External Email - Use Caution
Hi experts,
I have been attempting to analyze a group of subjects through the longitudinal
TRACULA pipeline and have run into many issues regarding the preprocessing step
making use of the thalamic segmentation. I've combed through the archives on
t
External Email - Use Caution
Hello FreeSurfer devs,
I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per
subject using an HCP server. I have used the example dmrirc page
(https://secure-web.cisco.com/1JykEBcpM6vAD_4qy69NGW33wNc83B-TuXM37yVrgXaTHoNwBQkiBWLQw
to:cnw...@uwm.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 27, 2018 at 4:28 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] longitudinal TRACULA -prep error
Exte
External Email - Use Caution
Hello,
I'm running into an error in the longitudinal TRACULA pipeline that I'm not
sure how to resolve. I saw this error in the message board but there was no
resolution to the problem so I thought I'd ask again. I've successfully run the
recon-all
surfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Longitudinal TRACULA study
Hi,
I want to clarify some aspects longitudinal TRACULA processing before
processing my data.
For example, I have 3 timepoints of data of the same participant:
sub
Hi,
I want to clarify some aspects longitudinal TRACULA processing before
processing my data.
For example, I have 3 timepoints of data of the same participant:
sub101_01
sub101_02
sub101_03
All of these have structural and diffusion data (same scanner, same acquisition
parameters). I processe
ari...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Saturday, July 29, 2017 at 8:31 AM
To: FS maling list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] longitudinal TRACULA
Hi,
I've run cross-sectional TRACULA on
Hi,
I've run cross-sectional TRACULA on one subject, three different
timepoints. Now I'm trying to run a longitudinal analysis on the same
subject's 3 timepoints. My understanding was that for TRACULA, unlike for
morphometry, I don't need to first run cross sectional before longitudinal,
the only
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks again for the help! And congrats on tracula — it's a great tool, and
vard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks again for the help! And congrats on tracula — it's a great tool, and the
online support is really good :)
I do have a follow-up question, if that’s OK. I’m currently running bedpost,
and it gives
se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks so much for your help! Sorry for the delay in replying -- just wanted to
make sure the was problem was indeed solved. Since I'm using a ser
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks so much for your help! Sorry for the delay in replying -- just wanted to
make sure the was problem was indeed solved. Since I'm using a server for which
o: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Barbara - If you're using the 5.3 version, then you'll have to download the
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
This should fix the problem. But if there's a vers
2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks so much for your quick reply. I've only tried version 6.0 to determine
whether the error was possibly version-related, but that doesn’t seem to be the
case… I'm actually wo
edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error
Dear FreeSurfer experts,
I’m running tracula on longitudinal data but I’ve encountered the following
error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see below)
trac-preproc -c /Doc
nt: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error
Dear FreeSurfer experts,
I’m running tracula on longitudinal data but I’ve encountered the following
error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see belo
Dear FreeSurfer experts,
I’m running tracula on longitudinal data but I’ve encountered the following
error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see below)
trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log
/Documents/TRACULA/TEST/S0001.01_T1/scr
harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in
Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process tha
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:
#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#
ington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of "Harms,
Michael"
Reply-To: Freesurfer support list
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer s
iversity School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: on behalf of "Harms,
>Michael"
> Reply-To: Freesurfer support list
> Date: Wednesday, June 29, 2
PM
To: Freesurfer support list
Subject: [Freesurfer] longitudinal tracula
Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves
of a given subject to be included in a single dmrirc file? My initial
thought was “no”, that it would be fine to run one scan wave pe
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula
Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a sing
Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file? My initial thought was “no”, that it would be fine to run one scan wave
per subject per dmrirc file (as long as the “baselist” variable is set
Hi Emad - I believe that it's not finding your freesurfer recons. They
should be under the $SUBJECTS_DIR and have the same names for time points
and longitudinal template as what is under your tracula output directory
(if the latter is different from SUBJECTS_DIR).
Best,
a.y
On Fri, 1 Apr 2
Hi Emad - The error happens at the very beginning, so I'm wondering if
something went wrong in the previous steps, before -path. Can you please
send me the entire trac-all.log of one of your subjects? Thank you!
a.y
On Wed, 30 Mar 2016, Emad Ahmadi wrote:
Hi Anastasia,
I hope you’re enjoy
Hi Anastasia,
I hope you’re enjoying your evening!
I’m doing longitudinal TRACULA analysis on two subjects, each having two time
points. I have already taken the steps of longitudinal recon-all and trac-all
-prep & -bedp.
Now I’m trying to do trac-all -path, but it gives me an error that I can
Hi Francesco - Please attach your dmrirc, and also the tracula log file of
your subject (scripts/trac-all.log). It's hard to guess what went wrong
without looking at the complete output.
Thanks,
a.y
On Thu, 29 Jan 2015, Francesco Siciliano wrote:
Hi,
I have been unsuccessful in getting lon
Hi,
I have been unsuccessful in getting longitudinal tracula to run. I have been
directing my dmrirc file to skip the registration-based B0-inhomogeneity
compensation (by setting it to 0). However, when I try to run trac-all prep, I
get an error message asking to specify a field map for each in
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