External Email - Use Caution
Hi
Thank you for your reply! mri_info
mris_info fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii
returns the follwoing:
==================================================
gifti_image struct
version = 1
numDA = 2
gim->meta nvpairs struct, len = 4 :
nvpair: 'Caret-Version' = '5.65'
nvpair: 'Date' = '2013-03-25T14:06:59'
nvpair: 'UniqueID' = '{ca14b266-2bf9-4910-8f46-7faecc9e1946}'
nvpair: 'encoding' = 'XML'
gim->labeltable giiLabelTable struct, len = 1 :
key 0, rgba (1.000, 1.000, 1.000, 0.000), label '???'
--------------------------------------------------
gim->darray[0] giiDataArray struct
intent 1008 = NIFTI_INTENT_POINTSET
datatype 16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim = 2
dims = 163842, 3, 0, 0, 0, 0
encoding 3 = GZipBase64Binary
endian 2 = LittleEndian
ext_fname =
ext_offset = 0
darray->meta nvpairs struct, len = 9 :
nvpair: 'AnatomicalStructurePrimary' = 'CortexRight'
nvpair: 'AnatomicalStructureSecondary' = 'MidLayer'
nvpair: 'Caret-Version' = '5.64'
nvpair: 'Date' = '2011-12-15T15:06:35'
nvpair: 'GeometricType' = 'Spherical'
nvpair: 'UniqueID' = '{1adeebae-d730-4e6c-8e93-b14805a6139f}'
nvpair: 'comment' = 'Imported from rh.sphere
scaled to fsaverage.rh.Midthickness_mni.mws.164k_fs.coord
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map
Deformation Map File: fsaverage.R.registered-to-fs_LR.164k_fs_LR.deform_map'
nvpair: 'configuration_id' = 'Unknown'
nvpair: 'topo_file' = 'fsaverage.R.closed.164k_fs_R.topo'
darray->coordsys giiCoordSystem struct
dataspace = NIFTI_XFORM_TALAIRACH
xformspace = NIFTI_XFORM_TALAIRACH
xform[0] : 1.000000 0.000000 0.000000 0.000000
xform[1] : 0.000000 1.000000 0.000000 0.000000
xform[2] : 0.000000 0.000000 1.000000 0.000000
xform[3] : 0.000000 0.000000 0.000000 1.000000
data = <set>
nvals = 491526
nbyper = 4
numCS = 1
darray->ex_atrs nvpairs struct, len = 0 :
--------------------------------------------------
--------------------------------------------------
gim->darray[1] giiDataArray struct
intent 1009 = NIFTI_INTENT_TRIANGLE
datatype 8 = NIFTI_TYPE_INT32
ind_ord 1 = RowMajorOrder
num_dim = 2
dims = 327680, 3, 0, 0, 0, 0
encoding 3 = GZipBase64Binary
endian 2 = LittleEndian
ext_fname =
ext_offset = 0
darray->meta nvpairs struct, len = 5 :
nvpair: 'Caret-Version' = '5.616'
nvpair: 'Date' = '2011-01-24T21:13:13'
nvpair: 'TopologicalType' = 'Closed'
nvpair: 'UniqueID' = '{15ec5dcb-b08c-420e-a8f9-057cbd2c0706}'
nvpair: 'comment' = 'Imported from rh.sphere'
data = <set>
nvals = 983040
nbyper = 4
numCS = 0
darray->ex_atrs nvpairs struct, len = 0 :
--------------------------------------------------
gifti_image struct
swapped = 0
compressed = 1
-- darray totals: 6 MB
gim->ex_atrs nvpairs struct, len = 2 :
nvpair: 'xmlns:xsi' = 'true'
nvpair: 'xsi:noNamespaceSchemaLocation' = 'true'
==================================================
Best
Karin
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: Monday, February 26, 2024 4:21:01 PM
To: Freesurfer support list
Subject: [ext] Re: [Freesurfer] mris_convert reading surf.gii files?
Your mris_convert command looks correct. I’m able to do the conversion like
this with dev version:
mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot
I’m wondering which Freesurfer you are running. If you do ‘mris_info surf.gii’,
what does it report?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Westin, Karin
Sent: Saturday, February 24, 2024 6:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_convert reading surf.gii files?
External Email - Use Caution
Hi
I'm trying to create an .annot file from a label.gii file using an HCP
fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii
fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the
error
** failed to open GIFTI XML file
'fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
mrisReadGIFTIdanum: gifti_read_image() returned NULL
Is there a better way to read/open CIFTI files using mris_convert?
Best and thanks
Karin
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