Hi Maria – Can you please run the mri_info command on the same nifti volume on
the same computer and let us know what the output is?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Maria Economou
mailto:meconom...@sheffield.ac.uk>>
Reply-To: Freesurfer support list
mai
Hi Yuwen - This file is generated by the command dmri_paths, which is run
before the dmri_pathstats command. You can see the exact command lines in
scripts/trac-all.cmd (and the full output in scripts/trac-all.log).
Best,
a.y
From: freesurfer-boun...@nm
Hi Colleen - Do the DWIs of your subjects have any slices that are in the brain
but look very dark, almost like the background? That's what those measures
capture, and not all subjects have that. If your subjects don't have that, then
there's nothing to be concerned about!
Best,
a.y
_
Any
suggestions on how to better match on motion?
Thanks,
Colleen
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, July 18, 2017 6:46 PM
To: Freesurf
Hi Derek – The version in the distribution is the only version that exists. One
option for what you’re trying to do is to use the *.byvoxel.* stats files and
average the values, say, in the first 1/3 of points.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Derek A Pi
nge the
threshold. How should the threshold value be determined in order for us to
match on dropout?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesd
Hi Marisa – Did you check the archives of this email list? I believe this error
has come up before.
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Marissa Pifer
mailto:marissapi...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
D
Hi – Is this on ubuntu by any chance? I remember it cropping up a while ago,
and I think you had to change something in the first line of the script. It
should be in the archives.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Lars M. Rimol" mailto:lari...@gmail.com>>
Repl
Hi Lars – That’s correct, you don’t need to run cross-sectional TRACULA first,
you just need to run longitudinal recon-all before you run longitudinal
TRACULA, and it expects that the time points and base template subject IDs are
the same for recon-all and for TRACULA. It sounds like the time po
Hi Yuwen - TRACULA is pretty forgiving in terms of imperfections in the
recon-all output. TRACULA uses only the aparc+aseg, after mapping it into
the subject¹s diffusion space, which is typically lower-res than the
structural. Also, TRACULA only uses the relative positions of white matter
voxels to
Hi Walter – I’d check on the structural segmentation and its registration to
the DWIs. Open dmri/dtifit_FA.nii.gz and label/diff/aparc+aseg.bbr.nii.gz and
check if they’re well aligned and if the segmentation looks fine.
On a separate note (and I don’t know if it’s related to the error you’re as
Hi Ariel – Have you run freesurfer on the structural images of your subjects?
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in
your configuration file?
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Lin, Yizhi" mailto:l...@union.edu
support list
Subject: Re: [Freesurfer] TRACULA ERROR!!
Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons were
found in SUBJECTS_DIR in my configuration file. Thanks.
best,
Ariel
On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia
mailto:ayend
Hi Ariel – Have you run freesurfer on the structural images of your subjects?
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in
your configuration file?
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.
You can use the wmparc, which includes ROIs of the WM underlying each cortical
area, right below the grey-white boundary surface. These are the relevant
tutorials:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalRO
What effect are you trying to measure with MD on the cortex?
From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am
the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia
wrote:
What effect are you trying to measure with MD on the cortex?
From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, Augus
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from
a lower-res (diffusion) space to a higher-res (T1) space, so it should be
smooth already, relatively to measure derived from the T1. And MD varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "
Hi Mina - The part that takes long is running bedpost. If you run trac-all with
the -jobs flag, it'll write out a text file with command lines that can be run
in parallel.
https://surfer.nmr.mgh.harvard.edu/fswiki//trac-all#Parallelprocessing
I do have long-term plans for not using bedpost, but
t: Re: [Freesurfer] Mean diffusivity on cortex?
Thank you both.
How can I deal with partial volume in this case? Would it be possible to use
the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea.
Best Wishes,
Shane
On Friday, August 11, 2017, 6:19:45 PM GMT+1, Ye
Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can
reinitialize those bad cases, by adding “set reinit = 1” in your config file
and changing the path list and subject list to specify only the tract and
subjects that you want. Then rerun trac-all --prior and trac-all —p
Hi Fred – Because of your language setting, unix is using commas instead of
decimal points and this is messing something up. Try changing your environment
with "setenv LANG en_US.UTF-8” .
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fred Sampedro
mailto:freds
Hi Christopher – If you have not resolved this, please send along the bvals and
gradient table files. It seems to expect a 35th volume in your nifti file,
which has 34 volumes.
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Ferrier, Christopher Q."
mailto:cfe.
Hi - Yes, it sounds like there is no drop-out in your data, so there is no
reason to use drop-out measures to compare across subjects.
Best,
a.y
On 8/30/17, 1:34 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
이 정환"
wrote:
>Hello
>
>I’m attempting to analysis diffusion MRI using TRACU
Hi Abby - You can try first reinitializing without increasing the number of
control points, and if that doesn’t work then increase them. Increasing the
number of control points increases the degrees of freedom in the shape of the
path, which can be good, e.g., for the corpus callosum of subject
Hi Anna - There was no method for intra-subject (diffusion to structural)
registration selected in your config file, so some steps were skipped. Change
the 0 to a 1 in this line: "set doregbbr = 0" and then rerun the preprocessing
(you can skip the steps before the intra-subject registration if
Hi Batool - Please send over your (actual and not made up :) config file and
trac-all.log.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool
[br2...@cumc.columbia.edu]
Sent: Tuesday, October 10,
Hi Chintan - Freesurfer is open source, so all of our source code is available,
but trac-all is actually a shell script, so you can find it under
$FREESURFER_HOME/bin/.
TRACULA just expects the output files of bedpostX, and does not care if they
were generated on GPUs or CPUs. Just provide the
er-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Friday, October 6, 2017 11:26:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA qc: forceps minor and major
Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can
reinitialize those bad cas
Hi Chintan - What makes you think that it's bedpostx_gpu? Does the problem go
away when you use regular bedpostx?
It's hard to guess what's going on. If you send me a subject that works and a
subject that doesn't (zip all tracula dirs of these subjects) here, I'll take a
look:
https://gate.nmr.
Hi - It's hard to tell from the screenshot. Can you please send your entire log
file from scripts/trac-all.log? The error seems to be related to the gradient
table, so if you can also send that and the b-value table, that'd be great.
Best,
a.y
From: freesurfer
Hi Zheng - I'll need the trac-all.log file, the gradient table, and the b-value
table. Please do not send other data at the moment.
Thanks,
Anastasia.
From: 郑凤莲 <13181786...@163.com>
Sent: Tuesday, October 31, 2017 9:48:52 PM
To: Yendiki, Anasta
Hi Fred - The longitudinal stream processes the diffusion data from all time
points jointly, which, for most of the processing steps, will not be the same
as processing each time point independently. It also uses the aparc+aseg from
the longitudinal recon-all stream, which will not be the same a
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 Duncan - We actually use a "robust max", i.e., the 99th percentile of the
values in path.pd.nii.gz. This is to avoid cases where the absolute max is an
outlier, which would cause the threshold to be too high and the isosurface in
freeview to be generated from too few voxels.
Best,
a.y
__
Hi - If there is no error message in your scripts/trac-all.log file, that means
that it was able to read the information from the dicoms. You can double-check
if the gradient table was read correctly by inspecting the outputs of the
tensor fit with: freeview --dti dmri/dtifit_V1.nii.gz dmri/dtif
Hi Knut Jørgen - TRACULA and AnatomiCuts are completely different software
tools that serve completely different purposes. TRACULA is for reconstructing a
set of pre-defined, named tracts automatically, based on prior information on
the anatomy of these tracts from a set of subjects were the sam
Hi Carissa - It loks like bedpost ran fine. Can you please attach your entire
log file (scripts/trac-all.log)? It's hard to tell what went wrong just from
the end of it.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Carissa Nicole Weis
...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Thursday, January 11, 2018 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of
bedpostx?
Hi Carissa - It loks like
ACULA.
The diffusion images were acquired with fairly common parameters: 3 B=0 images,
35 different gradient directions at B=800 with 70 slices per direction at a
voxel size of 2x2x2mm for a 128x128 matrix.
Thanks for your help!
Carissa
From: on behalf of "Yendiki,
Anastasia&
oun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Saturday, January 13, 2018 3:49 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA path segmentation fault error because of
bedpostx?
Those are pretty standard dimensi
Hi Linnea – Before the stats are computed, the probability distribution of the
paths is thresholded to 20% of its peak value, so voxels with very low
probability will not affect the outcome.
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Linnea Marie Dramdal Borg
Hi Nicole – You can skip the eddy current correction, check the TRACULA
tutorial for how to do so. BET thresholds don’t matter here, because TRACULA
will make a brain mask out of the freesurfer segmentation and use it to mask
your DWIs.
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harva
RESEARCH TECHNICIAN POSITION IN NEUROIMAGING
POSITION SUMMARY: Applications are invited for a research technician at
Washington University in St. Louis. This well-established laboratory studies
the structural and functional organization of the human brain using multi-modal
imaging: including m
Hi - Is this the only output that you get? This is the first line of text that
you see when you run trac-all? To figure this out we'll need the full terminal
output (which is also saved in scripts/trac-all.log), as well as your config
file.
Thanks,
a.y
From:
Can you attach your configuration file please?
On 1/29/18, 2:58 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Renew Andrade" wrote:
>Dear Anastasia:
>All the output I get is the if Expression Syntax.
>___
>Freesurfer mailing list
>Freesurfer
As a sanity check, you can downsample one of the data sets that fail to 2mm
iso, and see if it runs that way. This would tell you if it's a data size issue.
From: Carissa Nicole Weis
Sent: Monday, January 29, 2018 5:53:59 PM
To: Yendiki, Anastasia
Subjec
Subject: Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)
What is the configuration file or where can I find it?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
d.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Yendiki Anastasia config file
Here is the configuration file. I think is the default by tutorial.
___
Freesurfer mailing l
A two-year postdoctoral fellowship in the Center for Observational and
Real-World Evidence (CORE) division at Merck, applying quantitative methods to
improve healthcare quality/outcomes and reduce cost:
https://taleo.msd.com/careersection/merck_external_career_section/jobdetail.ftl?job=POS00024
Hi Donatas – All sounds fine. You can process single time points, and you can
process subsets of time points if the DWI data from one of them is unusable.
The T1 base template is only used as a reference space for longitudinal
TRACULA, so it shouldn’t make a huge difference if one additional tim
Hi John – The problem is the funky format of the numbers in that registration
file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in
all the other registration files in the xfms/ directory in this same format? It
probably has something to do with how your unix environment v
Hi Donald – TRACULA doesn’t use deterministic ROIs, instead it assigns a
probability to any ROI to be the one that the specific tract intersects or
neighbors at a specific position along that tract’s trajectory. These prior
probabilities are computed from the training subjects that make up the T
need to do my own tracula runs to get them?
Or am I missing something?
I am a total newbie on tracula.
Best – Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 4:34 PM
To: Freesu
e those .txt files
readily available somewhere? Or do I need to do my own tracula runs to get them?
Or am I missing something?
I am a total newbie on tracula.
Best – Don
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-b
ed. The outcome was identical, but
I can send the files in again if you need.
Thank you for helping
John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi John – The problem is the funky format of the numbers in that registration
file. It ex
, you will get FLIRT matrices saved in hexadecimal format. If you upgrade
your FSL to a more recent version, you should be okay.
On Fri, Feb 16, 2018 at 2:10 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ dir
nd ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and
fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks.
John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Sorry to hea
wrote:
Anastasia,
Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I
should probably ask IT department for the recommended. Is that the latest
stable version?
John
On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
OK, so t
Hi M - You generally want to register the lower-res to the higher-res image. In
this case, that’s diffusion to T1. Check the diffusion processing tutorial on
the freesurfer wiki for how you can apply the inverse transform to the
aparc+aseg to get it into diffusion space.
Best,
a.y
From:
mailt
ectj/mri/aparc+aseg2diff.mgz --reg register2b0.dat
--no-save-reg
Does this look right?
Thank you very much,
M.
On Fri, Feb 16, 2018 at 4:08 PM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi M - You generally want to register the lower-res to the higher-res image. In
this case, tha
Hi Katherine - If you mean the .trk format, that's not for storing labels, it's
for storing tractography streamlines (i.e., a bunch of curves that are stored
as sequences of x,y,z point coordinates). You can convert the FreeSurfer labels
to nifti volumes, and see if the software that you're tryi
Hi Carissa – These are MNI coordinates. These mean paths are created only for
visualizing group results. However the actual FA, etc measures that are used
for group analyses are generated in each subject’s native space.
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf
Hi Daniel - Just make sure that spatial resolution is isotropic, and collect as
many different directions as you have time for. Otherwise, we do not have
strict requirements.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Alejandro Reyna
Probably not a good idea, depending on how the data are balanced across
acquisition protocols. If you find differences between time points of subjects
or between subjects, you want to be ensure that those differences are not
because of acquisition differences. If, for example time point is alway
r that in a
second level?
Thanks,
M. Cano
De: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] en nombre de Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Enviado: lunes, 19 de marzo de 2018 12:39
Para: Freesurfer support list
Asunto: Re: [
Hi Desiree - It looks like this is happening for the corticospinal tract. Is
there anything going on with that scan in the area of that tract, let's say
slices cut off from the top of the motor cortex or from the brainstem?
Best,
a.y
From: freesurfer-boun...@n
Hi Don - See:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newb
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - See:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html
Best,
a.y
arvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - If the output files described here show up in the end, all is well
its probability, i.e. 0-255 -->
0.0 – 1.0
Thanks again – best – Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list
Subject: Re: [Freesur
mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
The volume would have to be normalized to a total sum of 1 for the voxel values
urfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
This wouldn't work because these 18 tracts do not include all tracts in
el values map to probability. That’s
why I described the wrong headed way I was thinking about it … so you could
tell me where I’m going wrong.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf
wfully low … what am I missing?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don -
Hi Samantha - You display a .trk file that was generated in any possible tool,
as long as that tool preserves the image orientation information in the header
of the .trk file. If that info is not there, there is no way for freeview to
guess how to display everything in the same space.
Best,
a.y
Yes, you can. The only thing that TRACULA uses from the structural is the
aparc+aseg, and specifically the relative positions (left, right, anterior,
etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
It's safe to assume that those positions will not have changed betw
d.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, May 02, 2018 2:10 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a
different MR sessions
Yes, you can. The only thing that TRACULA uses fro
Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial,
to pass a text file that contains the paths to all the stats files that you
want to include in the table. These can be from multiple subjects and/or tracts.
http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics
Hi Loic - The command that computes the motion measures is dmri_motion, and it
can take either the eddy_correct or eddy format as input. The former format
contains affine registration matrices with respect to the reference frame
(which usually is the first b=0). The latter format contains the
s
This is not entirely surprising. You have a b-value that’s quite high (b=3000)
and eddy_correct will not work well with such high b-values, because is tries
to register the b=3000 images to a b=0 image, and the b=3000 images do not have
enough anatomical detail to be registered correctly. You ca
Hi Tim – The best method to use will depend on the data you have. If you have
very high b-values, you should use eddy. You can turn off the eddy current part
of the preprocessing with “set eddy=0” in the config file, and run trac-all on
your corrected images.
Best,
a.y
From:
mailto:freesurfer
Hi Loic – In simple terms, motion will cause a rigid transformation of the
brain (translation and rotation only), whereas eddy currents will add non-rigid
effects (scaling/stretching). By registering each DWI to the first b=0 image,
and then extracting the translation and rotation part of the tr
The output of TRACULA is a probability distribution that tells you how likely
each voxel is to be part of the tract that you’re looking at. Voxels with low
probability values are not very likely to be part of the tract. Setting the
threshold in freeview to 20% means that you only want to display
Hi Montse – In case you’re still having trouble with this subject, I would
check the structural segmentation (aparc+aseg from recon-all) and see if
there’s anything wrong in parts of the brain that the ATR goes through. If that
looks fine, then sending along the entire trac-all.log file would he
You should probably be suspicious.
From: Katherine Damme
mailto:katherine.da...@gmail.com>>
Date: Wednesday, September 5, 2018 at 1:48 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>,
Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>>
Subject: Mean FA values for maj
Hi Qianwen – You don’t have to do (1) and (2), trac-all –stat does that for
you. For a description of the measures, see the tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
and the course slides:
http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt
Best,
a.y
...@qq.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 12, 2018 at 9:47 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] 回复： questions about trac-all -stat
External Email
Hi Heidi – Do you have write permission to create the output directory
/data_int/heidi/forHeidi/Preprocessed?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Heidi Emmanuel Foo
mailto:heidifo...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.ha
Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Heidi – Do you have write permission to create the output directory
/data_int/heidi/forHeidi/Preprocessed?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Heidi Emmanuel Foo
mailto:heidifo.
Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config
all defaults and kicked
off the process with -s and -i flags.
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700
Hi Matt – It looks like some sort of registration issue. When you
Hi Vinny - This error is during the diffusion-to-structural registration. Can
you send the entire log file (scripts/trac-all.log)?
Best,
a.y
On Sep 19, 2018 8:39 PM, Vinny K wrote:
External Email - Use Caution
Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I g
External Email - Use Caution
Hi Anastasia,
Nope, I don't actually get any output and/or log file.
Regards,
Heidi Foo
On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Heidi - The config file that you sent looked fine to me. What is th
44 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vinny - This error is during the diffusion-to-structural registration. Can
you send the entire log file (scripts/trac-all.log)?
Best,
a.y
On Sep 19, 2018 8:39 PM, Vinny K
mailto:vinit.k.srivast...@gmail.
at one for Tracula.
I'm assuming I can have both the stable and dev versions installed and modify
the .bashrc profile to point to the correct freesurfer version that I wish to
use?
Vinny
On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vin
noisy and
pixelated than others.
This is a mTBI subject with no other anatomical brain anomalies scanned with a
Siemens 3T.
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700
Do th
- Use Caution
Hi Anastasia,
I think I ran trac-all -c config.txt.
Regards,
Heidi
On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
What is the trac-all command line that you run?
From:
freesurfe
omalies scanned with a
Siemens 3T.
Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700
Do the raw images look like that too?
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailt
abels?
Thanks/Vinny
On Thu, Sep 20, 2018 at 8:32 AM Vinny K
mailto:vinit.k.srivast...@gmail.com>> wrote:
Thanks Anastasia, I'll give this approach a try.
On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
That's correct! You can
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