[Freesurfer] aseg2feat for PPI seeds for FSL
Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Thanks. Michelle ___ 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] aseg2feat for PPI seeds for FSL
Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ 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 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] aseg2feat for PPI seeds for FSL
Dear Doug and the Freesurfers, Ok, so is there a special filtered_func.nii generated from reg-feat2anat for each run or can I just use the feat? When one does a cross-subject PPI in FSL and enter each run from each person, isn't everyone in a different space? How do you account for this when doing setting up the PPI feat? Thanks. Michelle Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] aseg2feat for PPI seeds for FSL
Michelle Umali wrote: Dear Doug and the Freesurfers, Ok, so is there a special filtered_func.nii generated from reg-feat2anat for each run or can I just use the feat? No, just use the FEAT one. When one does a cross-subject PPI in FSL and enter each run from each person, isn't everyone in a different space? How do you account for this when doing setting up the PPI feat? Aren't you just getting a single time course? I have not done PPI analysis before, so I might not know what is required. doug Thanks. Michelle Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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 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
