grid mismatch when using 3dmaskave

AFNI Message Board
1

Hello,

I got a warning message when I used 3dmaskave as below:

Input dataset func_s1_right_decon14+orig[Pos-Neg_GLT#0_Coef] grid mismatch from mask.
Try the following command for grid comparison:
3dinfo -header_line -prefix -same_all_grid ./ROI_put_R+orig.HEAD ./func_s1_right_decon14+orig.HEAD

However, I ran the 3dinfo shown above and found that the grid information of the two data sets are the same, as below:

                     prefix	       =dim?	=delt?	=ornt?	=cent?	=obl?
                  ROI_put_R	  1	           1          	   1	           1	          1
      func_s1_right_decon14	  1	           1	           1	           1	          1

=========

I have two EPI scans (s1 and s3) in my experiment, with the same scanning protocol except different oblique angle between the scans.

3dinfo -header_line -prefix -same_all_grid …/s1/s1.nii …/s3/s3.nii
prefix =dim? =delt? =ornt? =cent? =obl?
s1.nii 1 1 1 1 0
s3.nii 1 1 1 1 0
=========
During preprocessing, I removed the oblique information with 3drefit -deoblique, for both the EPI scans as well as the anatomy image. The alignment between the EPI and anatomy images was good. However, the warning message only appeared for the s1 scan when I ran 3dmaskave, and also, the 3dinfo did not show any mismatch between the files of ROI_put_R+orig.HEAD and func_s1_right_decon14+orig.HEAD.
I am confused by the warning message.

Any suggestion or idea on the issue would be appreciated. Thank you very much.

– Nan

2

Try

3dinfo -extent -d3 ./ROI_put_R+orig.HEAD ./func_s1_right_decon14+orig.HEAD

to see if there’s anything odd or different between the two datasets. Also post the 3dmaskave command you used.

3

Thanks, Daniel! I found the problem. The scanning plans for the two scans were not identical. This could be the mistake by the scanning technician.

BTW, I think I found a bug in 3dinfo.
When I run “3dinfo -extent FILE1” and “3dinfo -extent FILE2”, it shows the extent information correctly; when I run “3dinfo -extent FILE1 FILE2”, it shows the extent information for the two files with the extents from FILE1.
My AFNI version is 18.0.11.

Below is the terminal information.

3dinfo -extent -d3 ${rootpath}/data_proc/${sbj}/s1/s1.nii
-107.147003 109.415497 -123.905998 92.656502 -41.609699 83.190308 3.437500 -3.437500 3.900000
3dinfo -extent -d3 ${rootpath}/data_proc/${sbj}/s3/s3.nii
-107.694000 108.868500 -122.811996 93.750504 -39.969002 84.831001 3.437500 -3.437500 3.900000
3dinfo -extent -d3 ${rootpath}/data_proc/${sbj}/s1/s1.nii ${rootpath}/data_proc/${sbj}/s3/s3.nii
-107.147003 109.415497 -123.905998 92.656502 -41.609699 83.190308 3.437500 -3.437500 3.900000
-107.147003 109.415497 -123.905998 92.656502 -41.609699 83.190308 3.437500 -3.437500 3.900000
3dinfo -extent -d3 ${rootpath}/data_proc/${sbj}/s3/s3.nii ${rootpath}/data_proc/${sbj}/s1/s1.nii
-107.694000 108.868500 -122.811996 93.750504 -39.969002 84.831001 3.437500 -3.437500 3.900000
-107.694000 108.868500 -122.811996 93.750504 -39.969002 84.831001 3.437500 -3.437500 3.900000
afni -version
Precompiled binary macosx_10.7_local: Jan 27 2018 (Version AFNI_18.0.11)

– Nan

4

Hi Nan,

Sorry about the confusion. I fixed that extents problem this past February.

  • rick
5

Hi Rick,

Thanks for your information. I will update the AFNI package.

– Nan