something went wrong with that process, don't know what
On 5/13/2022 10:35 AM, Zhang, Fan wrote:
External Email - Use Caution
Hi Dr. Greve,
I created the mgh file with “save_mgh” in MATLAB. I am not sure if it
showed empty here because the program failed to read it. I was able to
run the script with the same mgh files two months ago. I also just
verified the mgh file with the “load_mgh” in MATLAB and it showed the
dimension is [10242, 1, 1, 78].
Thanks,
Fan
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Thursday, May 12, 2022 10:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_surf2surf error
That mgh file has nothing in it (all dimensions 0). How did you create it?
On 5/12/2022 5:20 PM, Zhang, Fan wrote:
* External Email - Use Caution *
Hi Dr. Greve,
I got this when I ran the line you sent.
Thanks,
Fan
Hans-iMac-Pro:CCn_band fanzhang$ mri_info
lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
Volume information for lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
type: MGH
dimensions: 0 x 0 x 0
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 0.000
dof: 0
xstart: 0.0, xend: 0.0
ystart: 0.0, yend: 0.0
zstart: 0.0, zend: 0.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 0
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform not present
xform info: x_r =-1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000
: x_s = 0.0000, y_s =-1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm :
Orientation : ???
Primary Slice Direction: unknown
voxel to ras transform:
-1.0000 0.0000 0.0000 0.0000
0.0000 0.0000 1.0000 0.0000
0.0000-1.0000 0.0000 0.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000-0.0000-0.0000-0.0000
-0.0000-0.0000-1.0000-0.0000
-0.0000 1.0000-0.0000-0.0000
-0.0000-0.0000-0.0000 1.0000
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Thursday, May 5, 2022 3:33 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_surf2surf error
what happens if you run
mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
On 5/3/2022 11:54 AM, Zhang, Fan wrote:
* External Email - Use Caution *
Hello Everyone,
I am trying to run mri_surf2surf. But I got some errors saying
"no such file or directory" while in fact there are files in
the pathway. I was able to run this previously, so I am not
sure if this is relevant to the recent upgrade of the Mac
operation system (12.2.1). My FreeSurfer version is
(Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does anyone know how
to resolve this?
Thank you so much for the help!
Fan
mri_surf2surf --hemi lh --s fsaverage5 --sval
lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval
lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh
sysnameDarwin
hostname Hans-iMac-Pro.local
machinex86_64
userfanzhang
srcsubject = fsaverage5
srcval= lh.CCn_band.Seed1_20220314.V1.13subjs.mgh
srctype=
trgsubject = fsaverage5
trgval= lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame= 0
fwhm-in= 0
fwhm-out= 13
label-src= (null)
label-trg= (null)
OKToRevFaceOrder= 1
UseDualHemi = 0
Reading source surface reg
/Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg
Loading source data
MRIallocSequence(0, 0, 0, 0): bad parm
No such file or directory
Segmentation fault: 11
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