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 c
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 $SUBJECTS_DIR/subject/mri
> mri_aparc2aseg --s
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 a
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 th
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 the wm.mgz file to see
> if
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 t
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
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 ra
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?
>
> Th
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 sa
Hi Anastasia,
Is there a preferable method between CVS vs MNI registration when extracting
diffusion mesures from ROIs (white matter, ASEG etc)?
Best,
Yoon
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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.
___
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:
http://surfer.nmr.mgh.harvard.ed
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 in
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
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 f
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,
I’
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 parti
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
probabilit
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 Ha
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 f
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 when
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, th
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. http://www
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