What Doug said, but note that those decimals are getting dangerously close
to machine roundoff error territory, so I'd be cautious if the effect that
you're trying to detect is in that territory.
> You can add something like --mul 1000 to the mri_segstats command line
> to multiply the values by 1
Hi Pedro - Looks like the mri_convert command has trouble reading your
dicoms. Have you searched for that error message in the archives of the
freesurfer list? If nobody has encountered it before, then you can post
this as an mri_convert question so that the appropriate people look at it.
a.y
> H
Hi Pedro - Your config file needs to be a plain text file, not a rich text
format (rtf) file. If you run the cat command on your file, you'll see
that there are some formatting strings that were added by your text editor
in the beginning of the file and they include the curly brackets that give
you
Hi Stefano - As always, it'll be impossible to guess what's causing the
error without seeing at least the log from the command and the
configuration file.
a.y
> Hi list,
>
> I'm performing -stat step but this command produces sementation fault
> after loading affine registration .mat.
> Thanks,
>
The memory error was in the -path part, that's what you should try
rerunning. What you downloaded will have no effect on bedpostx itself.
> i just downloaded dmri_5.1_snow_leopard.tar.gz: from that web page and
> installed the new version of the dmri file in the freessurfer /boin
> directory
> I
The subject name needs to be the same for recon-all and trac-all. There is
no way for trac-all to guess that hpth_subj01 and Diff01 are the same
subject.
> Hi Anastasia,
> my original folder Diff01 in
> /Applications/freesurfer/subjects/subject_prova/Diff01 now
> contains:data.nii.gz (DWI), MPRAGE
Hi Stefano - The -prep option doesn't take an argument. Please run
trac-all with no arguments to see usage info.
a.y
> Hi list,
> I'm trying to run a test subject with TRACULA.
> I placed a folder in /Applications/freesurfer/subject/subject_prova which
> contains these files: data.nii.gz (DWI), b
Hi Juke - You can convert path.pd.nii.gz to a probability by normalizing
it to a sum of 1. The numbers in there are the number of occurrences of
the path in any specific voxel, among the 1000 or so paths that are
sampled by the MCMC algorithm.
Hope this helps,
a.y
> Dear Dr. Yendiki and TRACULA e
Hi Ansgar - From looking at your data, the reconstruction of the ccg
failed b/c it goes erroneously into an area superior of the cingulum. You
can see this clearly by looking at the slice view of the cingulum in
freeview (the isosurfaces in the 3D view don't always tell the whole
story).
It's pos
Hi Martijn,
Which pathway does it fail on? Is the pathology of your subject affecting
the structures in the aparc+aseg that surround that pathway?
a.y
> Dear all,
>
> I'm running Tracula on a brain with some pathology. During the preproc
> phase it fails with the following error:
>
> INFO: Rejec
You don't have to multiply the bvecs with anything yourself, it will do it
for you. Of course you should check that it does it correctly, check the
help of the flip4fsl script for how to do that.
> Could you give me something about the transpsition here?
> I checked the code flip4fsl and found the
Hi Colin - re: the first question, check out dmri_trk2trk.
Anastasia.
> Hello;
>
> first, regarding the information here:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms
>
> This looks to me very much like snippets of code to help people write
> their
> own code to read
Yes, it should be a concatenation of all existing pathway reconstructions
under dpath/... If you open it with trackvis --tv, you should be able to
see a 3d view of all the pathways. Sometimes the default threshold might
be too high for some pathways and you might need to adjust it individually
in f
Hi Ana - I'll try to post the fix later this week.
a.y
> Hello freesurfer users.
>
> I'm trying to process a trac-all
> and it works for a while, but i have always the same error when it going
> to
> process the error.
>
> this is the end of the message
>
> Loading cortex mask from
> /Application
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