ERROR: input(s) cannot have multiple frames

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1

hello guys,
i tried to run recon-all on subject.nii, i am getting the following error.
"ERROR: input(s) cannot have multiple frames!
Subject has 268 frames."

can someone help me out with this to know and resolve this error.

Thank,
Ritesh Mahajan

2

hi,

are you sure subject.nii is T1 MR image?

Alex

3

Hello Alex,

Yes, it is a T1 MR image.

Thanks,
Ritesh Mahajan

4

hi,

can you show me the output of:

mri_info subject.nii

Best,
Alex

5

Hello Alex,
Thanks for response.

Here is the output below :
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
WARNING: niiRead(): unknown time units 0 in subject.nii
INFO: this is an unsiged short. I'll try to read it, but
      it might not work if there are values over 32k
Volume information for subject.nii
          type: nii
    dimensions: 180 x 268 x 1 x 268
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: SHORT (4)
           fov: 180.000
           dof: 0
        xstart: -90.0, xend: 90.0
        ystart: -134.0, yend: 134.0
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 268
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 91.0000
              : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 135.0000
              : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 1.5000
Orientation : RAS
Primary Slice Direction: axial

voxel to ras transform:
                1.0000 0.0000 0.0000 1.0000
                0.0000 1.0000 0.0000 1.0000
                0.0000 0.0000 1.0000 1.0000
                0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant 1

ras to voxel transform:
                1.0000 0.0000 0.0000 -1.0000
                0.0000 1.0000 0.0000 -1.0000
                0.0000 0.0000 1.0000 -1.0000
                0.0000 0.0000 0.0000 1.0000

Thanks,
Ritesh Mahajan

6

see the problem:

dimensions: 180 x 268 x 1 x 268

freesurfer thinks it's 3D + time.

it should be:

dimensions: 180 x 268 x 268

to work

HTH
Alex