Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why? Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right? Thanks. All the best. Rujing Zha
2014-04-26
charujing123
On 04/26/2014 07:06 AM, charujing123 wrote:
Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why?
Which coordinate? are you looking at and on which surface?
Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right?
If left is negative, then it is RAS
Thanks. All the best. Rujing Zha 2014-04-26
charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug, Thanks doug. I saw the sig.mgh in freeview by typing this: freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:overlay=./sig.mgh I set the vertex number which is at the maxmum in freeview. And the "pic1" in the attachment displays the cluster information in the *.summary file. "pic2" in the attachment represents freeview snapshot. The arrow in these two files echo the different coordinates which is refered in the previous e-mail. Thanks again. All the best. Rujing Zha
At 2014-04-29 02:46:07,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
On 04/26/2014 07:06 AM, charujing123 wrote:
Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why?
Which coordinate? are you looking at and on which surface?
Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right?
If left is negative, then it is RAS
Thanks. All the best. Rujing Zha 2014-04-26
charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
The coords in the summary file are for the white surface, not the inflated. Try freeview again using the white surface
On 04/29/2014 07:50 AM, Rujing Zha wrote:
Hi doug, Thanks doug. I saw the sig.mgh in freeview by typing this: freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:overlay=./sig.mgh I set the vertex number which is at the maxmum in freeview. And the "pic1" in the attachment displays the cluster information in the *.summary file. "pic2" in the attachment represents freeview snapshot. The arrow in these two files echo the different coordinates which is refered in the previous e-mail. Thanks again. All the best. Rujing Zha
At 2014-04-29 02:46:07,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
On 04/26/2014 07:06 AM, charujing123 wrote:
Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why?
Which coordinate? are you looking at and on which surface?
Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right?
If left is negative, then it is RAS
Thanks. All the best. Rujing Zha 2014-04-26
charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
pic1.jpg
pic2.jpg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Rujing Zha