Re: [Freesurfer] bbregister problems with PET data

Thanks Martin and Doug, I'll give both robust_register with robent and mri_coreg a try. RE: Doug The PET tracer is Avid's amyloid compound -- F18-florbetapir (aka amyvid, aka AV45). The asymmetric signal is a result of the population -- individuals with a non-amnestic language dementia with under

[Freesurfer] ERROR running mkcontrast

Hi, I ran into an odd problem which I was able to fix but wanted to let others know about. This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3. I got the following error when I ran mkcontrast using batch files that previously worked fine: /private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn800

Re: [Freesurfer] Surface-based PET maps

Are those maps corrected for multiple comparisons or uncorrected? If corrected, how similar are the uncorrected? When doing a correction, you can get clusters that are just above significance in one analysis and just below sig in the other making it look like there are huge differences. I've lo

[Freesurfer] Fwd: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study

FYI Original message From: "Thomas,Robert" Date: 03/30/2016 5:52 AM (GMT+05:30) To: a...@nmr.mgh.harvard.edu Cc: Chol Shin Subject: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study A 5-year Post-Doctoral Fellowship is available in South K

Re: [Freesurfer] longitudinal pipeline surface error

Wow! I haven't thought about that but it's possible since we had a few study coordinators along the way. So it could be the case that the study coordinator didn't know the subject who came at follow-up. Hopefully it will be just a DICOM mismatch. Will see how it goes.. :) On Thu, Mar 31, 2016 at 1

Re: [Freesurfer] bbregister problems with PET data

btw, what tracer is this? And the asymmetry you are talking about is between the hemispheres? Is that typical for this tracer or is this a phenomena with this subject (or population)? On 03/30/2016 03:41 PM, Adam Martersteck wrote: > Hi Freesurfer team, > > I’m encountering a problem using bbreg

Re: [Freesurfer] DODS vs DOSS for correlation analysis

I thought it was disabled in 5.3, thanks for the heads up. On 03/30/2016 06:32 PM, Cassandra Wannan wrote: > Hi Doug, > > I'm using version 5.3. I had read about the bug but the release notes > for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue > must have been resolved. If no

Re: [Freesurfer] bbregister problems with PET data

Try using mri_coreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg On 03/30/2016 04:20 PM, Martin Reuter wrote: > Hi Adam, > > not sure robust_register robent will work on this type of stuff (never > tested it). I would recommend to keep the radius small (2,or 3), but >

Re: [Freesurfer] longitudinal pipeline surface error

I have seen cases where annonymization messed up ID's and individual time points came from a different subject. That could mess things up quite bad. (Also if the person sends their sibling or friend, because they don't have time to come to the follow up themselves, has also happened - not to me

[Freesurfer] Summer School course 'Genetics for Imagers', 8 August - 12 August in Nijmegen, The Netherlands

Dear Freesurfer users, I would like to promote our Radboud Summer School in Nijmegen (The Netherlands) which might be interesting for FSL imaging people that would like to expand their knowledge in the genetics area. This intensive one-week (8 August - 12 August 2016) course covers various aspe

Re: [Freesurfer] longitudinal pipeline surface error

Hi Martin, We ran this subject twice but we got the same error. The norm is not aligned. They almost look like two different brains. I double checked the exam numbers to make sure that these three exams belong to the same person. They indeed seem to belong to the same person but I will re-run reco

[Freesurfer] QDEC analysis

Dear FreeSurfer experts, I am trying to analyze some single time points of my longitudinal data in QDEC. I have 3 groups and created a file for the discrete factor "group" with three levels (1,2 and 3). I have done the same for gender (with 2 levels). The analysis with gender works just fine bu

Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi again, Claudia. As a temporary workaround, you can use this flag in your recon-all command: -itkthreads 1 This will tell the code not to multithread, which will make it slower, but should help avoid the problems you have experienced. Please let us know how that goes! Cheers, Eugenio Juan Euge

Re: [Freesurfer] stacked iteration in brainstem segmentation

In the hippocampal subfield segmentation, this happens once every 100-200 subjects. Three for seven is pretty bad. I'll take a look as soon as I can. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.b

Re: [Freesurfer] stacked iteration in brainstem segmentation

Hi Eugenio, we run the brainstem segmentation for 7 seven subjects and it succeded for 3 of them. Then we did not carry on with the others. The data are always 3D volumetric FSPGR acquired with the same sequence and scanner. Would you need any other info? Cheers, Claudia ___