[Freesurfer] Original Volume Space

External Email - Use Caution Hi Please tell me how do I use recon-all withkeeping original space without resampling?___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Job positions available. Science Programmer and Head Engineer in neuroimaging lab (LCBC, University of Oslo, Norway).

External Email - Use Caution I am delighted to advertise the following positions on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have available two new positions for excellent candidates. The main aim of

Re: [Freesurfer] temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces

Hi Neva if you upload a subject we will take a look. cheers Bruce On Wed, 19 Dec 2018, Neva M Corrigan wrote: External Email - Use Caution Hi,   I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes fo

[Freesurfer] using tkregister2 to check registration to custom atlas

External Email - Use Caution Hello Freesurfer Community, I am interested in seeing how well my subject scan registered to a custom atlas after being run through recon-all. From Freesurfer Wiki, although it is possible to see this in freeview, tkregister2 seems to be the best metho

[Freesurfer] Setting the origin in native space

External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Tal

[Freesurfer] using custom surface template

External Email - Use Caution Hello FreeSurfers, We use a custom surface template, generated according to the instructions in the SurfaceRegAndTemplates instructions for inter-subject co-registration. We then do cort

Re: [Freesurfer] Setting the origin in native space

Hi Ryan I think mri_convert -at should do the trick. cheers Bruce On Wed, 19 Dec 2018, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set

Re: [Freesurfer] using custom surface template

Hi Jason we use the parcellation to figure out where we don't need to deform the pial surface. I expect our standard parcellation is good enough for this, so maybe you can just run your own posthoc? cheers Bruce On Wed, 19 Dec 2018, Jason Tourville wrote: External Email - Use Cau

[Freesurfer] mri_segstats more decimals?

External Email - Use Caution Hi Freesurfer, Is there a way to print out more decimals with mri_segstats? The mean diffusivity values are very small and with only four decimals not really distinguishable from each other. Thanks for your help! Stephanie The information contain

Re: [Freesurfer] mri_segstats more decimals?

There is not a way to get more decimals but you can apply a scaling factor with --mul, eg, --mul 1000 will multiply the output by 1000 On 12/19/2018 04:01 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfer, > > Is there a way to print out more decimals

[Freesurfer] mris preproc for folding index

External Email - Use Caution Hi, Just like volume, I have "Folding Index" measures saved in lh/rh.aparc.stats files for each subject. If I am using mris_preproc *--meas volume* --out CV/lh.CV.mgh command to concat cortical volume files from all subjects, then how can I use this c

Re: [Freesurfer] mris preproc for folding index

something like --meas white.K or white.H On 12/19/2018 04:23 PM, Martin Juneja wrote: > > External Email - Use Caution > > Hi, > > Just like volume, I have "Folding Index" measures saved in > lh/rh.aparc.stats files for each subject. > > If I am using mris_preproc *--meas volume* --out C

Re: [Freesurfer] PNM Gui

Hello Freesurfer developers, I just wanted to kindly follow up to my previous message. I'm working from a remote Martinos linux server, so I've found that sometimes I don't have proper permissions to run important scripts, such as the physiological noise modeling processing pipeline that I ref

Re: [Freesurfer] [EXTERNAL] Re: mri_segstats more decimals?

External Email - Use Caution This is fantastic! You guys have thought of everything :) Thanks Doug!! Sent from my iPhone > On Dec 19, 2018, at 4:22 PM, Greve, Douglas N.,Ph.D. > wrote: > > External Email. Use Caution. > > There is not a way to get more decimals but you can ap

Re: [Freesurfer] PNM Gui

Hi Steven, PNM is an FSL tool, not freesurfer, but if you’re having remote-access permissions issues it might be best to contact the martinos help desk. Are you setting “output basename” to a writable directory? best Andrew From: on behalf of "Meisler, Steven Lee" Reply-To: FS Help Date:

Re: [Freesurfer] mris preproc for folding index

External Email - Use Caution Thanks Dr. Greve. That works, but both white.K and white.H are giving me very different output values. For example, for first few subjects I get: -0.00237-0.00450-0.00204 0.00113-0.00228-0.00958 -0.00314 0.00180-0.00452 if I

Re: [Freesurfer] mris preproc for folding index

I'll leave that up to Bruce and Rudolph On 12/19/2018 05:37 PM, Martin Juneja wrote: > > External Email - Use Caution > > Thanks Dr. Greve. That works, but both white.K and white.H are giving > me very different output values. > > For example, for first few subjects I get: > -0.00237    -

Re: [Freesurfer] PNM Gui

Hi Steven I don't think this is the right list to ask this question. Have you tried emailing Martinos help? cheers Bruce On Wed, 19 Dec 2018, Meisler, Steven Lee wrote: Hello Freesurfer developers, I just wanted to kindly follow up to my previous message. I'm working from a remote Marti

Re: [Freesurfer] mris preproc for folding index

External Email - Use Caution K and H are the Gaussian Curvature and the Mean Curvature. Both can be computed based on the 2 principal curvatures k1 and k2 of a surface. K and H are not identical to the folding index, though they are related to it via k1 and k2. k1 and k2 are als

[Freesurfer] Postdoctoral Fellow at Northwestern's Alzheimer's Disease Center

External Email - Use Caution *Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease is seeking candidates for a postdoctoral fellowship in Neuroimaging of Aging and Dementia. The fellow will focus on analyzing multimod

Re: [Freesurfer] mris preproc for folding index

a 2D manifold has two principal curvatures, usually called k1 and k2, which are the curvature in the direction of maximum curvature and minimum curvature (they are also the eigenvalues and eigenvectors of the Hessian of the surface if it is expressed as a function over the tangent bundle). The

[Freesurfer] surfreg cannot allocate memory

External Email - Use Caution Hello FreeSurfer Developers, I am using surfreg to map one of my subject "subj001" to "fsaverage_sym" by these commands: surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --lh --xhemi The first command worked well, howe

Re: [Freesurfer] surfreg cannot allocate memory

External Email - Use Caution Hello Haoran, You could try looking at your shell limits and see if the memory size is listed as something other than “unlimited”.   In bash shell, $ bash $ ulimit -a core file size          (blocks, -c) 0 data seg size           (kbytes, -d) unlimite