It seems to me that it failed to open the .gii file.

Can you check if ‘fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii’ exists and you have the read permission?

‘ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii’

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

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Hi I realized that the error occurs only with the Lh- file, that also gives this error

mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
** failed to open GIFTI XML file 'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
gifti_read_image() returned NULL

Is this a freesurfer error or is there something with the file?

thanks

Karin

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDU>
Sent: Thursday, February 29, 2024 10:05:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

The output from mris_info looks fine.

Are you still having trouble creating .annot file from a label.gii file? The command looks like this:

mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot

You need to provide full path to your input files.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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