[Freesurfer] Reminder: FSurf webinar tomorrow

Dear FreeSurfer Community, The Open Science Grid consortium (http://www.opensciencegrid.org) offers a service “FSurf” which allows large scale batch processing of MRI scans using FreeSurfer. FSurf supports the standard FreeSurfer workflow (autorecon-all) or workflows with arbitrary FreeSurfer

Re: [Freesurfer] Longitudinal Pipeline

Thanks Martin. Should I be worried about affine transform masking out the global atrophy if I am using the whole brain (no skull stripping)? Arman On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter wrote: > Hi Arman, > > should be possible by passing the - - affine

[Freesurfer] trac-all -stat

Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia - trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is

Re: [Freesurfer] trac-all -stat

Hi Amelia - This means that it can't find any of the tracts that you've specified (or any tracts period, if you haven't specified a list) for the subjects that you've specified in your config file. It'd be looking under: /data/dprojects/BIOS/tracula/$subj/dpath/ Best, a.y

Re: [Freesurfer] Longitudinal Pipeline

Hi Arman, should be possible by passing the - - affine flag. I think I also experimented around with a -base-affine flag to recon-all for that (instead of -base). It is experimental! Best, Martin > On 07 Apr 2017, at 13:34, Arman Eshaghi wrote: > > Hi, > > I

[Freesurfer] Survey on inputs for surface-based analysis pipelines

Hi list, We're working on FMRIPREP , a pipeline aimed at performing baseline preprocessing, and producing cleaned structural and functional data which can be fed into any of a number of analysis pipelines. We've recently begun incorporating surface

Re: [Freesurfer] TRACULA tract reconstruction

Hi Joelle – I tested one of your dicoms and the gradient table that mri_convert reads from it works just fine. So you can just pass your dicoms to TRACULA and it’ll do the rest. No need for you to specify the gradient tables. Best, a.y From:

Re: [Freesurfer] correlation coefficient R

Thank you so much Doug! It worked! I was just wondering which value I should report as the correlation coefficient of my analysis. This is the output I got: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -4 2037320373.0 Seg-004-0.1596

[Freesurfer] Fwd: wm edits not incorporated

Dear All, Regarding wm.mgz edits not incorporated into wm surface, which seems to have been reported on by several of us with FS 6.00. I followed Antonin's idea of editing 001.mgz by switching wm-intensity voxels clearly not wm (mostly in the subtemporal regions, at times close to bright dural

Re: [Freesurfer] manual edits

Hi John, Yes understanding how freesurfer deals with edits can be a bit confusing. I have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross sectional data in Freesurfer 5.3 so perhaps I can help. Recon-all is basically a script which runs a series of about 25 or so

Re: [Freesurfer] mri_concat pet images into 1 template image

Hi Doug, There is a bit of movement across the 3 acquisitions. How may I align everything together before running mri_concat? 1. Run bbregister or mri_coreg to register 1 acquisition to T1 2. Use the reg file to move the remaining 2 acquisitions ? Is there a quicker way? Thank you. --  Shane

[Freesurfer] Bits of dura being captured as GM ..

Hi Freesurfer Users, I am checking my data and there are many scans with a bit of dura being  captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects.  I am removing them manually them using Freeview, then running the autorecon-pial. But this will

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

I added --surf mytemplate lh to the command and now it works. Thank you so much!! - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 11. April 2017 20:13:21 Betreff: Re: [Freesurfer] glmfit mismatch between X