[Freesurfer] dmri_poistats

Dear Freesurfer experts, I would like to inquire about the tool "dmri_poistats" https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is included as a beta release ( in FS5.3 and FS 6.0). In literature review I found colleagues used the version 1.4 of this tool. e.g.

[Freesurfer] Using Freesurfer for skull stripping then reorienting images to use in FSL

Hello, We are using freesurfer to skull strip T1 images on a high-motion pediatric sample. We want to use freesurfer to get brain-only images and then do further analysis using FSL. The problem is that, in freesurfer, the images are in a different orientation than those in FSL. For example,

Re: [Freesurfer] TRACULA: narrow probability distributions

Yes, it shouldn't hurt. On Tue, 23 Aug 2016, Harms, Michael wrote: Ok. We’ll give it a try. Just to confirm, you're agreeing that increasing nburnin and nsample is a “good” thing, right? (e.g., 1000, and 15000, respectively?) If anything, we should be less likely to get narrow tracts

[Freesurfer] TRACULA: narrow probability distribution

Dear Anastasia, I’ve been looking at a lot of Tracula path.pd files and I’ve found that some probability distributions are only a single voxel wide, similar to the path.map file. The few none-zero voxels in these path.pd files have very high probability values. When an isosurface is generated

Re: [Freesurfer] TRACULA: narrow probability distributions

Ok. We’ll give it a try. Just to confirm, you're agreeing that increasing nburnin and nsample is a “good” thing, right? (e.g., 1000, and 15000, respectively?) If anything, we should be less likely to get narrow tracts when using larger nburnin/nsample values, right? thanks, -MH -- Michael

Re: [Freesurfer] TRACULA: narrow probability distributions

Hi Michael - Even if it starts very close to the true max of the distribution, in practice it'll never stay put. MCMC will accept a new sample path with probability 1 if the new sample has greater probability than the previous sample, and it will also accept it with some very small

Re: [Freesurfer] TRACULA: narrow probability distributions

Hi Anastasia, My interpretation of the “reinit” parameter is that it is for situations where a narrow probability distribution is assumed to be incorrect. But how do you know whether it is indeed incorrect, or whether in fact the true equilibrium distribution is (correctly) very narrow? In

Re: [Freesurfer] TRACULA: narrow probability distributions

Hi Dillan - There's a work-around for this, see the reinit variable at the bottom of the sample config file: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc I'm hoping to make this happen automatically soon! Best, a.y On Tue, 23 Aug 2016, Newbold, Dillan wrote: Dear Anastasia,

[Freesurfer] TRACULA: narrow probability distributions

Dear Anastasia, I’ve been looking at a lot of Tracula path.pd files and I’ve found that some probability distributions are only a single voxel wide, similar to the path.map file. The few none-zero voxels in these path.pd files have very high probability values. When an isosurface is generated

Re: [Freesurfer] Tracula ROI analysis CVS vs MNI reg

Hi Yoon - The wmparc and aseg ROIs are in the subject's native T1 space, so you don't need to register across subjects to get ROI-based diffusion measures. You just need to register between the subject's own T1 and DWIs - the recommended method for that is bbregister. You can find more in the

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

Hi Elijah - Does the directory in the error message exist? a.y On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, The error message occurs for other control points too, but it does not kill the -prior stage.  I have attached the full trac-all.log file. This error message is also found

[Freesurfer] PET surface sampling

Hi, I’m trying to use the PETsurfer Pipeline to perform BP analysis, but I’m not sure at which point in the pipeline to sample the data to the surface and what registration to use? I tried running the pipeline using dynamic kinetic modeling as described here:

[Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Hello freesurfer experts,  What's the difference between GLM surface based cortical thickness analysis and the cortical thickness analysis performed when using regions extracted from aparcstat table? Best, Paul Sent from my BlackBerry 10 smartphone. ___

[Freesurfer] Tracula ROI analysis CVS vs MNI reg

Hi Anastasia, Is there a preferable method between CVS vs MNI registration when extracting diffusion mesures from ROIs (white matter, ASEG etc)? Best, Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] permutation/monte carlo

On 08/23/2016 03:18 AM, maaike rive wrote: > > Dear Douglas, > > > Sorry to bother you with this, but after reading the thread about the > Eklund papers I'm getting confused about what I actually did when > correcting for multiple comparisons and I'd also like to know whether > I'm on the

Re: [Freesurfer] Recon-all Correcting Defect 0

See the cerebellum section here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting On 08/23/2016 06:10 AM, Heidi Foo wrote: > Hi Douglas, > > Yes it does seem like large parts of the cerebellum have been removed. > Is there anything I could do to get around this problem? > >

Re: [Freesurfer] sig.sum files shows more clusters than sig.mgh image

Can you send the command line, the sum file, and a pic of the surface? On 08/23/2016 04:39 AM, Oana Georgiana Rus wrote: > > Dear Freesurfer experts, > > I have run an analysis on GM Volume in Freesurfer. > > The interested contrast was patients vs. controls. (/command mri_glimfit/) > > I then

Re: [Freesurfer] qcache for qdec longitudinal analysis

Thank you very much. I will be looking forward to this. Nick Corriveau-Lecavalier ?tudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur ? la recherche, Association ?tudiante des cycles sup?rieurs en psychologie de l'Universit? de Montr?al (A?CSPUM) Universit? de

Re: [Freesurfer] [Martinos-faculty] Open position as MRI physicist at Copenhagen University Hospital, Denmark (fwd)

FYI The Neurobiology Research Unit (NRU) at Copenhagen University Hospital, Rigshospitalet has an opening for a MRI physicist position. The position entails design, development, implementation and evaluation of novel multimodal MRI acquisition protocols and image analysis techniques in relation

Re: [Freesurfer] Recon-all Correcting Defect 0

Hi Douglas, Yes it does seem like large parts of the cerebellum have been removed. Is there anything I could do to get around this problem? Thanks. Regards, Heidi On Tuesday, 23 August 2016, Douglas N Greve wrote: > It looks like there is a very large defect. Check

Re: [Freesurfer] qcache for qdec longitudinal analysis

Hi Nick, when using the 2 stage model (mris_long slopes ) you do not need the qcache. In qdec you will not look at thickness, but at the percent change or the rate of thickness changes as computed by long_slopes. For that to work, you need to create/modify the .qdecrc file so that qdec finds

[Freesurfer] sig.sum files shows more clusters than sig.mgh image

Dear Freesurfer experts, I have run an analysis on GM Volume in Freesurfer. The interested contrast was patients vs. controls. (/command mri_glimfit/) I then ran /mri_surfcluster/ command to get a text file with the significant clusters FDRcorrected and their peak coordinatesn- resulting in

Re: [Freesurfer] voxel values in destrieux file

ok thanks a lot ! do you know when it will be fixed in the recon-all as well ? Cheers, Pierre On Fri, Aug 19, 2016 at 7:45 PM, Douglas Greve wrote: > The error is in recon-all. If you want to fix this one outside of recon-all > you can run > cd

[Freesurfer] permutation/monte carlo

Dear Douglas, Sorry to bother you with this, but after reading the thread about the Eklund papers I'm getting confused about what I actually did when correcting for multiple comparisons and I'd also like to know whether I'm on the safe side. I used pre-cashed Monte Carlo simulation with a