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Hi friendly Freesurfers,
I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can view in tksurfer. Is there a way/formula to convert these easily, ideally into MNI coordinates?
I tried loading the label into Matlab with freesurfer_read_label.m converting to Talairach with freesurfer_label2tal.m and then also converting those coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not match with the Talairach/MNI coordinates shown for the corresponding vertices in tksurfer.
Thank you,
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. ________________________________
Hi Joel
I believe they are stored in "tkreg ras" by default. In any case, mri_label2label should let you map them to pretty much any space you like.
cheers Bruce On Fri, 27 Sep 2019, Berger, Joel wrote:
External Email - Use Caution
Hi friendly Freesurfers,
I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can view in tksurfer. Is there a way/formula to convert these easily, ideally into MNI coordinates?
I tried loading the label into Matlab with freesurfer_read_label.m converting to Talairach with freesurfer_label2tal.m and then also converting those coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not match with the Talairach/MNI coordinates shown for the corresponding vertices in tksurfer.
Thank you,
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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Thanks so much for the quick and clear reply Bruce. I'll look into doing that.
Cheers,
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: 27 September 2019 12:52:47 To: Freesurfer support list Subject: [External] Re: [Freesurfer] Converting .label coordinates to MNI
Hi Joel
I believe they are stored in "tkreg ras" by default. In any case, mri_label2label should let you map them to pretty much any space you like.
cheers Bruce On Fri, 27 Sep 2019, Berger, Joel wrote:
External Email - Use CautionHi friendly Freesurfers,
I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can view in tksurfer. Is there a way/formula to convert these easily, ideally into MNI coordinates?
I tried loading the label into Matlab with freesurfer_read_label.m converting to Talairach with freesurfer_label2tal.m and then also converting those coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not match with the Talairach/MNI coordinates shown for the corresponding vertices in tksurfer.
Thank you,
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.
________________________________ 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@nmr.mgh.harvard.edu
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Berger, Joel -
Bruce Fischl