Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf.
In my lab we generally process ?h.thickness files with the next two commands before statistically analysis:
"mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h"
To keep with this protocol, my questions are 1) how do I use "mris_thickness" properly so that I don't overwrite the files registered to fsaverage_510? 2) in "recon-all -qcache", will it do the trick by substituting "fsaverage_sym" for "fsaverage_510"?
Thank you in advance, Cherry
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf.
In my lab we generally process ?h.thickness files with the next two commands before statistically analysis:
"mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h"
To keep with this protocol, my questions are
- how do I use "mris_thickness" properly so that I don't overwrite
the files registered to fsaverage_510?
I think it will recreate the basic ?h.thickness file and will not touch registrations.
- in "recon-all -qcache", will it do the trick by substituting
"fsaverage_sym" for "fsaverage_510"?
Yes, that should work.
Thank you in advance, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug
On 03/28/2013 12:51 PM, Douglas N Greve wrote:
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf.
In my lab we generally process ?h.thickness files with the next two commands before statistically analysis:
"mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h"
To keep with this protocol, my questions are
- how do I use "mris_thickness" properly so that I don't overwrite
the files registered to fsaverage_510?
I think it will recreate the basic ?h.thickness file and will not touch registrations.
- in "recon-all -qcache", will it do the trick by substituting
"fsaverage_sym" for "fsaverage_510"?
Yes, that should work.
Thank you in advance, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial since the files are smoothed in the first place.
Any suggestions?
Cherry
On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug
On 03/28/2013 12:51 PM, Douglas N Greve wrote:
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf.
In my lab we generally process ?h.thickness files with the next two commands before statistically analysis:
"mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h"
To keep with this protocol, my questions are
- how do I use "mris_thickness" properly so that I don't overwrite
the files registered to fsaverage_510?
I think it will recreate the basic ?h.thickness file and will not touch registrations.
- in "recon-all -qcache", will it do the trick by substituting
"fsaverage_sym" for "fsaverage_510"?
Yes, that should work.
Thank you in advance, Cherry
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: 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.
Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug
On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial since the files are smoothed in the first place.
Any suggestions?
Cherry
On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >> Dear Freesurfer experts, >> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >> subjects to the subject of fsaverage_sym following the instructions on >> this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all >> the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. >> >> In my lab we generally process ?h.thickness files with the next two >> commands before statistically analysis: >> >> "mris_thickness -max 10 subjid ?h thickness_max10" >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >> >> To keep with this protocol, my questions are >> 1) how do I use "mris_thickness" properly so that I don't overwrite >> the files registered to fsaverage_510? > I think it will recreate the basic ?h.thickness file and will not touch > registrations. >> 2) in "recon-all -qcache", will it do the trick by substituting >> "fsaverage_sym" for "fsaverage_510"? >> > Yes, that should work. >> Thank you in advance, >> Cherry >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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.
I see. Then I think I'd better just follow the instructions on the Xhemi page. Thanks!
On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug
On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial since the files are smoothed in the first place.
Any suggestions?
Cherry
On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >> Dear Freesurfer experts, >> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >> subjects to the subject of fsaverage_sym following the instructions on >> this page: http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemi<http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>. After all >> the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. >> >> In my lab we generally process ?h.thickness files with the next two >> commands before statistically analysis: >> >> "mris_thickness -max 10 subjid ?h thickness_max10" >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >> >> To keep with this protocol, my questions are >> 1) how do I use "mris_thickness" properly so that I don't overwrite >> the files registered to fsaverage_510? > I think it will recreate the basic ?h.thickness file and will not touch > registrations. >> 2) in "recon-all -qcache", will it do the trick by substituting >> "fsaverage_sym" for "fsaverage_510"? >> > Yes, that should work. >> Thank you in advance, >> Cherry >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Doug,
As I'm trying to run mris_preproc on this page ( http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I want to know what the --xhemi argument is for. Is it for calculating the difference between lh and rh thickness?
I wanted to calculate a asymmetry index for each vertex, which is (lh-rh)/[(lh+rh)/2] rather than (lh-rh). Can I do that using mris_preproc and how?
Thanks, Cherry
On Thu, Mar 28, 2013 at 1:32 PM, Ejoe Yizhou Ma ym850@nyu.edu wrote:
I see. Then I think I'd better just follow the instructions on the Xhemi page. Thanks!
On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug
On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the "smooth" step in freesurfer tutorial since the files are smoothed in the first place.
Any suggestions?
Cherry
On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: >> Dear Freesurfer experts, >> >> I'm trying to investigate lh-to-rh asymmetry, so I register my >> subjects to the subject of fsaverage_sym following the instructions on >> this page: http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemi<http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>. After all >> the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. >> >> In my lab we generally process ?h.thickness files with the next two >> commands before statistically analysis: >> >> "mris_thickness -max 10 subjid ?h thickness_max10" >> "recon-all -qcache -measure thickness_max10 -target fsaverage_510 >> -fwhm 10 -no-isrunning -s subjid -hemi ?h" >> >> To keep with this protocol, my questions are >> 1) how do I use "mris_thickness" properly so that I don't overwrite >> the files registered to fsaverage_510? > I think it will recreate the basic ?h.thickness file and will not touch > registrations. >> 2) in "recon-all -qcache", will it do the trick by substituting >> "fsaverage_sym" for "fsaverage_510"? >> > Yes, that should work. >> Thank you in advance, >> Cherry >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Ejoe Yizhou Ma