Just guessing here, but it looks like it is reading in 2x the number of
voxels than expected, so maybe it is a "double" image instead of a
"float"? If so, can you convert it to float to see if it works?
On 1/27/2023 2:09 AM, Siamak Sorooshyari wrote:
External Email - Use Caution
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
<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:
External Email - Use Caution
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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