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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_niftiihdr =
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 10813440ERROR: 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
<dgr...@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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