Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

2024-02-29 Thread Westin, Karin 
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 
 on behalf of Huang, Yujing 

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 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:41 PM
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

2024-02-29 Thread Westin, Karin 
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 
 on behalf of Huang, Yujing 

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 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
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
encoding3 = 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] :  1.00  0.00  0.00  0.00
xform[1] :  0.00  1.00  0.00  0.00
xform[2] :  0.00  0.00  1.00  0.00
xform[3] :  0.00

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

2024-02-29 Thread Westin, Karin 
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 
 on behalf of Huang, Yujing 

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 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 2:40 PM
To: Freesurfer support list 
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
encoding3 = 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] :  1.00  0.00  0.00  0.00
xform[1] :  0.00  1.00  0.00  0.00
xform[2] :  0.00  0.00  1.00  0.00
xform[3] :  0.00  0.00  0.00  1.00
data   = 
nvals  = 491526
nbyper = 4
numCS  = 1
darray->ex_atrs nvpairs struct, len = 0 :
--
--
gim->darray[1] giiDataArray struct
intent   1009 = NIFTI_INTENT_TRIANGLE
datatype8 = NIFTI_TYPE_INT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 327680, 3, 0, 0, 0, 0
encoding3 = 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   = 
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:x

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

2024-02-29 Thread Westin, Karin 
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
encoding3 = 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] :  1.00  0.00  0.00  0.00
xform[1] :  0.00  1.00  0.00  0.00
xform[2] :  0.00  0.00  1.00  0.00
xform[3] :  0.00  0.00  0.00  1.00
data   = 
nvals  = 491526
nbyper = 4
numCS  = 1
darray->ex_atrs nvpairs struct, len = 0 :
--
--
gim->darray[1] giiDataArray struct
intent   1009 = NIFTI_INTENT_TRIANGLE
datatype8 = NIFTI_TYPE_INT32
ind_ord 1 = RowMajorOrder
num_dim   = 2
dims  = 327680, 3, 0, 0, 0, 0
encoding3 = 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   = 
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 
 on behalf of Huang, Yujing 

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 
 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

[Freesurfer] mris_convert reading surf.gii files?

2024-02-24 Thread Westin, Karin 
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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