Hi Gonzalo - The input to TRACULA can be any file that can be converted to
nifti by mri_convert. See:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#line-156
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Gonzalo Rojas Costa
External Email - Use Caution
Hello,
I just wanted to follow-up on my last message. I will be thankful if you can
respond at the earliest time of your convince.
Thanks and all the best,
Ela
From: Salar Dini, Elaheh
Sent: Wednesday, January 26, 2
External Email - Use Caution
Dear Anastasia,
Thank you so much for the response. Interestingly, when I try to open the two
reconstructed brains at the same time, they don't overlay. Am I correct to
assume then that we have to run recon-all using version 7.2.0? I'm providing a
s
Hi Ela - When you overlay the aparc+aseg from 6.0 and the one from 7.2, is
there a notable difference? Is there any chance that the brain is cut off? The
error happened in the anterior commissure, that's a tract that does goes fairly
close to the ventral surface of the brain, and in the part of
External Email - Use Caution
Thanks Anastasia. That is exactly what happened and we have fixed it.
best,
Alan
On Tue, Oct 15, 2019 at 5:37 PM Yendiki, Anastasia
wrote:
> Hi Alan - It looks like it may be due to a mismatch between the
> bvals/bvecs files and the number of volum
Hi Alan - It looks like it may be due to a mismatch between the bvals/bvecs
files and the number of volumes in your DWI data. I think it's expecting to
find a b=0 volume as the 64th volume, but your DWI nifti has only 63 volumes.
a.y
From: freesurfer-boun...@nmr.
ehalf of June Kang
Sent: Saturday, November 3, 2018 7:35:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged
tracts are defined?
External Email - Use Caution
It’s just huge data collected from general population. Some data can
gt;>
> Sent: Saturday, November 3, 2018 12:24:54 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged
> tracts are defined?
>
> External Email - Use Caution
> Thanks, Professor Anastasia,
>
>
vard.edu
on behalf of June Kang
Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged
tracts are defined?
External Email - Use Caution
Thanks, Professor Anastasia,
I am testing HCP data
External Email - Use Caution
Thanks, Professor Anastasia,
I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right
uncinate fasciculus (more than 25%), which not happened with my own
64-direction data with Siemens Tr
They are not random, they are 20% of the maximum value. If you want to generate
stats at a different threshold, you can find the dmri_pathstats command line in
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).
On Nov 1, 2018 9:01 PM, June Kang wrote:
External
Hi Gabriela - When you define a list of items in the config file, i.e.,
anything between two parentheses "( ... )", the items in the list need to be on
the same line, or, if you want to split them across multiple lines, there has
to be a backslash "\" at the end of each of the intermediate lines
Hi Noa - If you're still having this issue, please send the complete
trac-all.log file and your configuration file. It's impossible to guess
what goes wrong without seeing the full output.
Best,
a.y
On Fri, 30 Oct 2015, Golan, Noa wrote:
> Hi,
> I am currently analyzing DTI data and I am havi
Hi Emily - One should be a symbolic link to the other, so they should be
the exact same file.
a.y
On Tue, 16 Dec 2014, Emily Louise Belleau wrote:
__
Hel
Hi Lars - Just like you have to do before you run any freesurfer programs,
you'll have to run a script that comes with freesurfer and sets up all the
necessary environment variables. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
Hope this helps,
a.y
PS: Please send e
It looks like there may be something wrong with the bval file. Are you
using a different one for this particular subject?
On Wed, 7 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Here is the trac-all log. Thanks so much:
csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSur
Hi Anastasia:
Here is the trac-all log. Thanks so much:
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO:
Please attach the file trac-all.log. I can't tell what's going on just by
looking at the end of it.
On Wed, 7 Aug 2013, Alan Francis wrote:
Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:
mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeS
Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:
mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
--mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_reco
Yes, please attach the dmrirc and trac-all.log. Thanks!
a.y
On Wed, 7 Aug 2013, Alan Francis wrote:
> Hi Anastasia:
>
> For one brain I got this error message :
>
> csh::alanf@cerebro
> [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
> : trac-all -prep
> -
Hola Fernando - Please send questions about tracula to the freesurfer list
and not me personally, so that all users may benefit.
This issue will be resolved in the next version. For now, if you're on a
unix system that doesn't have the jot command, you'll just have to specify
the runlist in
Hi Gabor - The info that tracula uses is which aparc+aseg labels each
pathway neighbors at each point along its trajectory. It learns this
information from the 33 subjects in the atlas, where the pathways were
labeled manually, and then applies that knowledge to reconstruct the
pathways in you
Hi Gabor - Tracula doesn't use the BA labels, only the labels in the
aparc+aseg. I hope this answers your question.
a.y
On Sun, 16 Sep 2012, Gabor Perlaki wrote:
> Dear Anastasia,
>
> Earlier I was posted an issue about BA44/pars triangular:
> http://www.mail-archive.com/freesurfer@nmr.mgh.har
This probably means that bedpostx didn't process all the slices in your
DWIs. Someone else reported something like that recently, not sure what
may be causing it, but since it's independent of trac-all, I'd check on
the FSL list archives.
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
they a
Can you please check that the x-y-z dimensions of the bedpostx output
files are the same as the dimensions of the DWIs?
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
Thanks for your response!Attached are the requested files
The error occurs here are shown on my terminal:
Loading b-values
fr
Hi Natalia - I'd need to see at which point in the processing the error
occurs, since this is a very generic error message. Can you please include
your trac-all.log and dmrirc?
Thanks,
a.y
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
Hi Anastasia!I finally made tracula -prep work without er
Hi Natalia - This is an error that will occur if lowb_brain_mask does not
exist. The command that generates lowb_brain_mask is "bet" - can you find
that line in the log file and run it directly on the command line and see
if you get an error?
On a separate note, have you opted to use a DWI m
Do these files that it's trying to load exist? If not, the actual error
happened earlier, when they were being generated. Looking at the entire
trac-all.log instead of just the end might shed some light on this.
On Fri, 10 Aug 2012, Natalia Sánchez wrote:
Hi!I am running tracula for the fir
Thank you very much. We would like to do the weighted measure, as we
believe it would be more sensitive and robust to WM abnormalities in
our patient population.
Minjie
On Thu, Jun 28, 2012 at 11:52 AM, Anastasia Yendiki
wrote:
>
> Yes, if you wanted to do a weighted average of your measure. O
Yes, if you wanted to do a weighted average of your measure. Or you could
just theshold and binarize path.pd and use it a simple ROI to do an
unweighted average.
On Thu, 28 Jun 2012, Minjie Wu wrote:
> Dear Dr. Yendiki,
>
> Thank you very much for your quick response. To calculate the weighted
Dear Dr. Yendiki,
Thank you very much for your quick response. To calculate the weighted
DTI measure, per your previous emails, we would need to normalize
path.pd.nii.gz, right? If this is the case, we could use the following
equation correct for weighted measurement:
dti_para (DTI parameter imag
Hi Minjie - These commonly used measures are provided for your
convenience. You can always use the reconstructed path distribution volume
path.pd.nii.gz, thresholded or not, as a mask to average your measurement
of choice.
a.y
On Thu, 28 Jun 2012, Minjie Wu wrote:
> Dear TRACULA Developer &
Thanks Anastasia! The pathstats.allvoxel.txt was pasted at the end of
this email as in the previous one.
I will rerun dmri_paths command for the fmajor path and will send you
the log.txt file.
Thanks,
Minjie
[minjiewu@ccmfsl1 fmajor_P
Hi Minjie - There was no attachment to your email. The fmajor issue that
you're describing sounds like an initialization issue. That single curve
that you describe is where the algorithm starts at and b/c something is
wrong with it, it doesn't move from there. Does the curve seem to go into
a
Hi Priti,
Thank you very much for the detailed instructions. The tracts with
empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts.
After your email, I have checked all 10+ subjects with such problems.
They all share similar motion problems (the parietal or temporal part
of brain is cut
Hi Minjie,
The pathstats.byvoxel.txt gives the statistics of the higest probability
streamline of the posterior distribution of the tract and the
pathstats.overall.txt gives you average diffusion values for the whole
tract.
Please refer to the following:
http://surfer.nmr.mgh.harvard.edu/fswiki/
Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2
Hi Shannon - Which version of FSL do you have? Older versions didn't use
to save the mean_dsamples.nii.gz, but that was a
Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2
Hi Shannon - Which version of FSL do you have? Older versions didn&#
our help and patience,
~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Questio
hanks again for your help and patience,
~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracul
Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
run
Hi Maryam - You could compare the different measures like FA or MD across
subjects along the length of the pathway.
There will be a different number of points along the pathway for each
subject, so you'd have to interpolate the data points from all your
subjects to do a point by point comparis
No, if usemaskanat = 1, then the diffusion mask that comes from applying
bet to the lowb volume will not be used for tractography. A dilated
version of aparc+aseg will be used as a mask instead, which is typically
more reliable than trying to find the right bet threshold.
On Fri, 10 Jun 2011
Hi Anastasia
If I have T1 data available in my FS subject directory and I have
Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
then will the B0 brain mask we spoke of below be used?
Deryk
Hi Deryk - This variable is only used to average lowb images to create a
mask, so in your case you can set it to 2 and it'll just use the first 2
volumes from your nii file. Sorry for the confusion!
a.y
On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:
Dear Tracula Users
Does Tracula assum
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