can you cc the list so that others can help?
On Wed, 5 Mar 2014, Koschutnig,
Karl (karl.koschutnig@uni-graz.at) wrote:

Hi Bruce,

thanks for the fast answer!

1) convert from mgz to nii

mri_convert wm.mgz wm.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from wm.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, -1.86265e-08, -5.40167e-08)

j_ras = (7.82311e-08, 1.52504e-08, -1)

k_ras = (2.23517e-08, 1, -1.59052e-08)

writing to wm.nii...

2) and back to mgz

mri_convert wm.nii wm.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from wm.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, -1.86265e-08, -5.40167e-08)

j_ras = (7.82311e-08, 1.52504e-08, -1)

k_ras = (2.23517e-08, 1, -1.59052e-08)

writing to wm.mgz...

3) the difference between the original wm and the converted one

mri_diff wm.mgz wm_orig.mgz Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08)

... for more details:

mri_diff

FREESURFER_HOME /usr/local/freesurfer

cwd /media/Data/FREESURFER/Fage_P026a/mri

cmdline mri_diff wm.mgz wm_orig.mgz --log diff

timestamp 2014/03/05-15:26:19-GMT

sysname Linux

hostname fMRI-04

machine x86_64

user fmri

v1 wm.mgz

v2 wm_orig.mgz

pixthresh 0.000000

checkres 1

checkacq 1

checkpix 1

checkgeo 1

checkori 1

checkprec 1

absdiff 1

diffabs 0

diffpct 0

rss 0

ssd 0

rms 0

logfile diff

v1 vox2ras ----------

-1.000 0.000 0.000 130.238;

-0.000 0.000 1.000 -128.800;

-0.000 -1.000 -0.000 121.348;

0.000 0.000 0.000 1.000;

v2 vox2ras ---------

-1.000 0.000 0.000 130.238;

-0.000 0.000 1.000 -128.800;

-0.000 -1.000 -0.000 121.348;

0.000 0.000 0.000 1.000;

Volumes differ in geometry vox2ras r=1 c=1 0.000000

best

Karl

________________________________________

Von: Bruce Fischl [fischl@nmr.mgh.harvard.edu]

Gesendet: Mittwoch, 5. März 2014 16:00

An: Koschutnig, Karl (karl.koschutnig@uni-graz.at)

Cc: freesurfer@nmr.mgh.harvard.edu

Betreff: Re: [Freesurfer] different thickness after converting wm.mgz in nifti and back

Hi Karl

why is there any difference in either geometry or pixel values after

converting back and forth? Can you send us your mri_convert command lines

and screen output?

cheers

Bruce

On Wed, 5 Mar 2014, Koschutnig, Karl

(karl.koschutnig@uni-graz.at) wrote:

Dear experts,

our group decided to make all the white matter edits in brainvoyager (don't ask me why;-). So we converted the wm.mgz into nii and then into the brainvoyager format vmr, made the edits and the same way back into freesurfer. We started the recon-all -autorecon2-wm … and found massive reduction in the thickness. So far so bad.

To figure out the problem we started at the beginning of the conversion-mess and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the same reduction in the thickness. Finally, here comes my question. Is it possible that due to interpolation errors in the mri_convert routine this reduction can be explained?

PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: Volumes differ in geometry row=1 col=1 diff=0.000000 (5.96046e-08)

Please fin attached the reconstructed white matter surface (red = original, yellow = after converting the wm from nii in mgz and back)

thank you so much

best Karl

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