Hi Anastasia,
Just to be clear, is this what you mean by a more diffuse volumetric
distribution. Here is a snapshot of the right inferior longitudinal fasiculous.
I am just getting a better sense of what to look for in terms of bad vs. good
tracts.
Emily
- Original Message -
From: "An
Hi all,
I was wondering how you go about looking at dtifit_V1 (the primary eigenvector
of the tensors) displayed as lines in freeview?
Emily
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Hello,
I was looking at a trac-all log file to get my bearings on what is being done
and making sure things were done successfully,
I did not get any errors for this subject but when I was looking at the right
uncinate fasciculus: It would say "Path from initial control points not
entirely in
Hi Anastasia,
So probtractx uses the output from the bedpost stage (which I ran in Tracula).
I noticed that the bedpost stage (in the dmri.bedpostx folder) also outputs a
no_dif_brain mask. I guess what I am worried about is that if bedpost creates
this no_dif_brain mask, that is what will be u
Hi Anastasia,
Thank you so much, this is really helpful.
I have one other question. So, at the bedpost stage, the no_dif_brain mask is
used correct (looking at the fsl webpage), or at this stage the freesurfer
segmentation is used as well?
If in addition to using tracula, lets say if I also wa
Hello,
I have a few questions about Tracula. I am very new to DTI, so I hope you can
bare with me.
1.) I have been checking my registration at the prep stage. I am very new to
this so it may be that I am not looking at the right files.
I looked at my eddy current corrected diffusion data (whic
Hello,
I was wondering if it is better to keep the FA results from a DTI analysis in
diffusion space for group analysis or if you should warp them into standard
space as you would typically do with functional MRI data.
Emily
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Hi Anastasia,
Although the website says: In addition to the tract-based analysis that can be
performed on the tract-based averages of anisotropy and diffusivity, the same
maps could also be used for other voxel-based and ROI-based group analyses.
So this makes me think that this type of group
Hi Anastasia,
On a related note, with tracula, you can't let's say track the amygdala to the
vmpfc (there is a study already demostrating that there is a white matter tract
that connects these two structures). Can I do something like that...take
the amygdala as the seed and the vmpfc as the
Hello,
I recently modified my script so that it would work on a cluster. I had been
running it successfully locally but am now having some trouble on the cluster.
The only thing I changed in the dmrirc script were some pathways. However, I
keep getting an error of must specify as many dicoms as
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my
colleagues was able to run his data off of our cluster ( the whole pathway
including bedpost) without any problem. However he (Jon Wieser) made an
individual dmrirc configuration file script f
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the
subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets
sent to a different processor on the
Hi Douglas,
Thanks for the reply. I am very new to Freesurfer and am more used to scripting
with AFNI.
Would you mind giving me a bit of sample code to get used to what this may look
like? Can I script this in a .tcsh file?
Also, once I convert the aseg to MNI space, can I simply average or a
Hello,
I am finding that my bedposting is not completing successfully. I was able to
get my first two subjects to run successfully, however, for the other two
subjects that I have run I have gotten the following message:
For some reason the bedpostX process DOES NOT appear
to have successfully
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to warp
these grey matter masks to MNI space. I have been trying to use @auto_tlrc in
AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group grey
matter
Hello,
I had some questions about setting the dmrirc file for batch processing for DTI.
I set the subject list I put in the 6 subjects I wanted to process. Then in the
dcmlist I put in the pathway to the data files for each subject. I put a space
in between each subjects pathways. Then I put
Hello,
I was wondering what output from the recon-all freesurfer scripts would be best
to make a grey matter only mask?
Thanks,
Emily
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gt;
>> elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
>> Use this variable to specify the input DWI data, one entry per subject. The
>> file names are assumed be relative to the directory specified in dcmroot
>> above.
>>
>>
Hello,
I am running into the following error when I try to run trac-all:
set: No match.
ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several
attempts at debugging it.
I was wondering if you had any suggestions? Attached
Hello Anastasia,
Is it okay to run my DTI data on Freesurfer 5.3 when all my recon-all scripts
for the structural data were run in Freesurfer 5.0?
And I can download the tracula program straight from the tracula Wiki? And it
will work for Linux?
Thanks so much!
Emily
- Original Message -
- Original Message -
From: ebell...@uwm.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 10, 2013 3:14:06 PM
Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in
your
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