External Email - Use Caution
Hi again and sorry for the very confusing questions...
I now (without really knowing what I did) managed to get
mris_convert --annot left.fsaverage_MY_PARC_2_164.label.gii
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
lh.MY_PARC_164k_1.annot
to run without errors. However it creates an .annot file with a rh.lh -prefix,
eg rh.lh.MY_PARC_164k_1.annot
I've checked multiple times that the .label.gii file used as input is really
Left Hemisphere. I tried just renaming the .annot file but then
mri_aparc2aseg --old-ribbon --s subject --annot MY_PARC_164k_1 --o
MY_PARC_164k_1.mgz
gives the following error
Loading lh annotations from ~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot
error: No such file or directory
error: # elements (163842) in
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot and # vertices (154818)
don't match
ERROR: MRISreadAnnotation() failed
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot
best and thanks for the help
karin
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: Thursday, February 29, 2024 10:59:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?
All these filenames are too similar. You mentioned at least 3 different files.
mris_info
fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
mris_info
fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii (ok)
mris_convert
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
ls -lt
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (ok)
Make sure the file exists and provide full path to mris_info/mris_convert
command.
If you continue to have problems with mris_info/mris_convert, share the .gii
and we will take a closer look.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:41 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 again this gives
ls -lt fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
-rw-rw-r-- 1 karin karin 4323015 feb 29 21:54
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
best
karin
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:29:25 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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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