Re: [Freesurfer] Two timepoints - same subject, correlation matrix
Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the /exact same number /so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ 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. ___ Freesurfer mailing list Freesurfer@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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ 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] Two timepoints - same subject, correlation matrix
Got it : aseg2feat --feat featdir --seg aparc+aseg On 06/22/11, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the /exact same number /so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ 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. ___ Freesurfer mailing list Freesurfer@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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ 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] Two timepoints - same subject, correlation matrix
On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ 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] Two timepoints - same subject, correlation matrix
Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the /exact same number /so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ 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. ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Two timepoints - same subject, correlation matrix
Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ 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.
