[Freesurfer] flash v.s. mprage

looking at the docs available it seems that in general flash is prefered but it seems that for cortical thickness studies you may still favor the mprage ? all with good parameter setting of course. thanks in advance for any clarifying comments you may have Greg ___

[Freesurfer] nonlinear models in longitudinal analysis

Dear Freesurfer experts, I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to

Re: [Freesurfer] Information on automatic segmentation method

Hi Dorothy yes, this is referred to in our 2002 Neuron paper - we use the CMA segmentation procedure/definitions (see the references in that paper) cheers Bruce On Thu, 8 May 2014, dorothee schoemaker wrote: Hi, From what I understand, Freesurfer's automatic segmentation pipeline is partl

[Freesurfer] Information on automatic segmentation method

Hi, >From what I understand, Freesurfer's automatic segmentation pipeline is partly >based on a training set of subjects manually segmented. Is there a way to get >more information on which protocol/guideline was used to manually segment (or >define anatomical boundaries) these subjects at the

[Freesurfer] Information on automatic segmentation method

Hi, >From what I understand, Freesurfer's automatic segmentation pipeline is partly based on a training set of subjects manually segmented. Is there a way to get more information on which protocol/guideline was used to manually segment (or define anatomical boundaries) these subjects at the baseli

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Hi Emil how do the surfaces look before you apply the T2 deformation? And how do they look visualized over the T2 instead of the T1? cheers Bruce On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: Hi, I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm isotropic T1 (MPRAGE

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

Thank you, that solved it :-)cheers > Am 08.05.2014 um 15:56 schrieb Bruce Fischl : > > then you probably want to use mri_label2vol to sample it into the volume. > If the output name has the extension .nii it will be in nifti format > > cheers > Bruce > > > >> On Thu, 8 May 2014, Jutta Ernst

[Freesurfer] 2x3 ANOVA question

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DOSS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

It's a label file... On 05/08/2014 02:56 PM, Bruce Fischl wrote: > and what format is your ROI in? > On Thu, 8 May 2014, Jutta Ernst wrote: > >> Hi >> >> Nifti would be great and the software would be Data Processing Assistant for >> Resting-State fMRI (DPARSF). >> >> Cheers, Jutta >> >> >> On 05

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

then you probably want to use mri_label2vol to sample it into the volume. If the output name has the extension .nii it will be in nifti format cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: > It's a label file... > > > On 05/08/2014 02:56 PM, Bruce Fischl wrote: >> and what format is you

Re: [Freesurfer] Longitudinal design

Hi Tudor I'll leave ths stats question to Martin or Jorge, but I'm not sure why the wiki would say out longitudinal stream is not optimal. It is certainly as optimal as we have had the resources to make it, although there are a long list of things we would still like to do. cheers Bruce On Th

Re: [Freesurfer] Longitudinal design

Sorry for the repeat, wasn't sure whether this was received the first time. Tudor On 6 May 2014 19:55, Tudor Popescu wrote: > Dear FS list, > > I have structural data from a learning study (pre&post-training scans, > with 3 groups). Although the training was only one week, I'm guessing from > a

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

and what format is your ROI in? On Thu, 8 May 2014, Jutta Ernst wrote: > Hi > > Nifti would be great and the software would be Data Processing Assistant for > Resting-State fMRI (DPARSF). > > Cheers, Jutta > > > On 05/08/2014 02:38 PM, Bruce Fischl wrote: > > Hi Jutta > > we need more detail

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

Hi Nifti would be great and the software would be Data Processing Assistant for Resting-State fMRI (/DPARSF/). Cheers, Jutta On 05/08/2014 02:38 PM, Bruce Fischl wrote: Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to

Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

Hi Jutta we need more details - what format are you trying to conver the ROI to? What software are you planning to use to do the connectivity analysis? cheers Bruce On Thu, 8 May 2014, Jutta Ernst wrote: > > > Dear Freesurfer's > > I draw a roi to extract the cortical thickness for my two

Re: [Freesurfer] ADNI freesurfer annotation/labels file

Hi Tanya what kind of labels do you mean? If it is the cortical parcels they are in the label subdir in the *.annot files. cheers Bruce On Wed, 7 May 2014, Tanya wrote: > Hi Freesurfers,I'd like to work with ADNI freesurfer data to do analysis on > cortical segments, but could not find the anno

[Freesurfer] Fwd: extracting rois for connectivity analysis

Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta ___