Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

13 3:10 PM, "Bruce Fischl" wrote: > >> actually Matt Glasser points out that a brief description is in his paper >> that is coming out soon, and there is also some description in Andre's >> multi-echo mprage paper >> Bruce >> On Tue, 7 May 2013, I

Re: [Freesurfer] MRI artifacts detection

Question from the MR Physics peanut gallery: How are you defining/measuring SNR for the anatomical sequences? (Sticking to Siemens.) The way I think about this, if what you have are the dicoms from an mprage which was collected with a receiver array, acceleration and pre-scan normalization, the

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl wrote: > no, of course not :) > > On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] > wrote: > >> Hi Bruce, >> >> Out of curiosity and for reference for my users, do you have a paper on the >

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov On May 7, 20

[Freesurfer] multi-echo mprage

Hi All, I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the "best-practices" for using data from this type of sequence in Freesurfer? Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm

Re: [Freesurfer] mprage resolution for surfaces/thicknes?

;t think there > should be any problem (although it has been a long time since we used to > get those - 1.5T and single channel) > > cheers > Bruce > On Tue, 5 Mar 2013, Inati, Souheil > (NIH/NIMH) [E] wrote: > >> A colleague has some mprage scans collected on a 3T

[Freesurfer] mprage resolution for surfaces/thicknes?

A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in plane, 1.3mm thick. The SNR and CNR are pretty good. I figured I'd ping the list to see if anyone have any experience running scans with the slightly thickish voxels through the recon-all pipeline. Anything I ought to l

[Freesurfer] Import/export out of curry

Has anyone used freesurfer segmentations/labels in Curry? -- Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] mri_convert feature request?

lem is that the formats don't support it. Sorry > for the run around. > > D > > On Tue, Aug 28, 2012 at 1:46 PM, Inati, Souheil (NIH/NIMH) [E] > wrote: >> Hi Bruce and Freesurfers, >> >> The standard part of the nifti_1 header specifies that the first three

Re: [Freesurfer] mri_convert feature request?

data and sampling pattern, including things like diffusion encoding, physiological signals, etc. Here's a link: http://ismrmrd.sourceforge.net Cheers, Souheil On Aug 28, 2012, at 12:39 PM, Bruce Fischl wrote: > Hi Souheil, > > does NIFTI store the MR parameters? > > thanks

Re: [Freesurfer] mri_convert feature request?

On most (all?) scanners TR is stored as an integer. For example, on siemens it's in microseconds and then stored as a long. (this is the value in the protocol, not the actual execution TR, but when/if there are no bugs, then this is correct). When you convert a long to float (single or double

Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

for > which we have segmentations, or you could post your sequence parameters so > we could at least try to see if there are any datasets around that match it > more or less. > > cheers > Bruce > > > On Mon, 16 Jan 2012, Inati, Souheil (NIH/NIMH) [E] wrote: > >>

[Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

Hi All, I have a very small set of patients and I would like to compare the volumes of subcortical structures and thickness across the cortex to those of a large normative set. I don't need all the underlying data, just means and standard deviations. Is such a set of measures available? Than