Re: [Freesurfer] Extract the entorhinal cortex as a mask

2018-06-13 Thread Erik O'Hanlon
External Email - Use Caution Sorry Bruce, Yep Thanks. I didn't spot that label just the 216. Worked perfectly. Thanks again Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 12 June 2018 19:04:32 To:

Re: [Freesurfer] Extract the entorhinal cortex as a mask

2018-06-13 Thread Bruce Fischl
glad to hear it Bruce On Wed, 13 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Sorry Bruce, > > > Yep Thanks. I didn't spot that label just the 216. Worked perfectly. > > > Thanks again > > > Erik > > > From:

[Freesurfer] PREDOCTORAL POSITION at King's College London

2018-06-13 Thread Walter Hugo Lopez Pinaya
External Email - Use Caution Dear colleagues, We are looking for a predoctoral research assistant with knowledge of neuroimaging to work on a research project involving the application of machine learning techniques to neuroanatomical data. The project will lead to the

Re: [Freesurfer] Running qcache on old FS data

2018-06-13 Thread Douglas N. Greve
I have no idea how to make it work with data that old. You can "fool" it by copying or soft linking lh.curv to lh.white.K. You can probably get it to at least finish. On 06/06/2018 03:41 PM, Jamie Hanson wrote: > > External Email - Use Caution > > > Hello all, > > I was trying to run 

Re: [Freesurfer] Error during QDEC

2018-06-13 Thread Douglas N. Greve
can you send the fsgd file? On 06/12/2018 02:32 AM, Seung-Gul Kang (강승걸) wrote: > Dear Freesurfer experts, > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit

Re: [Freesurfer] dwi.ecclog file

2018-06-13 Thread Daumail, Loic Jean
Dear Mrs Yendiki, thank you for your response. However, for my configuration file, containing : " setenv SUBJECTS_DIR /autofs/space/avadhuti_001/users/gdesbord/CALM_data/CALM_001 set subjlist = ( 02_recon ) set dcmlist = (

Re: [Freesurfer] Group Analysis Covariates

2018-06-13 Thread Douglas N. Greve
On 06/11/2018 11:07 PM, Hua, Jessica wrote: > > > Dear Freesurfer Experts: > > > I analyzed my data following the guidelines on the FSL Tutorial/Group > Analysis page . I am trying to plot the adjusted values (covariates: > age, sex, and ICV) for the significant clusters for each of my >

[Freesurfer] hippocampus subfields and manual editing

2018-06-13 Thread Lara Foland-Ross
External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

2018-06-13 Thread Tudor Popescu
External Email - Use Caution Hi Bruce, I am guessing that Martin might be unavailable for now, judging by the date of his last input to the list. However, my intuition is that there is something really trivial that's causing this chain of (circular!) errors... For any more

Re: [Freesurfer] hippocampus subfields and manual editing

2018-06-13 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace

Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

2018-06-13 Thread Sally Grace
External Email - Use Caution Hi Eugenio, Great. We have already run our subjects through recon-all for FS5.3. EG. recon-all -s [subjects_dir] We have two dev versions of freesurfer installed on our server: freesurfer/devel-20180612 and freesurfer/devel-20171013. Does it make

Re: [Freesurfer] Group Analysis Covariates

2018-06-13 Thread Douglas N. Greve
trategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> > > > RCSI LEADING THE WORLD TO BETTER HEALTH > > [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png] > > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruc

[Freesurfer] Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease

2018-06-13 Thread Arnaud Boré
External Email - Use Caution *Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease* We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor Learning and Plasticity Laboratory*, at McGill University. The suitable candidate will join a team of

[Freesurfer] Post-doc position in neuroimaging pain research

2018-06-13 Thread Lussier,Desiree
External Email - Use Caution Postdoctoral Research Positions in Neuroimaging Pain Research Pain Research & Intervention Center of Excellence University of Florida, Gainesville, Florida Dr. Yenisel Cruz-Almeida and Dr. Natalie Ebner are currently accepting applications for

[Freesurfer] Cortical Thickness Using N30R83 Atlas

2018-06-13 Thread Ryan Flores
External Email - Use Caution Hello all, I am hoping to obtain structural information (e.g., cortical thickness, surface area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI space. The atlas differentiates between the hemispheres by using odd/even