Betreff: Re: AW: [Freesurfer] different thickness after converting wm.mgz in nifti and back
can you cc the list so that others can help? On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschutnig@uni-graz.atmailto: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.edumailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 5. März 2014 16:00 An: Koschutnig, Karl (karl.koschutnig@uni-graz.atmailto:karl.koschutnig@uni-graz.at) Cc: freesurfer@nmr.mgh.harvard.edumailto: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.atmailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
There will be small differences, but I don't think the differences you are showing are the problem (they are tiny). The wm.mgz should be of type uchar. Check to see whether it still is after you save it from BV doug
On 03/05/2014 11:37 AM, Koschutnig, Karl (karl.koschutnig@uni-graz.at) wrote:
*Betreff:* *Re: AW: [Freesurfer] different thickness after converting wm.mgz in nifti and back*
can you cc the list so that others can help? On Wed, 5 Mar 2014, Koschutnig, Karl (karl.koschutnig@uni-graz.at mailto:karl.koschutnig@uni-graz.at) wrote:
Hi Bruce, thanks for the fast answer!
- 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...
- 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...
- 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 mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 5. März 2014 16:00 An: Koschutnig, Karl (karl.koschutnig@uni-graz.at mailto:karl.koschutnig@uni-graz.at) Cc: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Koschutnig, Karl (karl.koschutnig＠uni-graz.at)