Sent: Friday, April 22, 2022 11:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA question
External Email - Use Caution
Hi:
Is it possible to use input diffusion files in MOSAIC IMA Siemens
file format directly? Or is it necessary to convert to nifti file
format
External Email - Use Caution
Hi:
Is it possible to use input diffusion files in MOSAIC IMA Siemens
file format directly? Or is it necessary to convert to nifti file
format first?
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of
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,
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
Subject: [Freesurfer] TRACULA Question
External Email - Use Caution
Dear Anastasia,
I have run trac -all -prep in 2 different conditions:
a) prerequisite recon-all step was done using freesurfer 7.2.0
b) prerequisite recon-all step was done using freesurfer 6
The first time everything ran
External Email - Use Caution
Dear Anastasia,
I have run trac -all -prep in 2 different conditions:
a) prerequisite recon-all step was done using freesurfer 7.2.0
b) prerequisite recon-all step was done using freesurfer 6
The first time everything ran smoothly without an error,
External Email - Use Caution
Dear Freesurfer experts,
I am a beginner in the use of TRACULA. I tried to run the preprocessing
step of the trac-all command and it seems that all have worked fine.
However, at the end of the command TRACULA finished with an error. This is
the final
edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Tuesday, October 15, 2019 10:26:32 AM
> *To:* Freesurfer
> *Subject:* [Freesurfer] Tracula question
>
>
> External Email - Use Caution
>
> Dear Anastasia -
>
> I tried running tracula pre
...@nmr.mgh.harvard.edu
on behalf of Alan Francis
Sent: Tuesday, October 15, 2019 10:26:32 AM
To: Freesurfer
Subject: [Freesurfer] Tracula question
External Email - Use Caution
Dear Anastasia -
I tried running tracula preproc. However, it gave me an error message. Could
you please shed
External Email - Use Caution
Dear Anastasia -
I tried running tracula preproc. However, it gave me an error message.
Could you please shed some light on this?
Thank you,
Alan
[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc
INFO: SUBJECTS_DIR is
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 have
t;
> 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 a
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 with
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
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
External Email - Use Caution
In the visualization step of Tracula processing, freeview -tv
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171),
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show
figueirolo...@mgh.harvard.edu>
Sent: Wednesday, December 6, 2017 5:18:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA question
Hi,
I am trying to run TRACULA and I am having the same error, after reviewing my
directory and the configuration file:
"ERROR: run list is
Hi,
I am trying to run TRACULA and I am having the same error, after reviewing my
directory and the configuration file:
"ERROR: run list is longer than subject list"
The number of inputs is the same number of subjects. I've read some old emails
with similar errors but none of the suggested
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
Hi,
I am currently analyzing DTI data and I am having issues with one file in
particular. When I run the tracheal -path -c step, all of the files are
generated except the pathstats text files.
Any thoughts?
Thanks!
Noa
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Freesurfer mailing list
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:
__
?Hello,
I was wondering what the difference was between the dwi.nii.gz and thd
data.nii.gz files.
I know based on the website description that the dwi.nii.gz file is the DWI
after all corrections have been made but I was unsure about the data.nii.gz
file.
I
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
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 -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107
Too many ('s.
ERROR: must
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
-c
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
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
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:
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
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
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:
Dear Anastasia,
Earlier I was posted an issue about BA44/pars triangular:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html
Because TRACULA also uses the cortical parcellation it may be
important to handle this issue somehow. Is it handled in TRACULA
analysis? Does it
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
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
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
Hi!
I am running tracula for the first time and I am encountering the following
error:
Loading brain mask of output subject from
/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain_mask.flt.nii.gz
niiRead(): error opening file
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
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
Dear TRACULA Developer User,
I am wondering if it is possible to add other DTI measurements to the
pathstats.overall.txt along with those DTI parameters already included
(FA, MD, AD, RD)?
Thank you very much.
Minjie
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Freesurfer mailing list
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
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
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
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 - 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
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
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:
Hello Tracula Developer User,
I found a few subjects have pathstat.overall.txt information but with
blank voxel information in pathstats.byvoxel.txt. For such tracts,
they usually len_min = len_max = len_avg. Anyone know what happened
for the fiber tracking? Is it possible to extract the byvoxel
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't
, 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 while ago.
How
[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 Question, step 2
Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
...@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 Question, step 2
Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get
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
Hi Anastasia,
I am trying to run Tracula for the first time in our lab and
I'm getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I've attached the configuration file I'm using and
the error message is below...
_
Hello Tracula Developers Users,
I can follow how to use the diffusion measures from
pathstats.overall.txt for each subject to run a group
analysis on the tracts.
On the other hand I noticed there is also the
pathstats.byvoxel.txt which contains various
diffusion measures in each voxel along the
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
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
Dear Tracula Users
Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
the config file tutorial (below), are the first X number of volumes in the
4Dnii.gz file or will the Tracula routines know from the bvals file where
the B0 scans are ordered in the file? For example, I
Dear Tracula Users
Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
the config file tutorial (below), are the first X number of volumes in the
4Dnii.gz file or will the Tracula routines know from the bvals file where
the B0 scans are ordered in the file? For example, I
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
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
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