Yes, type 3 is an MGH/MGZ file.

On Jul 11, 2009, at 1:42 PM, Bruce Fischl wrote:

Hi Lars,

can you send us the whole command line and output? I think type 3 is an MGH/MGZ file. Does mri_info work on it properly?

cheers Bruce On Sat, 11 Jul 2009, Lars M. Rimol wrote:

...

Hi,

What does it mean when mris_surf2surf produces the error message that the input file cannot be read "as type 3" ?

The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file.

Thank you!

yours, LMR

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

hmm, not sure what's going on. Can you also send the output of mri_info? If you try to load the file as an overlay in tksurfer does it work? On Sat, 11 Jul 2009, Lars M. Rimol wrote:

Hi Bruce,

Yes, mri_info works on all these files, and it states that it's an mgh file and the dimensions look allright and it says: type FLOAT (3).

Here's the output for the left hemisphere (with command line)

[lmr@localhost area]$ mri_surf2surf --s fsaverage --sval

/home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh

--hemi lh --fwhm 30 --tval

/home/lmr/subjects/analysis/TOP_sm100.s30_lh_cc2_11072009.mgh

srcsubject = fsaverage

srcval =

/home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh

srctype =

trgsubject = fsaverage

trgval =

/home/lmr/subjects/analysis/TOP_sm100.s30_lh_cc2_11072009.mgh

trgtype =

surfreg = sphere.reg

srchemi = lh

trghemi = lh

frame = 0

fwhm-in = 0

fwhm-out = 30

label-src = (null)

label-trg = (null)

Reading source surface reg /home/lmr/subjects/fsaverage/surf/lh.sphere.reg

Loading source data

mghRead(/home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh,

-1): could not open file

ERROR: could not read

/home/lmr/subjects/analysis/TOP_sm100_lh_cc2_11072009.mgh

as type 3

yours, LMR

...

Date: Sat, 11 Jul 2009 13:42:03 -0400 From: fischl@nmr.mgh.harvard.edu To: larilin@gmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot read file as type 3

Hi Lars,

can you send us the whole command line and output? I think type 3 is an MGH/MGZ file. Does mri_info work on it properly?

cheers Bruce On Sat, 11 Jul 2009, Lars M. Rimol wrote:

...

Hi,

What does it mean when mris_surf2surf produces the error message that the input file cannot be read "as type 3" ?

The file is an .mgh which I converted from an .mgz using mri_convert (mri_convert oldfile.mgz newfile.mgh). I get the same error when I use the .mgz file.

Thank you!

yours, LMR

hmmm, no idea why this would happen. Do you want to put it on the filedrop for us (we'll need everything to run mri_surf2surf to replicate the error) On Sat, 11 Jul 2009, Lars M. Rimol wrote:

Yes, I can load it as an overlay in tksurfer.

Here's the mri_info output:

[lmr@localhost area]$ mri_info TOP_sm100_lh_cc2_11072009.mgh

Volume information for TOP_sm100_lh_cc2_11072009.mgh

type: MGH

dimensions: 163842 x 1 x 1 x 216

voxel sizes: 1.0000, 1.0000, 1.0000

type: FLOAT (3)

fov: 163842.000

dof: 1

xstart: -81921.0, xend: 81921.0

ystart: -0.5, yend: 0.5

zstart: -0.5, zend: 0.5

TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees

nframes: 216

ras xform present

xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 81921.0000

: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.5000

: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.5000

talairach xfm :

Orientation : RAS

Primary Slice Direction: axial

voxel to ras transform:

1.0000 0.0000 0.0000 0.0000

0.0000 1.0000 0.0000 0.0000

0.0000 0.0000 1.0000 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 1.0000 -0.0000 -0.0000

-0.0000 -0.0000 1.0000 -0.0000

0.0000 0.0000 0.0000 1.0000

PS! I originally had this file (TOP_sm100_lh.mgh), which I reduced in Matlab, i.e. I removed 150 of the 366 subjects and then saved the new matrix with save_mgh. Both the original file and the new one crash in msi_surf2surf, both are viewable in tksurfer and their mri_info info looks similar to me.

[lmr@localhost area]$ mri_info TOP_sm100_lh.mgh

Volume information for TOP_sm100_lh.mgh

type: MGH

dimensions: 163842 x 1 x 1 x 366

voxel sizes: 1.0000, 1.0000, 1.0000

type: FLOAT (3)

fov: 163842.000

dof: 1

xstart: -81921.0, xend: 81921.0

ystart: -0.5, yend: 0.5

zstart: -0.5, zend: 0.5

TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees

nframes: 366

ras xform present

xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 81921.0000

: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.5000

: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.5000

talairach xfm :

Orientation : RAS

Primary Slice Direction: axial

voxel to ras transform:

1.0000 0.0000 0.0000 0.0000

0.0000 1.0000 0.0000 0.0000

0.0000 0.0000 1.0000 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 1.0000 -0.0000 -0.0000

-0.0000 -0.0000 1.0000 -0.0000

0.0000 0.0000 0.0000 1.0000