So you're saying that the dimension changed after you ran freeview and
saved the volume? Can you replicate it? ie, if you make a copy of the
brainmask.mgz, then edit the copy, does it do the same thing every time
you make a copy and edit it?
On 7/29/16 12:09 PM, Isabelle Deschamps wrote:
Dear FreeSurfer experts,
I am trying to fix the skull strip manually for a group of
participants. For all participants except 4, I get an error when
running recon-all -autorecon-pial -subjid S07_FS, after editing
manually in Freeview the brainmask.
In freeview, I followed the instruction for Edits to the brainmask
(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon)
I open freeview using this command on my participant's data:
*freeview -v pial_edits_before/mri/brainmask.mgz \*
*-f pial_edits_before/surf/lh.white:edgecolor=yellow \*
*pial_edits_before/surf/lh.pial:edgecolor=red
pial_edits_before/surf/rh.white:edgecolor=yellow \*
*pial_edits_before/surf/rh.pial:edgecolor=red *
Then, I follow these instructions, which are on the website.
*To fix this type of error you can simply edit away the offending
voxels from the brainmask.mgz volume. To do this you will need to
select the edit voxels tool and set the brush to a size and shape
comfortable for you. A circle brush of radius 2 works well for this
edit. Then you can simply use the shift key and your mouse button to
erase the voxels in the brainmask.mgz, or you can set the brush value
to 1 (so that the edits can be detected if you decide to run
"recon-all -show-edits") and simple draw over the voxels you want to
disappear.*
Then I save the brainmask volume using the save volume button.
When running *recon-all -autorecon-pial -subjid S07_FS* to correct the
pial surface, I get the following error:
ERROR: dimension mismatch between source and mask
The source of the problem is the the brainmask, in which one of the
dimensions is no longer 256. It is either 255 or 254. Prior the
modifications, the brainmask and the T1 had the same dimensions 256^3.
Following the brainmask edits, one dimension (it varies for the 4
problematic participants) is no longer 256. I do not understand why
for all participants except 4, the brainmask edits worked. I followed
the exact same procedure for all participants.
Any ideas or suggestions?
Thank you in advance for the help,
Isabelle
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