I am extremely grateful for your replying!
To make it clear for you, I would like to outline the process. Hope this is helpful.
The whole process is made up of following steps:
1. Download 13 different ROIs in matlab-WFU Human atlas-AAL (e.g. Frontal_Sup_L.nii), and then, for each ROI run the following code
"3dcalc -prefix WFU_Frontal_Sup_L.nii.gz -a Frontal_Sup_L.nii -expr 'step(a-0)'
3dresample -master SB92_noBrainstemCereb.nii.gz -dxyz 3 3 3 -prefix WFU_Frontal_Sup_L_3mm.nii.gz -input WFU_Frontal_Sup_L.nii.gz
3drefit -space MNI WFU_Frontal_Sup_L_3mm.nii.gz"
2. These 13 ROIs were grouped into the original mask by 3dcalc "a*1+b*2+...m*13". However, this original mask didn't fill in the brain well, leaving much empty space especially in the marginal area, so I chose to use the Draw Plungin to fill it——"Choose dataset for copying"- "Save" botton, get a COPY file, and then run the following code:
"3dcalc -a COPY_WFU_Frontal_Sup_L_3mm.nii.gz -b WFU_Frontal_Sup_L_3mm.nii.gz -expr 'a+b' -prefix aaa_Frontal_Sup_L.nii.gz
3dcalc -a aaa_Frontal_Sup_L.nii.gz -b SB92_noBrainstemCereb.nii.gz -expr 'a*b' -prefix Frontal_Sup_L_Edited1.nii.gz"
For each ROI, I repeated this process several times to get a dream one, which filled the border completely.
3. So far, no problem arose. Each ROI can be viewed in the AFNI. However, when I used the previous method, 3dcalc "a*1+b*2+...m*13" ,to make up a new mask. This mask also couldn't be viewed in the AFNI, and had the same "data bytes needed" error. Something wrong must had happened at this time. But I ignored it and found another way to avoide this error. Specifically, I calculated 3-4 ROIs each time (e.g. 3dcalc "a*1+b*2+c*3"), and then added them together. By this way, I got the ROI13_Mask.nii.gz.
I don't know what happen here, but I can view the ROI13_Mask.nii.gz in the AFNI, and the value related with each ROI is correct. When I tried to separate each ROI, that error arose again, as I had mentioned before.
-Here is the output of "nifti_tool -disp_nim -infiles ROI13_4.nii.gz"
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header file 'ROI13_4.nii.gz', num_fields = 63, fields:
all fields:
name offset nvals values
------------------- ------ ----- ------
ndim 0 1 3
nx 8 1 64
ny 16 1 76
nz 24 1 64
nt 32 1 1
nu 40 1 1
nv 48 1 1
nw 56 1 1
dim 64 8 3 64 76 64 1 1 1 1
nvox 128 1 311296
nbyper 136 1 1
datatype 140 1 2
dx 144 1 3.0
dy 152 1 3.0
dz 160 1 3.0
dt 168 1 0.0
du 176 1 0.0
dv 184 1 0.0
dw 192 1 0.0
pixdim 200 8 0.0 3.0 3.0 3.0 0.0 0.0 0.0 0.0
scl_slope 264 1 0.0
scl_inter 272 1 0.0
cal_min 280 1 0.0
cal_max 288 1 0.0
qform_code 296 1 4
sform_code 300 1 4
freq_dim 304 1 0
phase_dim 308 1 0
slice_dim 312 1 0
slice_code 316 1 0
slice_start 320 1 0
slice_end 328 1 0
slice_duration 336 1 0.0
quatern_b 344 1 0.0
quatern_c 352 1 -0.0
quatern_d 360 1 0.0
qoffset_x 368 1 -94.5
qoffset_y 376 1 -130.5
qoffset_z 384 1 -76.5
qfac 392 1 1.0
qto_xyz 400 16 3.0 -0.0 0.0 -94.5 0.0 3.0 -0.0 -130.5 0.0 0.0 3.0 -76.5 0.0 0.0 0.0 1.0
qto_ijk 528 16 0.333333 0.0 0.0 31.5 -0.0 0.333333 0.0 43.5 0.0 -0.0 0.333333 25.5 0.0 0.0 0.0 1.0
sto_xyz 656 16 3.0 -0.0 -0.0 -94.5 -0.0 3.0 -0.0 -130.5 0.0 0.0 3.0 -76.5 0.0 0.0 0.0 1.0
sto_ijk 784 16 0.333333 0.0 0.0 31.5 0.0 0.333333 0.0 43.5 -0.0 -0.0 0.333333 25.5 0.0 0.0 0.0 1.0
toffset 912 1 0.0
xyz_units 920 1 2
time_units 924 1 0
nifti_type 928 1 1
intent_code 932 1 0
intent_p1 936 1 0.0
intent_p2 944 1 0.0
intent_p3 952 1 0.0
intent_name 960 16
descrip 976 80
aux_file 1056 24
fname 1080 1 'ROI13_4.nii.gz'
iname 1088 1 'ROI13_4.nii.gz'
iname_offset 1096 1 607359616
swapsize 1104 1 0
byteorder 1108 1 1
data 1112 1 (raw data of unknown type)
num_ext 1120 1 1
ext_list 1128 1 ecode = 4, esize = 607359248, edata = <?xml
------------------------------------------------------------------------------------------------------------------
Besides, I also ran the "nifti_tool -disp_nim -infiles ROI13_Mask.nii.gz". The output of it is almost the same, except that the valve of iname_offset is 5568464 and the esize of ext_list is 5568112.
Thank you again very much.
Wind
Edited 1 time(s). Last edit at 03/17/2022 11:31PM by Wind.
