[Freesurfer] mris_thickness qcache for xhemi surfaces
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 ___ 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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
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 gr...@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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. ___ 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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
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 gr...@nmr.mgh.harvard.edu mailto:gr...@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 gr...@nmr.mgh.harvard.edu mailto:gr...@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
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 gr...@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/Xhemihttp://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:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 http://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 mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 gr...@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/
