Hi FreeSurfer community,
I have several questions regarding FreeSurfer's surface integral measurements.
Perhaps there is a documentation page that answers these questions that someone
can point me to that I haven't been able to find, or perhaps someone knows the
answers to these questions off
If you have a 3mm MNI152 space, then you should run bbregister to
fsaverage to create a new register.dat file. Alternatively, you can
register it directly to 32k_fs_LR and cut out the middle man (make sure
to use --9 to account for scaling). Please ignore my comment about
fsaverage. In that cas
yes
On 4/3/17 1:34 PM, Juan Baldermann wrote:
> Is ist correct that the pcc.mgh file give's me pearson's correlation
> coeeficient for each vertex?
>
> Best, Carlos
>
>
>
> Dr. med. Juan Carlos Baldermann
> Wissenschaftlicher Mitarbeiter, Assistenzarzt
> AG Neuro
You can use mri_segstats to generate a file for each subject (use the
ROI volume as the --seg). Then use asegstats2table to create your final
table
On 04/04/2017 12:18 PM, Ostrowski, Lauren wrote:
> Hello experts,
>
> We are looking to generate a stat file containing the number of voxels
> in
you can try playing with the --reorder flag in mri_convert
On 04/05/2017 10:11 AM, Jeffrey Crawford wrote:
>
> Hello everyone!
>
> I have two types of scans of the same participant. One was an Axial
> scan (Image 1) and the other is a Cortical Scan (Image 2), both with
> the same dimensions (25
Hello all,
I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of
parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go
about this using the aseg.stats output (using asegstats2table), but am
running into inconsistencies.
The basic calculation for VBR is:
(Total Ven
I believe what I am seeing in the long stream is the edits not properly taking
effect.
I uploaded a subject with two timepoints, and only baseline edits to the wm as
dsemanek2.zip about a week and a half ago. There doesn’t seem to be any
significant changes to the surfaces in the base or either
Hi Erik
I see. I defer to Thomas on this issue
Bruce
On Wed, 5 Apr 2017, ERIK JAHNER
wrote:
Hi Bruce,
Thanks for the quick response. Sorry, I meant 6mm radius (for regions such as
fusiform face area and visual word form area). I am using the same seeds that
are suggested to be associated
Hello FreeSurfer Community,
I am attempting to use mri_watershed to create BEM surfaces, but for some of my
subjects part of the cerebellum is being cut off. Adjusting the threshold was
not sufficient, so I attempted to add a seed point in the cerebellum using the
following command:
mri_water
Dear Freesurfers,
I am trying to implement the methods mentioned in this paper to deal with
partial volume effects when quantifying metabolites: https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title
The first step it mentions is: A binary mask must first be created, which
represen
Dear Kristen,
looking at the source code of mri_watershed, the seed point has to be specified
in the format:
-s i j k
and the option can be specified more than once when you want to add more seed
points (30 seed points is maximum).
i.e., when you want to input seed points in coordinates 50,60,
Dear Freesurfer Experts,
1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If
there were no significant regions for Group-Gender interaction in mean cortical
thickness in the QDEC analysis, can I conclude that gender does not influence
the effect of group on thickness? T
Hello,
I am getting an odd bug on selxavg3-sess. I am getting the error message,
*ERROR: cannot find [rest of file path]/fmc.sm0*
I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am
confused because the output of preproc-sess for no smoothing is
fmc.nii.gz, *NOT
*fmc.sm0.nii.gz w
Dear David,
I did not see your data, but maybe couple of relevant remarks could be useful:
1.
By default the wm.mgz edits are not propagated from cross to the base, but from
the cross to long. And surfaces in long are initialized from the base.
Therefore the wm.mgz has to be OK both in the cros
Dear Freesurfer Developers,
I was trying to use the recon-all -autorecon1 -subjid bert and got an error.
When I checked I found the error was coming while executing the below command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc
./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mr
Dear Freesurfer Experts,
1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If
there were no significant regions for Group-Gender interaction in mean cortical
thickness in the QDEC analysis, can I conclude that gender does not influence
the effect of group on thickness?
Hi,
as you advise I have run selxavg3-sess with the -svres option.I found a folder
called "res" which contain "res-001.nii". Is it the f.nii fully
processed?ThanksStefano
Messaggio originale
Da: "Douglas Greve"
Data: 14-mar-2017 17.38
A:
Ogg: Re: [Freesurfer] R: Re: Whole prepro
I get these pincher errors as well in VirtualBox.
One thing that may fix it is to disable 3D acceleration for the graphics in the
VM settings.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael ONeill
Sent: Thursday, 23 March 2017 11
Hi Douglas,
I am wondering, where did you find the mini 152 T1 map? :)
Regarding this...
Would it be better to instead run recon-all on a higher-res MNI atlas? and
then run mri_vol2surf for that segmentation?
Cheers,
*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonanc
Freesurfer devs,
In freesurfer 6 stable I'm having a problem at the careg stage of the long. The
relevant recon-all log is pasted below. Could you point me to where to debug
this problem?
Cheers,
Chris.
mri_ca_register -rusage
136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.
Dear All,
I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I'm running matlab 2015a 64bit on a linux machine.
I'm using MRIread, which in turn calls load_nifti.
I'm getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in loa
It happens when I use -bigventricles.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson
Sent: Thursday, 6 April 2017 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] long mri_ca_register error
Freesurfer devs,
Furthermore, the res-001.nii which is produce in produced in the res folder in
not the same dimension of f.nii.I would do the whole FAST preprocessing on
f.nii., maintaining the same dimension and open it with FSL.ThanksStefano
Messaggio originale
Da: std...@virgilio.it
Data: 5-apr-
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