How should I know the slice acquisition order just with NIFIT format?

AFNI Message Board
1

Dear all,

    How should I know the slice acquisition order(such as sequence,alternative.....) just with NIFIT format?(the scanner information:mobile 1.5T Siemens Avanto)

    I have already tried some ways but there are no effects to obtain the information of the slice time :

    1.   3dinfo -VERB filename.nii.gz | grep offsets

       the results : 
              
        ++ 3dinfo: AFNI version=AFNI_17.3.05 (Nov 27 2017) [64-bit]

    2.   3dinfo -slice_timing filename.nii.gz

      the results :  
      0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000


    I am confused about the slice time order,and I have the file just the NIFIT format not DICOM format ,so if any comman just like Dimon and anything others will work out???


  Thanks a lot!
   Fairy
2

Dear all,

   My problem have been already settled down.Actually,if you don't have a dataset with DICOM format and even no useful information about the slice timing order keep in the header file which with NIFIT format,there are no way to  know the slice acquisition order entirely just with command.But there are another two ways which we can use to obtain the information of the slice time partially:

   1. nifti_tool -disp_hdr -field slice_code -field slice_duration -field slice_start -field slice_end -infile filename.nii.gz

      the results : 

     N-1 header file 'NDARHL358LGQ_Resting_State_2.5mm.nii.gz', num_fields = 4
       name                offset  nvals  values
      ------------------- ------  -----  ------
        slice_code           122      1    0
        slice_duration       132      1    0.0
        slice_start           74      1    0
        slice_end            120      1    53

    Then you can get some useful information just like the "slice_start" is "0",the " slice_end" is "53" and so on.



    2. You can also use the graph display in the afni viewer to check slice timing.The important thing we will know is the the slices are acquired interleaved or not. 
       The more details attached.   https://en.wikibooks.org/wiki/Neuroimaging_Data_Processing/Slice_Timing

Thanks a lot!
Fairy

3

Hi Fairy,

I am not sure what state you have gotten to, but that NIFTI
file does not contain any slice timing information. You either
need to go back to the DICOM files, or, much more likely,
inquire from the person who acquired the data (since it
usually is not in the DICOM files, either).

  • rick