To try to understand the problem as to why the brainmask.mgz and T1.mgz files are not the same size, I decided to skip that step and make edits to the white matter only. At this point, all files (i.e. T1.mgz, brainmask.mgz and the wm.mgz) have the same
dimensions 256^3.
I removed offending voxels from the wm.mgz file using Freeview as per the instructions found on this website:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview. For all participants except 4, the modifications did not result in in errors. However, for the same 4 participants that had problems with the brainmask.mgz file, I have problems
with the wm edits after running :
recon-all -autorecon2-wm -autorecon3 -subjid S08_FS
This is the error that I got:
ERROR: mri_segment-MRIcheckVolDims: volume1 height=255 != volume2 height=256.
Darwin Isabelles-iMac.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
recon-all -s S08_FS exited with ERRORS at Tue Aug 9 13:44:25 EDT 2016
It appears that for these 4 participants that are problematic, any corrections made to the brainmask or wm.mgz file changes the dimensions of those files.
The original wm.mgz file had the following dimensions:
mri_info /Users/Isabelle/Desktop/wm/S08/wm.mgz
Volume information for /Users/Isabelle/Desktop/wm/S08/wm.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
whereas the modified wm.mgz file has the following dimensions:
mri_info /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/wm.mgz
Volume information for /Volumes/Flynn/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri/wm.mgz
type: MGH
dimensions: 255 x 255 x 256
voxel sizes: 1.0000, 1.0000, 1.0000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -127.5, xend: 127.5
ystart: -127.5, yend: 127.5
zstart: -128.0, zend: 128.0
I am installing Freesurfer on another Mac running El Capitan to see if the problem persists. Any ideas as to what is causing the problem?
Thanks,
Isabelle
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: brain mask and T1 are not the same size (Isabelle Deschamps)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Aug 2016 13:21:09 +0000
From: Isabelle Deschamps <isabelle.deschamps.1@ulaval.ca>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <56102043-B30A-4E16-B1B8-8CDF75269E98@ulaval.ca>
Content-Type: text/plain; charset="us-ascii"
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160808/c03a96e3/attachment-0001.html
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 150, Issue 11
*******************************************
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.