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:
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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,
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
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
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
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
___
Freesurfer mailing
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
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
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
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 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
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
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
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
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
to the directory specified in dcmroot
above.
Jon
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: ebelleau ebell...@uwm.edu, freesurfer
freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 22, 2013 1:47:05 PM
Subject: Re
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?
- 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
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
21 matches
Mail list logo
