Re: [Freesurfer] Two Stage Longitudinal Model

Hi Martin, Thank you for your reply. I am glad to hear that I am doing that correctly. I am running into an error when I attempted to run my GLM. I have looked at my fsgd and qdec files for errors, however I cannot seem to find anything. The error is in the attached .txt file named

[Freesurfer] Longitudinal analysis

Hi FreeSurfer Team, We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease

Re: [Freesurfer] Amygdala subfields

to clarify: the amygdala subregion atlas is built and will be released early 2017. Dorit On Oct 31, 2016, at 11:46 AM, Dorit Kliemann wrote: > Hi Sascha, > yes, we have developed an amygdala nuclei atlas similar to the hippocampal > subfields . Its currently being tested and

Re: [Freesurfer] fsaverage_sym LR-flipchecks

Hi Doug Thanks for the reply. It's actually just a normal first level fMRI analysis ran once on subj1 and once on subj1 after flipping the anatomical and BOLD data for subj1. After flipping I ran recon-all on the flipped subject (treating as new subject - so for this sub LH == RH) Top left

Re: [Freesurfer] Creating overlay files automatically

Look up the specs for nifti files. The spec is publicly available. If you are doing this in matlab, you can use our MRIwrite.m On 10/31/16 6:01 AM, Eloy Geenjaar wrote: Dear Douglas, Thanks for the quick response, I do know that nifti or mgz files are used for the overlay, I was trying to

Re: [Freesurfer] Recon-all Exiting without Error

To answer your question, you need to tell recon-all what to do. Eg, -all On 10/31/16 10:47 AM, Harms, Michael wrote: Hi, Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users.

Re: [Freesurfer] Amygdala subfields

Hi Sascha, yes, we have developed an amygdala nuclei atlas similar to the hippocampal subfields . Its currently being tested and to be implemented (hopefully) soon. Stay tuned. Dorit > From: "sf" > Subject: [Freesurfer] Amygdala subfields > Date: 31 October 2016 at

Re: [Freesurfer] values of 0 in the beta.mgh files

If you use the --no-prune flag, then it will consider all subjects at a vertex regardless of whether it is 0 or not. But is this really what you want to do? >>Thank you so much for the reply. Yes I do se now, that single subjects which have certain vertexes with a value of 0 thus excludes

Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

Hey Martin, Thank you for the reply. Yes, I ended up recreating the table solely within a text editor and it worked so it was some sort of formatting issue. Thank you for your time. Quinn From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Amygdala subfields

Hi all, is there any possibility to segment amygdala subfields with freesurfer? Similar to the hippocampal subfields segmentation? Cheers - Sascha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Obtain images extracted from aseg.mgz that have been corrected for partial volume effects

Hi Bruce, This would be most helpful. And yes, I think multiple labels for each voxel that are the coefficients that explain the observed intensity of that voxel would be a good format. I am thinking that anyone could then correct for pve of structures taken from the aseg.mgz file in matlab (or

Re: [Freesurfer] Recon-all Exiting without Error

Hi, Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the

[Freesurfer] Recon-all Exiting without Error

Hi, I have just started using FreeSurfer and I am trying to do the subcortical segmentation on some Human Connectome Data. In the command line I typed, 'recon-all -i T1w_acpc_dc_restore_1.25.nii -subjid 100307' The following output was produced: WARNING: tcsh v6.17.06 has an exit code bug!

Re: [Freesurfer] Extend pial surface

Hi Noah it's impossible to tell from a single slice, but if you are talking about the right superior temporal gyrus I would guess that it is an incorrectly fixed topological defect. If you upload the subject to our ftp site we will take a look cheers Bruce On Mon, 31 Oct 2016, Noah

Re: [Freesurfer] [Question for recommended MRI protocols]

Hi Jeongsik the bandwidth, geometry and read-out matching ensure that there is no differential distortion between the scans, so unless you have a compelling reason I wouldn't change any of that. And you definitely, definitely cannot reduce the voxel size to 2mm iso and expect to get

Re: [Freesurfer] values of 0 in the beta.mgh files

On 2016-10-27 17:26, Douglas N Greve wrote: > Yes, if even one subject has a 0 at a vertex, then that vertex will be > excluded from analysis > > > On 10/27/2016 10:34 AM, Bruce Fischl wrote: >> Hi Linn >> can you show us a picture of the medial inflated surface with the >> overlay? >> The

[Freesurfer] recon-all steps question

Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1

Re: [Freesurfer] Creating overlay files automatically

Dear Douglas, Thanks for the quick response, I do know that nifti or mgz files are used for the overlay, I was trying to figure out how to write such files though. In what format do I have to write nifti or mgz files for Freeview to be able to load them correctly? Kind regards, Eloy