Hi Doug,
Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4
Thank you,
Kaley
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Wednesday, June 14, 2017 11:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 160, Issue 25
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Today's Topics:
1. Re: difference in T1 and T2 resolution (Douglas Greve) 2. Re: viewing surfaces in 3D using freeview (Ruopeng Wang) 3. Re: mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5 (Elijah Mak) 4. Re: difference in T1 and T2 resolution (John Anderson) 5. Re: recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension (Bruce Fischl) 6. Re: difference in T1 and T2 resolution (Douglas Greve) 7. Re: Brainmask Shifted (Douglas Greve) 8. Re: separate medial from lateral part in superiorfrontal parcel of Desikan-Killiany atlas (Bruce Fischl) 9. Re: Applying an affine transformation to a surface (Douglas Greve) 10. Re: Surface area of a define volume projection on cortical surface (Douglas Greve) 11. Re: viewing surfaces in 3D using freeview (Michael Davies) 12. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve) 13. Re: Merging outputs of mri_label2vol across hemi (Elijah Mak) 14. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve) 15. Re: Longitudinal Pipeline (Martin Reuter) 16. Re: viewing surfaces in 3D using freeview (Ruopeng Wang)
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Message: 1 Date: Wed, 14 Jun 2017 16:02:10 +0200 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] difference in T1 and T2 resolution To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9ddd5b02-e0df-ffbb-1515-e5bf02a622aa@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
This is not due to a difference between T1 and T2 resolution. The problem is that the two T1 volumes (001.mgz and 002.mgz) are difference sizes. It is probably not a good idea to try to combine them, but if you really want to, I can supply you with a solution.
On 6/14/17 1:12 PM, John Anderson wrote:
Thank you for your response. The log file is attached *Sent:* Tuesday, June 13, 2017 at 2:02 AM *From:* "Douglas Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
can you send the log file?
On 6/11/17 10:08 PM, John Anderson wrote:
In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8 MultiRegistration::loadMovables: voxel size is different /recons/subj1/mri/orig/002.mgz. Jon *Sent:* Sunday, June 11, 2017 at 2:12 PM *From:* "Matt Glasser" <matt@ma-tea.com> *To:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution What was the error message? Peace, Matt. From: <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of John Anderson <j.anderson@publicist.com <mailto:j.anderson@publicist.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, June 11, 2017 at 9:06 AM To: <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] difference in T1 and T2 resolution Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200 I tried to run "recon-all" but it failed to process the data. The command that I used is : pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache -T2pial -all" How can I analyze these images? Is it a correct procedure to conform the voxels using "mri_convert". Is this procedure correct? does it hurt the anatomy of the images? I highly appreciate your help John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
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