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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, May 5, 2022 3:33 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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:
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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
sysname Darwin
hostname Hans-iMac-Pro.local
machine x86_64
user fanzhang
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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