Hi Lorenzo,
The correct way to calculate the expected (not an integer value) number of
voxels belonging to a subfield is by summing ( intensity / 255 ) across all
voxels. Not sure where things go wrong: the integer values you report are a
bit suspicious, or perhaps some rescaling of image intensit
Hello FS experts,
I would like to study MRI, by using FS, to extract binary images of hippocampi.
My data images have sizes different from 256,256,256.
Is there any FS procedure to generate images 256, 256, 256 from my data set?
Does FS work only on images 256, 256, 256 ?
Thank you very much
Andre
Dear Koen,
thank you very much for your help!! by summing the intensities and dividing by
255 I get the same volumes estimated by freesurfer.
Thank you again and greets,
Lorenzo Pasquini
--- Ven 7/12/12, Koen Van Leemput ha scritto:
Da: Koen Van Leemput
Oggetto: Re: [Freesurfer] hippocampal s
Hello Andrea,
on one of the first FS steps your images will be scaled to fit 256x256x256
pixels.
Best regards,
Iven
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Andrea Tateo
Gesendet: F
What physical size do you need them? I use either convert in unix or photoshop
On Dec 7, 2012, at 1:36 AM, Knut J Bjuland wrote:
> Hi Bruce,
> Do you upsample the tiffs from tksurfer when making image for publications?
> Or do you use another program in FreeSurfer suite?
>
>
> Knut J
>
>
Hi Greg,
It's ok to smooth using FS tools, as long as the different sizes of the
faces of the ico7 are taken into account. This means that, after running
"rpncalc", the "smoothdpx" command can be skipped, and the data can be
converted to vertexwise and imported into qdec, which will then smooth it
Hi Andrea
sure, recon-all will handle whatever you give it and resample to 256^3,
but the accuracy will degrade as the resolution worsens. What resolution
are your images?
cheers
Bruce
On Fri, 7 Dec
2012, Andrea Tateo wrote:
Hello FS experts,
I would like to study MRI, by using FS, to ex
Hi
I saw an updated version of mri_glmfit in
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/.
Should I update this file in my freesurfer installation.
What do this fix? Is is not in the release notes? Along with mri_glmfir-sim
from Doug Greve ftp site.
Knut J
This is my dataset.I don't know another
Tenx
Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 7-dic-2012 17.09
A: "Andrea Tateo"
Ogg: Re: R: Re: R: Re: [Freesurfer] different MRI size
why do you have different matrix sizes? And I can't tell resolution
without knowing the FOV. Id
Hello
I am trying to run Tracula on a set of dicoms files. I have run
recon-all previously.
I am getting a message trac-preproc exited with ERRORS
Please can anyone advise me on this?
I have listed all the details (command, error/output, config file) below
Thank you so much for your help
best w
Hi Knut, no need to update. This looks like a pretty old file.
doug
On 12/07/2012 11:12 AM, Knut J Bjuland wrote:
> Hi
>
> I saw an updated version of mri_glmfit in
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/.
>
> Should I update this file in my freesurfer in
Hi Jorge,
Sorry, but I am not following :(
What is "/ni"/ ?
if "/ni/" is "/number of repeated measures for each subject"/ (as
/sortData/ help says) - then, for each subject we did only 2 repeated
measures, so /ni/ should be
/ni = [2];
/if "/ni/" is the "/vector of the same size as the number
Hi Alex
In your case ni is a vector of size 36
ni =[2 2 2 2... 2];
Note that it may happen that the number of repeated measures being different
across subjects for some longitudinal studies. In your case all subjects have
the same number of repeated measures (2).
this sID column - is this a simpl
Hi,
Do I work with aseg.fused.mgz or do I work with aparc files to get the most
accurate segmentation of brain structures?
I tried using freeview to look at segmentations. Is there a way to isolate
mgz files of very specific structures. I mean, is there an inbuilt tool
which can do that for me, o
Hi Prasanna,
not sure what you are asking and what this has to do with longitudinal.
But generally: subcortical segmentations are stored in the aseg.mgz file
(this is true also for the longituinal stream, do not look at the
aseg.fused.mgz , it is an intermediate step). Final results are in
aseg.mg
Hi Prerona - You need to uncomment the bvecfile and bvalfile definitions
in your configuration file.
Hope this helps,
a.y
On Fri, 7 Dec 2012, s0675204 wrote:
Hello
I am trying to run Tracula on a set of dicoms files. I have run
recon-all previously.
I am getting a message trac-preproc exit
Hi Doug,
I'm having a similar problem. Subjects had the opportunity to classify
stimuli into one of three categories (Good, Bad, Neutral). For some
subjects, one of more of the runs did not contain any stimuli that they
classified as Neutral. If I want to look at a contrast that compare
Good-Ne
Hi Keith,
if you don't have any Neutral in a session, you can't do a Good-Neutral
comparison. If you have multiple runs within a session, then it should
be ok.
doug
On 12/07/2012 03:02 PM, Keith Yoder wrote:
> Hi Doug,
>
> I'm having a similar problem. Subjects had the opportunity to
> classif
Ah, the subject was missing Neutral from all three runs. Removing them
from the sessid gets rid of the error.
Thanks!
Keith
--
Keith Yoder
PhD Student, Integrative Neuroscience
Social Cognitive Neuroscience Laboratory
The University of Chicago
5846 S. University Avenue, Kelly 312
Chicago, IL 6063
Hello
I think I spoke to soon!
It ended with errors again.
I get the error message: "bvecs and bvals don't have the same number of entries"
I saw on some older messages on the mail-base you said that we need to
check that the number of entries in the bvals is same as and bvecs is
3 times as muc
Can you please send the text files instead of pasting them in the email?
Thanks!
On Fri, 7 Dec 2012, s0675204 wrote:
Hello
I think I spoke to soon!
It ended with errors again.
I get the error message: "bvecs and bvals don't have the same number of entries"
I saw on some older messages on
Yes, I can see that each of the bvecs/bvals files is one long line. Was
that the case for the original files that you specified in the dmrirc?
On Fri, 7 Dec 2012, s0675204 wrote:
Hi Anastasia
I had attached the files, but maybe they did not go through to the
mailing list? So I am sending th
I see. Can you try formatting them in columns (1 column for the bvals and
3 columns for the bvecs)?
On Fri, 7 Dec 2012, s0675204 wrote:
yes! these are the original files
well these are the files i pointed to in my config file. and i think
the script copies them over to the dmrirc folder?
b
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