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

That mgh file has nothing in it (all dimensions 0). How did you create it?

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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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, May 5, 2022 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu <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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