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Hello all,
I am currently using the longitudinal implementation of Tracula with a dataset
of five subjects each with two time points. All follow-up time points were
acquired roughly three weeks after all baseline time points on a different
scanner (
only the long
stream.
Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Donovan Roediger
Sent: Wednesday, March 16, 2022 2:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA longitudinal - weird t
ope this helps,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nick Vogt
Sent: Friday, January 4, 2019 6:21:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula longitudinal tract reconstruction problems
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Thank you Anastasia!
I’ll try upping the nburnin to 2000, and then I’ve also had some success
increasing the nsample to 18000 (which presumably gives it more opportunities
to get unstuck and explore?).
For the longitudinal pipeline, what’s the best
Hi Nick - This likely means that it got stuck at the initial path for a while,
but eventually got unstuck and explored the space successfully. If you don't
like this look, you can try setting the nburnin parameter in the config file,
to something higher than the default 200. This sets the number
u<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA longitudinal stream: using multiple configuration
files?
Hi Freesurfer users
I wonder wether it makes a difference when using longitudinal TRACULA if all
timepoints are run with
Hi Freesurfer users
I wonder wether it makes a difference when using longitudinal TRACULA if all
timepoints are run within one process (1 configuration file including all three
timepoints) or if it is possible to split it into several independent processes
(with several different configuration
Hi again Deniz - This may be confusing but with longitudinal TRACULA there
are separate trac-all.log files in each time point's directory and in the
within-subject template's directory. The former are for things that are
run independently for each time point (mainly pre-processing) and the
la
Dear Anastasia,Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one.In the inter-subject registration step, I
Hi Deniz - It seems that it finds the folders of the 2 time points, but
not the folder of the longitudinal base template. This is the template
that longitudinal recon-all creates in its 2nd processing step. In your
case, it would be
/data_august/Deniz/DTI_long/subjects/med_AhJa94
Doe
rfer/tracula/bvecs.txt
>> > set bvalfile = /data/analysis/freesurfer/tracula/bvals.txt
>> > set doeddy = 1
>> > set dorotbvecs = 1
>> > set thrbet = 0.3
>> > set doregflt = 0
>> > set doregbbr = 1
>> > set doregmni = 0
>>
gt; set doregmni = 0
>> set doregcvs = 1
>> set usemaskanat = 1
>> set pathlist = ( lh.cst_AS rh.cst_AS \
>>lh.unc_AS rh.unc_AS \
>> lh.ilf_AS rh.ilf_AS \
>>fmajor_PP fminor_PP \
>>
15 4:00 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Date: Fri, 7 Aug 2015 18:23:41 -0400 (EDT)
From: Anastasia Yendiki
Subject: Re: [Freesurfer] TRACULA longitudinal processing fails when
inter-subject registration to CVS template
To: Freesurfer support list
Cc: Tracy Melzer
Messa
et trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
- END: subj2.dmrirc.long -
On 9/08/15 4:00 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Date: Fri, 7 Aug 2015 18:23:41 -0400 (EDT)
> From
Hi Daniel - You should be able to use CVS with longitudinal tracula,
although it's probably the least tested combination of options in there.
It sounds like this may be a bug. Can you please send me the full log file
and full config file? Thanks!
a.y
On Tue, 4 Aug 2015, Daniel Myall wrote:
Hi,
Is it possible to register to CVS template (and not the MNI template)
and use the longitudinal processing stream in TRACULA? If it should be,
then either there is a bug or I'm doing something wrong.
Using Freesurfer 5.3 with the 2014/05/26 TRACULA update on Ubuntu
14.04.2 (with a bunch o
Hi Kevin - The names should be the cross-sectional IDs, i.e., without the
.long.basename suffix.
Note that the version of longitudinal tracula originally included in
freesurfer 5.3 uses the cross-sectional aparc+aseg from freesurfer,
whereas the latest updated version (recommended) uses the
Getting ready to run longitudinal tracula. Does the sublist entries in the
dmrirc.long file refer to the cross-sectional or longitudinal processed subject
time points?
set subjlist = ( huey-scan1 \
huey-scan2 \
dewey-scan1 \
dewey-scan2 \
Hi Vincent - Overall measures for the whole tract would not be affected
by this type of error.
a.y
On Fri, 4 Apr 2014, Vincent Brunsch wrote:
> Great, thank you!
>
> Do you maybe know if these changes will only affect the "center
> variables"? I have almost completed my soon-due report about t
Great, thank you!
Do you maybe know if these changes will only affect the "center
variables"? I have almost completed my soon-due report about the
longitudinal analysis of "weighted average variables" (overall not
byvoxel along the MAP) and now I fear that results are maybe not correct
because
Hi Vincent - I suspect that this problem would be fixed by some recent
changes that I've implemented for the longitudinal stream of tracula, and
that I'm in the process of testing. As soon as we can get a new dev
version built, I'll let you know so you can test it.
Thank you for your patience!
Dear TRACULA experts,
I have used the longitudinal version and find that for some subjects'
tracts Len_Min is larger than Len_Center. How is this possible? (An
extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.)
Best, Vincent
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Hi Anastasia,
the files are here:
/autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr
The base is here:
/autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB
Freesurfer outputs:
/autofs/cluster/lazar/proj
Hi Vincent - If you upload the tracula dirs for this particular time
point, I'll take a look.
a.y
On Mon, 20 May 2013, Vincent Brunsch wrote:
> Hi Anastasia,
> Thanks for your help! I had this issue with 4 tracts in total. I just want to
> add that before rerunning dmri_pathstats not only pat
Hi Vincent - Thanks for bringing this to my attention. I can see what
might cause this glitch (only in the longitudinal case) and I'll fix it in
the next version.
In the meantime, if you delete one of the two identical lines from
cpts.map.txt, and then rerun the dmri_pathstats command line tha
Dear Anastasia,
When running the longitudinal tracula version on our 39 subjects I found
for some of them "nan"-values for the center_avg variables of some tracts.
When I have a look at the tract distribution and the highest probability
path, everything seems to be ok. However, when checking the c
Hi Catherine - Yes, for now treat each time point as a different subject
for trac-all purposes. (You can pass the time points' recon-all
directories either before or after longitudinal processing.) However,
there may also be a longitudinal version of tracula coming soon - but you
didn't hear
Hello Experts,
Please forgive another question.
I have run 59 people through the recon-all freesurfer longitudinal stream with
2 timepoints (tp1id, tp2id).
I want to run these subjects through "tracula" next, since the same people also
received repeated Tensor imaging.
To process everybody t
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