I am trying to use the NetPlotBrain library to plot the Dorsal Attention Network in the Glasser Atlas. However, the MNI coordinates seem to be plotting incorrectly on the library’s tools. Here’s what the plot is using, and I am using the Glasser360 atlas (glasser360MNI.nii.gz, from GitHub) in this link:
https://github.com/brainspaces/glasser360
This is what the plot looks like:
Does anyone know what to do for this?
Thanks,
Ani
Same issue, i am trying to plot using brainconn r package. I have tried to extract the centroid coordinates with afni, fsl and nibabel but all bring similar results. Nibabel from python seems more less right except that node index don’t seem to correspond to the rois as defined. Have you find a solution yet?
For what it is worth, I downloaded the NIFTI file from that GitHub repo, and just by trying to display the header information, it seems like there was some badness with it. This is the result of just running nifti_tool on it to display the header:
nifti_tool -disp_hdr -infiles ./glasser360MNI.nii.gz
** nifti_header_version: bad sizeof_hdr = 168430090
** ./glasser360MNI.nii.gz: bad nifti header version -1
** resetting invalid NIFTI version to 1
N-1 header file './glasser360MNI.nii.gz', num_fields = 43
all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr 0 1 168430090
data_type 4 10
<!DOCTYP
db_name 14 18 E html>
<html
la
extents 32 1 574449518
session_error 36 1 28261
regular 38 1 "
dim_info 39 1 10
dim 40 8 8224 8202 25632 29793 11617 28515 28524 11634
intent_p1 56 1 67422187560263187693568.0
intent_p2 60 1 285390924808294370932219015331840.000000
intent_p3 64 1 0.0
intent_code 68 1 24932
datatype 70 1 24948
bitpix 72 1 27693
slice_start 74 1 26473
pixdim 76 8 54969992417568985412357389811712.000000 70066966973833157804032.0 17841761196303659340660736.000000 0.0 71429295009271352534213830115328.000000 263070471475639091200.0 54958899314248201575050285940736.000000 70066966973833157804032.0
vox_offset 108 1 263020298561040416768.0
scl_slope 112 1 0.0
scl_inter 116 1 263010781188390387712.0
slice_end 120 1 24948
slice_code 122 1 45
xyzt_units 123 1 97
cal_max 124 1 0.0
cal_min 128 1 4515215449879990536104837120.000000
slice_duration 132 1 16930761507442511577088.0
toffset 136 1 273716066201068634112.0
glmax 140 1 1030972775
glmin 144 1 1937339170
descrip 148 80 tem" data-a11y-link-underlines="true"
>
<head>
<meta charset="utf-
aux_file 228 24 8">
<link rel="dns-pre
qform_code 252 1 25958
sform_code 254 1 25460
quatern_b 256 1 3024853282189717213806592.000000
quatern_c 260 1 0.056249
quatern_d 264 1 77455596791919140629456164487168.000000
qoffset_x 268 1 0.0
qoffset_y 272 1 73968382565394844355782416269312.000000
qoffset_z 276 1 0.0
srow_x 280 4 4616807007520475366555648.000000 17856807540992862686895857991680.000000 19363068665941709907121017978880.000000 4630426139518845732324900864.000000
srow_y 296 4 0.0 17849401607114688915570688.000000 3177438470043333886632450326528.000000 0.0
srow_z 312 4 0.0 270883230963020972687360.0 4296497166963830408871936.000000 4597719581775369065323332370432.000000
intent_name 328 16 ef="https://avat
magic 344 4 ars.
I’m not sure if that is part of the issue or not.
I couldn’t even copy the file:
3dcopy glasser360MNI.nii.gz tmp2.nii.gz
++ 3dcopy: AFNI version=AFNI_24.2.01 (Nov 7 2024) [64-bit]
** nifti_header_version: bad sizeof_hdr = 168430090
** nifti_image_read: bad nifti im header version -1
** failed to open input 'glasser360MNI.nii.gz' on non-AFNI write
Try including the view of the input dataset glasser360MNI.nii.gz
or use its fullname. That might take care of the error.
–pt
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