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
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:
- 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?
- 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
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:
- 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?
- 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%3E
-- Douglas N. Greve, Ph.D. MGH-NMR Center 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 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
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.
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:
- 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?
- 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 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
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Michelle Umali