Hi all,
I run into somthing that seems odd to me and wanted to consult -
I run the following script for getting the FA values from my DTI scans:
1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I1.dcm
--s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
/usr/lo
Dear members,
I would like to get your opinion on this issue - I have a dataset of over
400 subjects but under half of this data was acquired on a 1.5T scanner and
the rest was acquired on a 3T scanner. Would it be acceptable to conduct
cortical thickness analysis on the combined dataset? From rea
Dear Sinead,
we found global significant differences in thickness between 1.5T and
3T, in a group of subjects that was scanned at both scanners
(http://www.ncbi.nlm.nih.gov/pubmed/16651008). I think that nothing
stops you from doing the analysis, but maybe model in a field effect to
asset it i
Hi Sinead
I agree with Jorge - there is bound to be a substantial scanner effect. You
might be better off keeping the data separate and treating the 3T as a
confirmatory study.
cheers
Bruce
On
Mon, 18 Feb 2013, Jorge Jovicich wrote:
> Dear Sinead,
>
> we found global significant difference
Hi Bruce,
What if she created an FSGD file, and instead of just having "patients" and
"controls", she would have "patients1.5", "patients3", etc.? With over 400
subjects this should be feasible, i.e. the loss of d.f. is worth running the
combined analysis.
Chris
Hi Rotem
that does sound high. Have you checked the registation between your
diffusion data and the anatomicals?
cheers
Bruce
On Mon, 18 Feb 2013, Rotem Saar wrote:
> Hi all,
>
> I run into somthing that seems odd to me and wanted to consult -
> I run the following script for getting the FA
Hi Chris
you could do that but the increased variance may make it less. You also
could have a disease interaction such as changing tissue properties having
different effects at 1.5T and 3T. With that many subjects I would think the
more powerful statement is if you find maps that are similar wh
I ran trac-all -bedp -c /Studies/MJMRI/DTI/dmrirc_single_subject
the end of the output was:
52 slices processed
52 slices processed
53 slices processed
53 slices processed
54 slices processed
54 slices processed
55 slices processed
55 slices processed
56 slices processed
57 slices processed
5
Thank you all so much for your advice on this - The patient:control ratio
is disproportionate in both datasets and I will also be splitting the
subjects into genotype groups so I think I may consider running separate
analyses on the two datasets to see if we find similar results.
Thanks again for
Hi there,
Through the help of the Freesurfer Q&A staff I've been able to get ROIs
drawn in tksurfer into an augmented aparc+aseg file of an averaged subject.
I need to be able to get those ROIs, which are not part of the color LUT,
into Afni space.
For ROIs that are already in the LUT, getting th
Hi Paul
we usually call those labels and have an ascii label file format. Not
sure how to get that into AFNI, but I'm zure Ziad (ccd) knows.
cheers
Bruce
On Mon, 18
Feb 2013, Paul Beach wrote:
Hi there,
Through the help of the Freesurfer Q&A staff I've been able to get ROIs
drawn in tksurf
Hi Merlin,
Have you tried "wget -c" to resume an interrupted download? You can put the
command inside an infinite loop that will keep retrying even if the
connection is interrupted when you are not watching (say, overnight). The
following should work:
while (true) ; do wget -c -T 60
ftp://surfer.
Thank you for forwarding this.
I realize I need to further clarify my issue as well.
With the help of Doug Greve I've taken hand made ROIs in tksurfer,
repackaged them into a new annotation, and repackaged that into a new aseg
file for an average subject. Now (and this is where I'm stuck) I'm try
Hi Jon - There's a list of all bedpostx output files here:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
Do you see these files in the dmri.bedpostX directory?
a.y
On Mon, 18 Feb 2013, Jon Wieser wrote:
I ran trac-all -bedp -c /Studies/MJMRI/DTI/dmrirc_single_subject
the end
Hi Fabricio - Any format that the mri_convert command can take as input is
fine, so I'd try it on a sample data set and see. If this doesn't work,
you'll have to convert your data to nifti in advance, and provide the
gradient table and b-value table as well.
Hope this helps,
a.y
On Sun, 17
Hi Jon - So the files are there but there's to be a memory allocation
problem. Are you using the updated mac build from the tracula wiki page or
the one that was originally released with freesurfer 5.1?
a.y
On Mon, 18 Feb 2013, Jon Wieser wrote:
> Hi ,
>
> i have the following files in my dmr
Hi Jon - There was an updated build of the tracula executables
specifically for macos users that was posted a while back. See the tracula
wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Better yet, wait for 5.2 to be released later this week!
a.y
On Mon, 18 Feb 2013, Jon Wieser wr
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
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