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Can anyone help? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruss, Joel E Sent: Friday, October 19, 2018 9:26:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
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Doug-
Did you have any other ideas on this? I'm using FreeSurfer 6.0.0, if that helps any. I've tried the "mkheadsurf" command on three different subjects and all have the same issues. The coordinates I get in matlab are nowhere near what I see in Freeview.
-Joel
________________________________ From: Bruss, Joel E Sent: Tuesday, October 16, 2018 3:53:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
Attached is a screenshot showing what I see in Freeview and what I see in Matlab.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Tuesday, October 16, 2018 3:15:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
which coords are you looking at? They should be the "surface RAS" coords.
On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
External Email - Use CautionI couldn't remember if it's 1+ or 1-. Either way, either direction give similar coordinates that don't match up to what I can see in FreeView.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Tuesday, October 16, 2018 1:48:14 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation When you look at the vertex in matlab, are you correctly accounting for the fact that FreeView uses 0-based indexing and matlab uses 1-based? Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be using 234740 in matlab below
On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
External Email - Use CautionI'm trying to make a surface file from a subject's head and to map coordinates to that surface. If I run:
mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2
mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 $SUBJECTS_DIR/$sub/surf/lh.seghead
and then load lh.seghead in FreeView, it looks as I would expect. Clicking anywhere near a vertex gives the typical output, showing the closest vertex. All fine and well. However, if I load the file in
Matlab:
vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
my values are nothing near what I'm seeing in Freeview. For example, FreeView reports:
vertex 234741 [-78.50,14.50,26.50]
read_surf reports:
vertex 234740 0168.9800000000000
Of note, an error log tells me that:
MRISreadNewCurvature: incompatible vertex number in file $SUBJECTS_DIR/$sub/surf/lh.curv
How do I edit, update or create a curv file to play with the new surface file, or what can I do to get sensical surface coordinates from this data?
Thanks, Joel
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________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________
________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________