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I'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 0 168.980000000000 0
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
________________________________ 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. ________________________________
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 Caution
I'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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I 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
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.
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
________________________________ 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. ________________________________
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 Caution
I 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 Caution
I'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
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.
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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
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.
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
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.
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
________________________________ 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. ________________________________
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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
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.
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
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.
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
________________________________ 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. ________________________________
External Email - Use Caution
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
External Email - Use Caution
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
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.
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
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.
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
________________________________ 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. ________________________________
Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
External Email - Use Caution
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 Caution
I 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 Caution
I'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
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.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
External Email - Use Caution
Bruce-
Thank you for the reply. I'll try to summarize what I've done (and please see the attached jpeg showing my coordinate examples).
I needed to create a surface of the scalp/skull in order to query vertex coordinates in conjunction with some TMS localization. I ran:
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
I can load lh.seghead into freeview, cursor onto a vertex and note the coordinates. I then load the file into matlab via read_surf. I've since taken care to note that matlab is +1 in vertex number. I've also ran:
mris_curvature -w lh.seghead
as you suggested and reread the file in matlab. Attached are snippets from freeview and matlab showing that when I query lh.pial, I see the correct vertex coordinates in freeview and in matlab. When I do the same thing but use lh.seghead, the coordinates in matlab no longer match the vertex coordinates that I see in freeview., even after running mris_curvature -w.
How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for lh.seghead? If I load that file into matlab with read_surf, why do my coordinates not match what I see in freeview?
-Joel
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, November 5, 2018 11:12:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
External Email - Use CautionDoug-
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
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.
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
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.
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
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. ________________________________
The problem is a combination of things in that mri_tessellate writes out a file that read_surf.m cannot read. I have fixed this in our tree. You can get around it by using mri_mc instead of mri_tessellate (same exact command line). mri_mc uses marching cubes.
On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
External Email - Use Caution
Bruce-
Thank you for the reply. I'll try to summarize what I've done (and please see the attached jpeg showing my coordinate examples).
I needed to create a surface of the scalp/skull in order to query vertex coordinates in conjunction with some TMS localization. I ran:
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
I can load lh.seghead into freeview, cursor onto a vertex and note the coordinates. I then load the file into matlab via read_surf. I've since taken care to note that matlab is +1 in vertex number. I've also ran:
mris_curvature -w lh.seghead
as you suggested and reread the file in matlab. Attached are snippets from freeview and matlab showing that when I query lh.pial, I see the correct vertex coordinates in freeview and in matlab. When I do the same thing but use lh.seghead, the coordinates in matlab no longer match the vertex coordinates that I see in freeview., even after running mris_curvature -w.
How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for lh.seghead? If I load that file into matlab with read_surf, why do my coordinates not match what I see in freeview?
-Joel
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Monday, November 5, 2018 11:12:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
External Email - Use Caution
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 Caution
I 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 Caution
I'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
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.
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
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.
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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Doug-
I had time to play around with this, substituted the mri_mc command and.... success! Thank you so much for resolving this issue. Is this something that will be incorporated into the next release or will I have to remember to run this command for any other surfaces that I create?
-Joel
________________________________ 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: Thursday, November 8, 2018 9:26:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
The problem is a combination of things in that mri_tessellate writes out a file that read_surf.m cannot read. I have fixed this in our tree. You can get around it by using mri_mc instead of mri_tessellate (same exact command line). mri_mc uses marching cubes.
On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
External Email - Use CautionBruce-
Thank you for the reply. I'll try to summarize what I've done (and please see the attached jpeg showing my coordinate examples).
I needed to create a surface of the scalp/skull in order to query vertex coordinates in conjunction with some TMS localization. I ran:
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
I can load lh.seghead into freeview, cursor onto a vertex and note the coordinates. I then load the file into matlab via read_surf. I've since taken care to note that matlab is +1 in vertex number. I've also ran:
mris_curvature -w lh.seghead
as you suggested and reread the file in matlab. Attached are snippets from freeview and matlab showing that when I query lh.pial, I see the correct vertex coordinates in freeview and in matlab. When I do the same thing but use lh.seghead, the coordinates in matlab no longer match the vertex coordinates that I see in freeview., even after running mris_curvature -w.
How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for lh.seghead? If I load that file into matlab with read_surf, why do my coordinates not match what I see in freeview?
-Joel
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Monday, November 5, 2018 11:12:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
External Email - Use CautionDoug-
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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It will be in the next release. We may be depricating mris_tessellate in favor of mri_mc anyway. But I've already fixed it in mri_tessellate
On 11/9/18 3:31 PM, Bruss, Joel E wrote:
External Email - Use Caution
Doug-
I had time to play around with this, substituted the mri_mc command and.... success! Thank you so much for resolving this issue. Is this something that will be incorporated into the next release or will I have to remember to run this command for any other surfaces that I create?
-Joel
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, November 8, 2018 9:26:23 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
The problem is a combination of things in that mri_tessellate writes out a file that read_surf.m cannot read. I have fixed this in our tree. You can get around it by using mri_mc instead of mri_tessellate (same exact command line). mri_mc uses marching cubes.
On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
External Email - Use CautionBruce-
Thank you for the reply. I'll try to summarize what I've done (and please see the attached jpeg showing my coordinate examples).
I needed to create a surface of the scalp/skull in order to query vertex coordinates in conjunction with some TMS localization. I ran:
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
I can load lh.seghead into freeview, cursor onto a vertex and note the coordinates. I then load the file into matlab via read_surf. I've since taken care to note that matlab is +1 in vertex number. I've also ran:
mris_curvature -w lh.seghead
as you suggested and reread the file in matlab. Attached are snippets from freeview and matlab showing that when I query lh.pial, I see the correct vertex coordinates in freeview and in matlab. When I do the same thing but use lh.seghead, the coordinates in matlab no longer match the vertex coordinates that I see in freeview., even after running mris_curvature -w.
How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for lh.seghead? If I load that file into matlab with read_surf, why do my coordinates not match what I see in freeview?
-Joel
*From:* freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu *Sent:* Monday, November 5, 2018 11:12:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
External Email - Use CautionDoug-
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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Tuesday, October 16, 2018 3:15:16 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Tuesday, October 16, 2018 1:48:14 PM *To:* freesurfer@nmr.mgh.harvard.edumailto: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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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
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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. ________________________________
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Bruss, Joel E -
Greve, Douglas N.,Ph.D.