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?
External Email - Use Caution
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Westin, Karin Sent: Saturday, February 24, 2024 6:10 PM To: freesurfer@nmr.mgh.harvard.edumailto: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