String: "MATRIX(-0.15,0,0,9.44,0,-0.15,0,17.81,0,0,0.15,-6.765):128,218,128"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:    -9.610 [R] -to-     9.440 [L] -step-     0.150 mm [128 voxels]
A-to-P extent:   -14.740 [A] -to-    17.810 [P] -step-     0.150 mm [218 voxels]
I-to-S extent:    -6.765 [I] -to-    12.285 [S] -step-     0.150 mm [128 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is short
3dinfo /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/SIGMA_Anatomical_Brain_Atlas.nii.gz
++ 3dinfo: AFNI version=AFNI_20.3.03 (Dec  7 2020) [64-bit]

Dataset File:    /template/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/SIGMA_Anatomical_Brain_Atlas.nii.gz
Identifier Code: NII_DeJGSOJNSF-zX8FkVqSwyg  Creation Date: Sat May 21 21:55:18 2022
Template Space:  TLRC
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   65,445,120 (65 million) bytes
Geometry String: "MATRIX(-0.09,0,0,11.61,0,-0.09,0,17.6175,0,0,0.09,-6.96597):260,342,184"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:   -11.700 [R] -to-    11.610 [L] -step-     0.090 mm [260 voxels]
A-to-P extent:   -13.073 [A] -to-    17.618 [P] -step-     0.090 mm [342 voxels]
I-to-S extent:    -6.966 [I] -to-     9.504 [S] -step-     0.090 mm [184 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float

I hope I make my problem clear. I might missed out some steps. Could anyone helps me?

grandjeanlab commented 2 years ago

Hi, this is correct. I have informed the author of the template, but I don't kbow if it got updated.

Send me an email (joanes.grandjean@radboudumc.nl) and I will send you a copy of the atlas resampled into the template

DavidBarriere commented 2 years ago

Hi, I am fixing it for the next version of the SIGMA. A corrected version is coming.

David

grandjeanlab commented 2 years ago

I head from @DavidBarriere that the atlas was corrected and a new version is uploaded. @doulemint could you check if it works now?

Hierakonpolis commented 2 years ago

I am experiencing the same issue, I tried using the following files from all dowloadable versions of the atlas (1.1, 1.11, 1.2)

Atlas: SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/SIGMA_Anatomical_Brain_Atlas.nii Template: SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/SIGMA_InVivo_Brain_Template.nii

The affine matrices also seem to indicate that these volumes would reside in different spaces.

gdevenyi commented 2 years ago

@DavidBarriere?

DavidBarriere commented 2 years ago

Hi guys, Header checking and fixing in progress.

DavidBarriere commented 2 years ago

Could you please download and try the Sigma Wistar Rat Brain Templates and Atlases Version1.2.1 on NITRC platform ? https://www.nitrc.org/projects/sigma_template

You will find little changes in SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas folder with two additional folders :

I also add in vivo GM, WM and CSF masks within the SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template folder

Please send here your feedback.

D