Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans
I'd collect highres T1w as well and then refine the 1mm surfaces using that. Peace, Matt. From: SHAHIN NASR sha...@nmr.mgh.harvard.edu Date: Monday, February 25, 2013 1:39 PM To: Freesurfer freesurfer@nmr.mgh.harvard.edu, Bruce Fischl fis...@nmr.mgh.harvard.edu, Doug Greve gr...@nmr.mgh.harvard.edu Subject: [Freesurfer] High resolution fMRI and resolution of anatomical scans Hi, We are planning to collect high resolution functional MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed anatomical scans with 1 mm voxel size. The question is, do we need to re-collect anatomical scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] High resolution fMRI and resolution of anatomical scans
You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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] High resolution fMRI and resolution of anatomical scans
We always collect a low resolution whole brain mprage structural scan before the functional scans to help us position our slices. Can I use that? You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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] High resolution fMRI and resolution of anatomical scans
yes On 02/25/2013 03:23 PM, sha...@nmr.mgh.harvard.edu wrote: We always collect a low resolution whole brain mprage structural scan before the functional scans to help us position our slices. Can I use that? You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/ -- 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.
