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Dear Dr. Greve,

This happens on all the MEG inputs I've tried not just one or two (I'm using files/data from the OMEGA dataset). I've put some print statements in the load_nifti.m file to see the nitemsread and nvoxels variables that (I think) seem to be causing the problem. The below is what I see:  

  

IsIco7 = 

     0

  

dim = 

   176

   240

   256

     1

     1

     1

     1

ind0 =

  0×1 empty double column vector

dim =

   176

   240

   256

     1

     1

     1

     1

nvoxels =

    10813440

fp =

     3

  

ans =

     0

  

Siamak_1_in_load_niftii

hdr = 

  struct with fields:

        sizeof_hdr: 348

            endian: 'l'

         data_type: '          '

           db_name: '                  '

           extents: 0

     session_error: 0

           regular: 114

          dim_info: 54

               dim: [8×1 double]

         intent_p1: 0

         intent_p2: 0

         intent_p3: 0

       intent_code: 0

          datatype: 4

            bitpix: 16

       slice_start: 0

            pixdim: [8×1 double]

        vox_offset: 352

         scl_slope: 1

         scl_inter: 0

         slice_end: 0

        slice_code: 0

        xyzt_units: 18

           cal_max: 0

           cal_min: 0

    slice_duration: 0

           toffset: 0

             glmax: 0

             glmin: 0

           descrip: 'TE=3;Time=134612.108;phase=1                                                    '

          aux_file: '                        '

        qform_code: 1

        sform_code: 1

         quatern_b: 1.745223999023438e-04

         quatern_c: 0

         quatern_d: 0

         quatern_x: -87.776428222656250

         quatern_y: -94.240295410156250

         quatern_z: -1.479825134277344e+02

            srow_x: [4×1 double]

            srow_y: [4×1 double]

            srow_z: [4×1 double]

       intent_name: '                '

             magic: 'n+1 '

             sform: [4×4 double]

             qform: [4×4 double]

           vox2ras: [4×4 double]

               vol: [21626880×1 double]

     

nitemsread =

    21626880

   

ans =

     3

   176

   240

   256

     1

     1

     1

     1

ERROR: D:\MEG_OMEGA_data\controls\sub-0249_Siamak\ses-01\anat\sub-0249_ses-01_run-1_T1w.nii, read in 21626880 voxels, expected 10813440

ERROR: loading D:\MEG_OMEGA_data\controls\sub-0249_Siamak\ses-01\anat\sub-0249_ses-01_run-1_T1w.nii as analyze

I'm just not clear what is causing this mismatch. I can share my screen and show you if you are able to Zoom? In any case, please let me know what you think. 

Best,

Siamak

On Thursday, January 26, 2023 at 07:13:32 AM PST, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Does this happen on every volume or just with this one. If just this one, then it is probably a problem with the volume itself and not the code

On 1/25/2023 9:15 PM, Siamak Sorooshyari wrote:

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Dear FreeSurfer, 

I am using the FieldTrip software to process MEG data, it involves my using the function ft_read_mri() in MATLAB to read in the anatomical MRI file. 

I have tried feeding into this function a .nii.gz as well as the unzipped .nii version. 

In the latter case I get an error: 

ERROR: D:\...\anat\sub-0249_ses-01_run-1_T1w.nii, read in 21626880 voxels, expected 10813440

I contacted the FieldTrip folks and they mentioned that it's a FreeSurfer issue. I think I've isolated the issue to the load_nifti.m file with the "nitemsread" variable and "nvoxels" variables not matching in value. I am not clear why this would happen, how can this be fixed?  

Best, 

Siamak

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