Re: [Freesurfer] Getting combined bvals/bvecs

[Anastasia Yendiki]

Hi Marissa - You have to specify as many b-values and gradient vectors as 
there are volumes in your DWI data file. This means that, if you combine 
the AP and PA volumes, you also have to concatenate the bvals from the two 
into one file, and do the same with the bvecs. Make sure that the order in 
which the AP and PA volumes are combined is the same as the order in which 
the corresponding bvals and bvecs are combined.


Hope this helps,

a.y

On Wed, 14 Sep 2016, Marissa Pifer wrote:


Hello freesurfer experts,
I am trying to run tracula on subjects that have separate AP/PA direction DTI 
files. We combined the data
into one using topup, and would now like to run tracula on the subject. The 
problem is, the combined file
doesn't have a bvals/bvecs file. When I try to use the original bval/bvec 
files, I get the error that the
bvals and bvecs don't match up. I have tried combining the files into one, and 
then running a dicom to
nifty conversion to get a combined bvals/bvecs output, but that results again 
in two separate bvals/bvecs
files as well. I then tried just have two specified bvals and bvecs. This did 
not give us an error
message, but trac-prep took only a few seconds and did not complete the steps 
it was supposed to to create
the directories for trac-bedp to complete. I have attached our dmrirc.example 
file and the log for the
trac-prep step for your reference. 

The questions then are; is there a way to get one bvals/bvecs file that has the 
correct parameters for the
AP and PA combined file. Or, if not, is there a way to run tracula with two 
sets of bvals and bvecs (one
for the AP and one for the PA direction)? 

In case you need this information, the process is being run with freesurfer 
5.3, on a macbook pro OS X
version 10.9.5. 

Thank you in advance, 

Marissa 

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Re: [Freesurfer] Tracula movement

[Anastasia Yendiki]

You're right that this looks fine. Can you upload the entire DWI series 
for me here? Nifti is fine. Thanks!


https://gate.nmr.mgh.harvard.edu/filedrop2/

On Mon, 12 Sep 2016, Lars M. Rimol wrote:



 Re: [Freesurfer] Tracula movement

Anastasia Yendiki Mon, 12 Sep 2016 04:24:56 -0700

Hi Lars - This sounds like the subject was trying to climb out of
the scanner: 3cm average translational motion and 24% of the slices in
the series have drop-out. How do the images look?

a.y


Hi,

I don't have a lot of experience looking at dwi scans, but they don't seem
crazy to me. I have attached screenshots of the dwi, FA, and brain_anat_mni
images, and the gross anatomy looks fine to me. There are stripes in
brain_anat_mni, which I would guess indicate motion..

Thank you!


sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] Tracula movement

[Anastasia Yendiki]

Hi Lars - This sounds like the subject was trying to climb out of the 
scanner: 3cm average translational motion and 24% of the slices in the 
series have drop-out. How do the images look?


a.y

On Mon, 12 Sep 2016, Lars M. Rimol wrote:


HI,
Is there a rule-of-thumb upper level of acceptable head motion? The tutorial
gives these values as examples:

AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
0.489419 0.00398925 0 1
I have a subject with 

AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
30.018
0.209
24
1.6


I plan, of course, to use the index described in Yendiki et al. (2013) but
would such high levels nevertheless be considered disqualifying a priori?  



Thank you!



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Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

[Anastasia Yendiki]

Good to know, thanks for sharing this trick!

On Sat, 3 Sep 2016, Chung, Yoonho wrote:



I found out why it didn't work. One of the script that  bedpostx_postproc.sh
calls is written in python2. I set my default to python3 and therefore
caused the error in the last step. After I loaded python2 environment, i got
the merged files and finished properly. Thanks for your help as always!


Yoon


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Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz

[Anastasia Yendiki]

Hi Yoon - It sounds like FSL's bedpostx postprocessing script 
failed. You can run it like this:


bedpostx_postproc.sh /path/to/your/subject/dmri

This script merges the results from all the slices. It's possible that 
something went wrong with the slices (you ran out disk space for example).

If the slice results are ok, this'll do it.

Best,
a.y

On Fri, 2 Sep 2016, Chung, Yoonho wrote:



Hi Anastasia,


trac-all -prep completed without error.

I thought trac-all -bedp starts and ends without any error but trac-all path
failed with these messages.


Loading BEDPOST parameter samples from */dmri.bedpostX
niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz
 

I looked at the dmri.bedpostX directory and all slices exist in
the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp
phase did not create the 

merged samples in this directory.


I am currently runnning with 

FSL/5.0.6

Program versions:
$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
and freesurfer version 5.3


I looked through the mailing list to see if someone ran into a similar
problem but could not find a good solution. Do you have what may have caused
this? Any other files I would like to look into?


Thank you

Yoon


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Re: [Freesurfer] Tracula Error -preproc Segmentation fault (core dumped)

[Anastasia Yendiki]

Hi Kristina - I suspect there's some misregistration, or part of the brain 
mask (and hence the anatomical segmentation) missing or something like 
that. Do you mind uploading the tracula directories of this subject for me 
to take a look at?


https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks!

a.y

On Thu, 1 Sep 2016, Kristina Jelinkova wrote:



Hello everyone,


I've been using Tracula for a while now with much success (and help from the
archive) but I've run into an error I haven't been able to solve. I have
several subjects for which trac-all -preproc ends with Segmentation fault
(core dumped) 


I don't think it's a mistake with my directories, they appear correct and
I've ran numerous subjects successfully like this already. The dti data and
aparc+aseg also appear normal. I'm attaching the trac-all log and error log
from one of these problematic subjects. Any insight would be greatly
appreciate!


Thank you, 


Kristina Jelinkova


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Re: [Freesurfer] About TRACULA results

[Anastasia Yendiki]

Hi there - If you upload the tracula directories for me, I'm happy to try 
to figure out what's going on. Although honestly at this point it's worth 
waiting for the new version.


Thanks!

a.y


On Tue, 30 Aug 2016, Kang, XJ wrote:


Hi,

I am trying to computer the changes of cortical parcellations and fiber
pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied
the anatomical and DWI images from the same scan session into five
directories. Run recon-all and trac-all on the 5 same data sets, in order to
check the reproducibility of the analysis. 

Here are what I got: the Desikan-Killiany parcellations in both GM and WM,
and the subcortical structures, repeat well. No difference found in volume
or size of those structures. However, the volume and averaged DTI parameters
of the fiber pathways, which found in the file
~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5
sets.   tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example.

The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For
example, the changes of averaged FA  between the 5 data sets are :
  

?? ?  S1-S0, S2-S0, S3-S0, S4-S0

Corpus Callosum - Forceps Major                  ,  
-1.1   ,    6.0   ,    0.5   ,    1.3   ,
Corpus Callosum - Forceps Minor                 
,    0.1   ,    0.0   ,   -1.6   ,    0.0   ,
Right Anterior Thalamic Radiations                   
,    0.1   ,   -1.0   ,    0.5   ,    0.9   ,
Right Cingulum - Angular Bundle                   
,   -4.8   ,   -2.0   ,   -1.5   ,    3.8   ,
Right Cingulum - Cingulate Gyrus Endings    ,   
0.5   ,   -0.9   ,    0.4   ,   -2.3   ,
Right Corticospinal
Tract    ,    1.9  
,    0.6   ,   -2.2   ,    1.4   ,
Right Inferior Longitudinal Fasciculus
,   -2.2   ,   -0.8   ,   -1.3   ,    3.0   ,
Right Superior Longitudinal Fasciculus - Parietal Endings ,    0.8   ,  
-0.4   ,   -1.2   ,    0.2   ,
Right Superior Longitudinal Fasciculus - Temporal Endings ,   -4.9   ,  
-0.6   ,   -2.6   ,   -1.3   ,
Right Uncinate
Fasciculus  ,   
0.5   ,    1.6   ,   -0.9   ,    3.5   ,


Even larger changes for the volume of the pathways:
  

?? ?   S1-S0, S2-S0, S3-S0, S4-S0

Corpus Callosum - Forceps Major   
,    2.2   ,  -33.7   ,  -12.3   ,    1.1   ,
Corpus Callosum - Forceps Minor   
,   11.9   ,    4.8   ,    0.6   ,    7.2   ,
Right Anterior Thalamic Radiations     
,   -8.9   ,    2.2   ,  -12.5   ,    7.5   ,
Right Cingulum - Angular Bundle   
   ,  -38.1   ,   41.6   ,   34.8   ,    8.6   ,
Right Cingulum - Cingulate Gyrus Endings  ,  
24.4   ,   33.1   ,   21.3   ,   17.5   ,
Right Corticospinal
Tract  ,   
9.8   ,   -3.0   ,    2.2   ,   19.5   ,
Right Inferior Longitudinal Fasciculus 
,    7.2   ,   24.1   ,   -7.3   ,   23.8   ,
Right Superior Longitudinal Fasciculus - Parietal Endings  ,   17.2   ,  
10.2   ,   25.1   ,    9.9   ,
Right Superior Longitudinal Fasciculus - Temporal Endings ,   15.4   ,   
3.4   ,   -3.1   ,  -11.5   ,
Right Uncinate Fasciculus                       
            ,   13.3   ,   -1.2   ,   16.4   ,   -3.4   ,

Any expert has the experience on these? Thank you for your help.

XJ Kang


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[Freesurfer] Satellite Symposia - Resting-State and Brain Connectivity Conference

[Anastasia Yendiki]

Dear FreeSurfers - If you're attending the Resting-State and Brain 
Connectivity Conference in Vienna, you can now register for satellite 
symposia, including one on diffusion MRI.


Hope to see you there!

a.y

--

We are pleased to inform you that registration for the six Satellite 
Symposia at the Resting-State and Brain Connectivity Conference is open!


These specialised meetings will take place on Saturday, September 24th right 
after the Resting-State and Brain Connectivity Conference. So why not extend 
your stay in Vienna for the sake of maximizing knowledge gain, deepening the 
vivid scientific exchange and socializing with your community members?


The Satellite Symposia will will cover diffusion MRI, optogenetics, PET/MRI, 
TMS/fMRI and predictive analyses of neuroimaging data. 


We made sure to provide a large selection of topics for our six Satellite 
Symposia, so that everyone gets to choose the most interesting on their behalf:

 *  Symposium #1: Probing white-matter anatomy and microstructure with
diffusion MRI
 *  Symposium #2: Tackling connectivity using non-invasive brain
stimulation (fMRI/TMS, tDCS, tACS)
 *  Symposium #3: The Emerging Field of Predictive Analytics in
Neuroimaging: Applications, Challenges and Perspectives
 *  Symposium #4: Multi-modal fMRI from photons to protons
 *  Symposium #5: Dynamic Functional Connectivity
 *  Symposium #6: Network-Based Approaches for Neuroimaging: Graph
Theory Techniques for Brain Connectivity Research

http://www.restingstate.com/2016/satellite-symposia/

So don’t hesitate to register for a satellite symposium now!

We look forward to welcoming you to Vienna in September 2016!

On behalf of the local and international organizing committees

Christian Windischberger
Claus Lamm
Rupert Lanzenberger
Bharat Biswal
Mark Lowe
Christopher Pawela
Martin Walter
Susan Whitfield-Gabrieli___
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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Anastasia Yendiki]

No need to rerun anything. It's an issue with the format of those mean 
path files. Just view them in the standard 5.3 version of freeview for 
now.


On Fri, 26 Aug 2016, Elijah Mak wrote:


Hi Anastasia,

Yes indeed. I am using a dev version of freeview. I could give it another go 
with the freeview that came
with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on 
a v5.3? 

Thanks!

Best Wishes,
Elijah



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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Anastasia Yendiki]

Hi Elijah - Glad to hear that things worked out! Are you by any chance 
using the dev version of freeview?


a.y

On Fri, 26 Aug 2016, Elijah Mak wrote:


Hi Anastasia and others,
I am trying to visualise the *.path.mean.txt on MNI template after running 
trac-all -stat. I used this
command:

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
stats/*.path.mean.txt
However, it looks like something has gone wrong with the labelling and position 
of the tracts (note the
CST highlighted in green).

https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2014.41.37.png?dl=0

Everything was fine and correctly labelled when I checked the merged tracks.

Thanks again for your help!


Best Wishes,
Elijah

P.S. On another note, the reinit=1 trick works very well and I was able to 
reconstruct the tracts in
almost all cases. Thanks!




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Re: [Freesurfer] wmparc parcellation for thalamus and brainstem

[Anastasia Yendiki]

Hi Vasudev - These regions are part of the subcortical segmentation (aseg) 
volume:


http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

a.y

On Thu, 25 Aug 2016, Dev vasu wrote:


 
Dear all,


After running through  recon-all ,I have obtained wmparc parcellation file
(see the attached figure ). I would like to obtain parcellation at specific
regions of interest for my study i.e  Brain stem region and Thalamus region,
could you please let me know how i could perform parcellation for these two
specific regions of interest ( i.e. Brain stem and Thalamus ).


Thanks
Vasudev


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Re: [Freesurfer] dmri_poistats

[Anastasia Yendiki]

Hi Mohamad - This tool hasn't been worked on for over a decade, and there 
is nobody here who can support it. There are tools out there that do 
tractography without anatomical priors (in fact that's approximately all 
the tools out there), but none in freesurfer at the moment.


Best,
a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:


Hi Anastasia,
This tool is available in (FS 5.3 and FS v6.0) as version 1.0 Beta. But in the 
paper that I have pointed to, the folks used the version 1.4 of this tool. 
That's why I am a bit confused.

Kindly, are there any tools that can help to do tractography for the 
corticospinal tract  when T1 images are not available?


Thank you for any advice
Mohamad



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Wednesday, August 24, 2016 10:36 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] dmri_poistats


Hi Mohamad - This tool is *way* deprecated. It should not have been included in 
beta releases. Thanks for bringing this to our attention.

a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:



Dear Freesurfer experts,

I would like to inquire about the tool “dmri_poistats”
https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is 
included as a beta release ( in FS5.3 and FS 6.0).

 

In literature review I found colleagues used the version 1.4  of this
tool. e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/

 

Kindly, I have the following two questions:

1.   What is the final release of this tool?

2.   I have DWI images and no T1 images are available. Is it reliable to do 
tractography for the corticospinal tract using this tool?

 

Thank you for any advice!

Mohamad

 





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Re: [Freesurfer] dmri_poistats

[Anastasia Yendiki]

Hi Mohamad - This tool is *way* deprecated. It should not have been 
included in beta releases. Thanks for bringing this to our attention.


a.y

On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:



Dear Freesurfer experts,

I would like to inquire about the tool “dmri_poistats” 
https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is 
included
as a beta release ( in FS5.3 and FS 6.0).

 

In literature review I found colleagues used the version 1.4  of this tool. 
e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/

 

Kindly, I have the following two questions:

1.   What is the final release of this tool?

2.   I have DWI images and no T1 images are available. Is it reliable to do 
tractography for the corticospinal tract using this tool?

 

Thank you for any advice!

Mohamad

 


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Re: [Freesurfer] TRACULA: narrow probability distributions

[Anastasia Yendiki]

Yes, it shouldn't hurt.

On Tue, 23 Aug 2016, Harms, Michael wrote:



Ok.  We’ll give it a try.  Just to confirm, you're agreeing that
increasing nburnin and nsample is a “good” thing, right?  (e.g., 1000, and
15000, respectively?)  If anything, we should be less likely to get narrow
tracts when using larger nburnin/nsample values, right?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/23/16, 5:09 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Michael - Even if it starts very close to the true max of the
distribution, in practice it'll never stay put. MCMC will accept a new
sample path with probability 1 if the new sample has greater probability
than the previous sample, and it will also accept it with some very small
probability if it doesn't. This means that it'll still explore the space
around the max, even if it ends up returning to the max pretty quickly. So
most likely there's something weird about the initial path if it doesn't
move at all.

Best,

a.y

On Tue, 23 Aug 2016, Harms, Michael wrote:



Hi Anastasia,
My interpretation of the “reinit” parameter is that it is for situations
where a narrow probability distribution is assumed to be incorrect.  But
how do you know whether it is indeed incorrect, or whether in fact the
true equilibrium distribution is (correctly) very narrow?

In particular, my understanding of MCMC is that higher burn-in, and more
sampling iterations are only a “good” thing.  i.e., If we have the time
and compute resources, we shouldn’t hesitate to increase them from their
defaults, to help to make sure we are capturing the true equilibrium
distribution.  So, if increasing the nburnin and nsample values makes it
more likely to find spatially narrow tract distributions, isn’t that a
sign that the true distribution should indeed be narrow?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Dillan - There's a work-around for this, see the reinit variable at
the
bottom of the sample config file:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

I'm hoping to make this happen automatically soon!

Best,

a.y

On Tue, 23 Aug 2016, Newbold, Dillan wrote:


Dear Anastasia,

I’ve been looking at a lot of Tracula path.pd files and I’ve found that
some probability distributions are only a single voxel wide, similar to
the path.map file. The few none-zero voxels in these path.pd files have
very high probability values. When an isosurface is generated for these
tracts, it looks like a short thin blob somewhere in the usual tract
distribution. I’ve seen descriptions in the archives of similar “short
thin tracts,” but, from what I have seen, no one has offered a
satisfying
explanation for why these occur.

What I think is happening in these tracts is that a maximum-probability
(or local maximum) path is found during a burn-in iteration and all
following perturbations of that path are rejected. Since the probability
value in the path.pd is equal to the number of sample paths intersecting
that voxel, finding a local maximum early on results in a small number
of
very high-probability voxels. Consistent with this explanation, I’ve
found that this issue occurs more frequently when nburnin is set to 1000
(default = 200). A similar issue can occur if a local maximum is found
early during the sample iterations, and this results in a path.pd file
containing a small number of voxels with very high values surrounded by
a
larger area of low-value voxels. When a 20% threshold is applied, the
result is the same as when a local maximum occurs during a burn-in
iteration.

Does my understanding of this issue seem correct?

None of this would be a problem if my only aim were to find the single
path with the maximum a posteriori probability, but I’m concerned that
the average and weighted_average sats for these tracts will be less
accurate. Since these distributions include small fractions of the
number
of voxels included in most tract distributions, is it likely that the
average and weighted_average stats from these narrow distributions are
less representative of the whole tract and more subject to random noise?

Given these concerns, what

Re: [Freesurfer] TRACULA: narrow probability distributions

[Anastasia Yendiki]

Hi Michael - Even if it starts very close to the true max of the 
distribution, in practice it'll never stay put. MCMC will accept a new 
sample path with probability 1 if the new sample has greater probability 
than the previous sample, and it will also accept it with some very small 
probability if it doesn't. This means that it'll still explore the space 
around the max, even if it ends up returning to the max pretty quickly. So 
most likely there's something weird about the initial path if it doesn't 
move at all.


Best,

a.y

On Tue, 23 Aug 2016, Harms, Michael wrote:



Hi Anastasia,
My interpretation of the “reinit” parameter is that it is for situations
where a narrow probability distribution is assumed to be incorrect.  But
how do you know whether it is indeed incorrect, or whether in fact the
true equilibrium distribution is (correctly) very narrow?

In particular, my understanding of MCMC is that higher burn-in, and more
sampling iterations are only a “good” thing.  i.e., If we have the time
and compute resources, we shouldn’t hesitate to increase them from their
defaults, to help to make sure we are capturing the true equilibrium
distribution.  So, if increasing the nburnin and nsample values makes it
more likely to find spatially narrow tract distributions, isn’t that a
sign that the true distribution should indeed be narrow?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Dillan - There's a work-around for this, see the reinit variable at the
bottom of the sample config file:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

I'm hoping to make this happen automatically soon!

Best,

a.y

On Tue, 23 Aug 2016, Newbold, Dillan wrote:


Dear Anastasia,

I’ve been looking at a lot of Tracula path.pd files and I’ve found that
some probability distributions are only a single voxel wide, similar to
the path.map file. The few none-zero voxels in these path.pd files have
very high probability values. When an isosurface is generated for these
tracts, it looks like a short thin blob somewhere in the usual tract
distribution. I’ve seen descriptions in the archives of similar “short
thin tracts,” but, from what I have seen, no one has offered a satisfying
explanation for why these occur.

What I think is happening in these tracts is that a maximum-probability
(or local maximum) path is found during a burn-in iteration and all
following perturbations of that path are rejected. Since the probability
value in the path.pd is equal to the number of sample paths intersecting
that voxel, finding a local maximum early on results in a small number of
very high-probability voxels. Consistent with this explanation, I’ve
found that this issue occurs more frequently when nburnin is set to 1000
(default = 200). A similar issue can occur if a local maximum is found
early during the sample iterations, and this results in a path.pd file
containing a small number of voxels with very high values surrounded by a
larger area of low-value voxels. When a 20% threshold is applied, the
result is the same as when a local maximum occurs during a burn-in
iteration.

Does my understanding of this issue seem correct?

None of this would be a problem if my only aim were to find the single
path with the maximum a posteriori probability, but I’m concerned that
the average and weighted_average sats for these tracts will be less
accurate. Since these distributions include small fractions of the number
of voxels included in most tract distributions, is it likely that the
average and weighted_average stats from these narrow distributions are
less representative of the whole tract and more subject to random noise?

Given these concerns, what type of overall path statistics do you think
is most descriptive of a tract? Also, do you feel that higher nburnin and
nsample values should lead to superior results? I would have thought this
to be the case, but now it seems to me that setting either of these
values too high will result in narrow probability distributions and bad
statistics.

Thank you,
Dillan

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Re: [Freesurfer] TRACULA: narrow probability distributions

[Anastasia Yendiki]

Hi Dillan - There's a work-around for this, see the reinit variable at the 
bottom of the sample config file:

http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

I'm hoping to make this happen automatically soon!

Best,

a.y

On Tue, 23 Aug 2016, Newbold, Dillan wrote:


Dear Anastasia,

I’ve been looking at a lot of Tracula path.pd files and I’ve found that some 
probability distributions are only a single voxel wide, similar to the path.map 
file. The few none-zero voxels in these path.pd files have very high 
probability values. When an isosurface is generated for these tracts, it looks 
like a short thin blob somewhere in the usual tract distribution. I’ve seen 
descriptions in the archives of similar “short thin tracts,” but, from what I 
have seen, no one has offered a satisfying explanation for why these occur.

What I think is happening in these tracts is that a maximum-probability (or 
local maximum) path is found during a burn-in iteration and all following 
perturbations of that path are rejected. Since the probability value in the 
path.pd is equal to the number of sample paths intersecting that voxel, finding 
a local maximum early on results in a small number of very high-probability 
voxels. Consistent with this explanation, I’ve found that this issue occurs 
more frequently when nburnin is set to 1000 (default = 200). A similar issue 
can occur if a local maximum is found early during the sample iterations, and 
this results in a path.pd file containing a small number of voxels with very 
high values surrounded by a larger area of low-value voxels. When a 20% 
threshold is applied, the result is the same as when a local maximum occurs 
during a burn-in iteration.

Does my understanding of this issue seem correct?

None of this would be a problem if my only aim were to find the single path 
with the maximum a posteriori probability, but I’m concerned that the average 
and weighted_average sats for these tracts will be less accurate. Since these 
distributions include small fractions of the number of voxels included in most 
tract distributions, is it likely that the average and weighted_average stats 
from these narrow distributions are less representative of the whole tract and 
more subject to random noise?

Given these concerns, what type of overall path statistics do you think is most 
descriptive of a tract? Also, do you feel that higher nburnin and nsample 
values should lead to superior results? I would have thought this to be the 
case, but now it seems to me that setting either of these values too high will 
result in narrow probability distributions and bad statistics.

Thank you,
Dillan

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Re: [Freesurfer] Tracula ROI analysis CVS vs MNI reg

[Anastasia Yendiki]

Hi Yoon - The wmparc and aseg ROIs are in the subject's native T1 space, 
so you don't need to register across subjects to get ROI-based diffusion 
measures. You just need to register between the subject's own T1 and DWIs 
- the recommended method for that is bbregister. You can find more in the 
multimodal tutorial on the freesurfer wiki.

Best,
a.y

On Tue, 23 Aug 2016, Chung, Yoonho wrote:

> 
> Hi Anastasia,
> 
> 
> Is there a preferable method between CVS vs MNI registration when extracting 
> diffusion mesures from ROIs (white matter, ASEG etc)?
> 
> 
> Best,
> 
> Yoon
> 
> 
> 
>
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - Does the directory in the error message exist?

a.y

On Fri, 19 Aug 2016, Elijah Mak wrote:


Hi Anastasia,
The error message occurs for other control points too, but it does not kill the 
-prior stage. 

I have attached the full trac-all.log file.

This error message is also found in other subjects where I am struggling to get 
a good initialisation.

The ERROR: fio_pushd:subject/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri

Thank you!

Best Wishes,
Elijah
--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - This error occurs with one number of control points but not 
another? That would be very strange. I'd have to look at the full 
trac-al.log to figure it out, I can't guess what's going on just from this 
one line unfortunately.


a.y

On Fri, 19 Aug 2016, Elijah Mak wrote:


Hi Anastasia,
Thanks, it works, but only for MNI reg option. For the CVS stream, there was an 
error message during
-prior. 

ERROR: fio_pushd: 
/Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri

This error message did not halt the process though. Could this be a clue?

Thanks for your patience :)

Best Wishes,

Elijah





--

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Mmm, it sounds like the shape of the tract is too convoluted for it to 
find a good fit. I'd try increasing the # of control points.


On Fri, 19 Aug 2016, Elijah Mak wrote:


Hi Anastasia,
Thank you for looking into that subject. I have tried reinitiliasation a few 
times and in all cases, it
just could not find a satisfactory control point fit during the -prior stage. 
Therefore, the -prior
stage has been running for more than 10 hours now. This occurs in other a small 
number of other subjects
as well. 

WARN: Could not find satisfactory control point fit - try 596

How can I resolve this? And what type of problem could be reflected by  this? 
Bad aparc+aseg.mgz /
registration to template? 

If all else fails, I will exclude subjects using the criteria that you set in 
the Neuroimage paper:
where a subject was excluded if there were failures of reconstruction in 2 or 
more WM tracts. 

Thank you for your help!

Best Wishes,
Elijah




--

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Anastasia Yendiki]

Hi Taha - Once you've mapped from the volume onto the white surface, you 
should be able to display it on the inflated surface, and also to get 
thickness statistics (thickness is just the distance between corresponding 
points on the white and pial surface). You don't need to do anything to 
map from white to inflated within an individual.


Best,
a.y

On Fri, 19 Aug 2016, Taha Abdullah wrote:


Excellent! Thank you for the quick advice, I tried this initially but I was
using the wrong xfm format.
Since I have the FA map in subject ?h.white space, I have done the same with the
tract endings too. I am having some difficulties conceptually, in terms of
projecting the end points onto either the subject specfic or fsaverage inflated
surface. I assumed using mri_surf2surf would be sufficient to transform the
endpts from subject surface ?h.white space to the inflated surface, but it is a
scalar data file. Once the endpts are projected onto the inflated surface it
seems straightforward to extract the thickness values for further analysis.
Essentially replicating the attached image from Sølsnesa 2015.  If you have any
suggestions that would be much appreciated. Thank you very much!

Best,
Taha



On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Taha - Trying getting a .dat registration file from bbregister
  and using that as the input to mri_vol2surf. There's a multimodal
  tutorial on the freesurfer wiki that might be of help.

  Best,
  a.y

  On Thu, 18 Aug 2016, Taha Abdullah wrote:

Hello All,

I am trying to project FA map (dtifit_FA.nii.gz) and the
endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface
space.
I was following instructions on
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html,
under FreeSurfer
Registration, to create the various xfms files. 

Next, I registered the FA map to subject conformed space
using flirt 
 *  flirt -in dtifit_FA.nii.gz -ref
../../mri/orig.nii.gz -applyxfm -init
./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA
map onto fsaverage surface with the following command. 
 *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1
--cortex --hemi rh --trgsubject fsaverage --regheader
taha_brain
    --reg ./xfms_taha/fa2freesurfer.mat --o
FA_2fsavg_surf.mgh
Upon viewing in freeview the fsavg rh.white surface and
fa2FS.nii.gz (FA map in FreeSurfer space) did not allign
properly. I have tried some variations wtihout any luck.
I used the following command line for freeview.  
 *  freeview 
-f/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m
gh -v fa2FS.nii.gz
 *  Attached are some pics of the FA confomred map and
fsaverage.rh.white surface
Do I need a xfm file for taliarch allignment? Any advice
or insight would be greatly appreciated.

Thanks in advance,
Taha 

Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using
/usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz
as target reference.
Loading label
/usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface
/usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration 
 
/usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration 
 
 /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target has

Re: [Freesurfer] red and blue gradient color map for freeview

[Anastasia Yendiki]

Hi Eun Young - Not sure if anyone has a more elegant solution but it 
sounds like you could split your positive and negative activations into 2 
volumes and use the 2 different colormaps for them.

Best,
a.y

On Thu, 18 Aug 2016, Eun Young Choi wrote:

> Hi all,
> 
> I'd like to have a freeview color map that has both a red-yellow gradient and 
> a blue-light blue gradient (the typical
> colors for positive and negative fcMRI correlations) and ideally no color for 
> 0... None of the standard color maps in
> freeview work well and I can't seem to find one online. Has anyone created 
> one? Or know where I can view the text file
> for the standard color maps that come with freeview, so I can create one 
> myself?
> 
> Thank you!
> Eun Young
> 
>
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Re: [Freesurfer] Projecting FA map onto fsaverge surface

[Anastasia Yendiki]

Hi Taha - Trying getting a .dat registration file from bbregister and 
using that as the input to mri_vol2surf. There's a multimodal tutorial on 
the freesurfer wiki that might be of help.


Best,
a.y

On Thu, 18 Aug 2016, Taha Abdullah wrote:


Hello All,

I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz 
from TRACULA onto fsaverage surface space.
I was following instructions on 
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under 
FreeSurfer
Registration, to create the various xfms files. 

Next, I registered the FA map to subject conformed space using flirt 
 *  flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init 
./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA map onto fsaverage 
surface with the following command. 
 *  mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh 
--trgsubject fsaverage --regheader taha_brain
--reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh
Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in 
FreeSurfer space) did not allign
properly. I have tried some variations wtihout any luck. I used the following 
command line for freeview.  
 *  freeview -f 
/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh
 -v fa2FS.nii.gz
 *  Attached are some pics of the FA confomred map and fsaverage.rh.white 
surface
Do I need a xfm file for taliarch allignment? Any advice or insight would be 
greatly appreciated.

Thanks in advance,
Taha 

Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target 
reference.
Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration 
  /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration 
   /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (143161)
Reverse Loop had 26084 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 107182, nSrcLost =     0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979
nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882
Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to FA_2fsavg_surf.mgh
Dim: 163842 1 1


--
Taha Abdullah 
Department of Physiology
Northwestern University Feinberg School of Medicine 
Masters of Science Physiology and Biophysics, Georgetown University 2015
Work: (312)-503-0413

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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - You add "set reinit =1" to the config file, (and remember to 
set the pathlist and subjlist to only what you want to rerun), and then 
rerun the -prior and -path steps in that order.


Best,
a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:


Thanks for the tips on reinitialisation of tracts.

Apologies if I might have missed it in the online tutorial, do you have some
general guidelines for reinitialising?

Can I simply add "set reinit =1" to my configuration file, and then re-run
trac-all -path. Are there any other parameters I could tweak?

After running through more QC on other subjects, I have also noticed other
tracts that were not fully constructed. These tracts appear to be truncated
or blob-like, for a lack of better word :) I have attached the screenshot to
illustrate what I mean.

In these cases, I do the following QC routine after the general recon-all QC

1) freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz 
2) freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz
subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz 


Thanks a lot for your help, Anatasia!

Best Wishes,
Elijah


--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Anastasia Yendiki]

Hi Elijah - It looks like the CVS case needs to be reinitialized. In 
principle you're right that if the registration is good this shouldn't be 
a problem. It's hard to tell what might've caused this in an individual 
case without looking at the data. If you want me to look into it you can 
upload all the TRACULA directories of the subject for me here:

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks!

a.y

On Thu, 18 Aug 2016, Elijah Mak wrote:


Dear Anastasia and List,
I have been using TRACULA to process my DTI dataset using both the affine
MNI and non-linear CVS options.
In one subject, the forceps major (MNI) look very different from its CVS
counterpart (screenshot attached). I am just wondering what could lead to
this type of differences? I've checked the registrations and they look good
(overlaying FA on MNI/CVS).

Thanks!

Best Wishes,
Elijah


--

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ



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[Freesurfer] opening at the University of Sydney

[Anastasia Yendiki]

-- Forwarded message --
Date: Tue, 16 Aug 2016 22:55:47 +
From: Sasha Klistorner 

Research Fellow - Neuroimaging
Save Sight Institute and Brain and Mind Centre
Sydney Medical School
Reference no. 1332/0816

·   Join a collaborative and supportive research team
·   Bring your expertise in neuroimaging to this important research in 
multiple sclerosis
·   Full-time fixed term for one year, remuneration package: base salary 
$99K-$117K p.a., leave loading and up to 17% superannuation

The University of Sydney is Australia's first university and has an outstanding 
global reputation for academic and research excellence. It employs over 7600 
permanent staff, supporting over 60,000 students.

Save Sight Institute leads research into eye diseases and conditions, 
throughout Australia and internationally.
Our renowned team of laboratory and clinical researchers are at the forefront 
of ophthalmic breakthroughs, and our findings have already saved the sight of 
many people living with eye disease since the institute was formed in 1985.
The Brain and Mind Centre’s multidisciplinary research aims to set new 
standards in brain and mind sciences both in Australia and internationally, is 
dedicated to finding solutions that will lead to generational change. Our 
approach is based on the active collaboration of researchers from basic through 
to translational and clinical brain and mind sciences, students, patients and 
front-line carers.
We are seeking to appoint a Research Fellow to work under the combined 
supervision of Associate Professor Alexander (Sasha) Klistorner at the Save 
Sight Institute and Associate Professor Michael Barnett at the Brain and Mind 
Centre.  These world-class researchers are interested in the development of 
neuroimaging biomarkers of demyelination and axonal loss and the study of the 
mechanisms of axonal degeneration in multiple sclerosis using the visual system 
as a model. You will have the opportunity to actively participate in research 
in this area.
In this role you will:

* work closely with clinical, scientific, imaging and other relevant university 
staff at the Save Sight Institute and the Brain and Mind Centre, and the Sydney 
Neuroimaging Analysis Centre to develop and/or refine magnetic resonance 
imaging protocols and analysis pipelines relevant to the project
* be required to develop and implement a tool for the longitudinal analysis of 
diffusion tensor imaging (DTI) alterations in multiple sclerosis patients
* provide expertise across aspects of magnetic resonance imaging acquisition, 
protocol design and writing, analysis and interpretation of data relevant to 
the project; and contribute to writing peer-reviewed manuscripts
* take responsibility for the supervision of research assistants / image 
analysts working on the project or related projects where relevant

·   undertake administration relating to your own university activities.
You may also have the opportunity to work on other related team projects and to 
supervise postgraduate research students or projects and be involved in 
research training.
To succeed in securing this role you will have:
·   a PhD in neuroimaging or a related discipline
·   knowledge of MRI analytics, physics, mathematical and computational 
modelling
·   strong experience in MRI image processing and analysis
·   solid experience in basic neuroimaging toolboxes such as FSL, 
FreeSurfer or similar analytical packages
·   experience in Diffusion MR data analysis
·   demonstrated experience writing complex analytical reports and papers
·   ability to work both independently and as part of a multidisciplinary 
team
·   programming skills in bash-scripting, Matlab and/or Python
·   sound organisational skills and ability to effectively manage competing 
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Re: [Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

[Anastasia Yendiki]

Hi Yoon - Please see "FA ROI analysis" in the diffusion tutorial on the 
freesurfer wiki:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion_DtiIntegration#FAROIAnalysis

Best,

a.y

On Mon, 15 Aug 2016, Chung, Yoonho wrote:



Hi Anastasia,


Is it possible to extract diffusion measures FA, ADC etc. within
the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If
possible, can you show how it can be done? Thank you in advance.


Best,

Yoon


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Re: [Freesurfer] FreeSurfer TrackVis Transforms

[Anastasia Yendiki]

Hi - Check out the dmri_trk2trk command. In your case, you'd need to pass 
it a transformation file from the registration between your diffusion and 
structural data, which you can compute with bbregister.


Best,

a.y

On Mon, 15 Aug 2016, "김재명" wrote:



Dear expert.


Hi. I'm a newbie using Freesurfer software, and I want to transform the data
of .trk file which is from Trackvis tool.
(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms)


As there is an information for transforming trk file into the space of
Freesurfer surface, I read it several times but I couldn't implement it on
Linux console. 


The problem is that I cannot understand how to 'load the trk data from a
file' to use the header data such as voxel_size.


I also read TrackVis file format
(at http://trackvis.org/docs/?subsect=fileformat), and read other mails sent
from others, but couldn't solve the problem.


Could you give me a specific steps to solve this?



Many thanks

Jack.


[IMAGE]
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Re: [Freesurfer] How to run part of TRACULA

[Anastasia Yendiki]

Hi Nasia - They both have preprocessing steps because recon-all runs on 
the T1 and trac-all runs on the DWIs, so they preprocess different images.


You cannot skip any of the steps in recon-all and still get a 
segmentation. The point of the autorecon schemes is mostly to repeat only 
one part of the processing if you change something in between, not to skip 
part of the processing entirely.


Best,

a.y

On Sun, 14 Aug 2016, Athanasia Metoki wrote:


Dear Anastasia,

Thank you so much for responding so fast!
I see what you're saying and thank you for your input.

I have one more question if you don't mind taking a moment to respond. I
noticed that both trac-all and recon-all include some preprocessing steps
(eg. motion correction, eddy current correction, skull stripping). How come
and they both have these steps if one is supposed to run both commands? My
understandind is, if someone wants to run TRACULA from scratch, they would
need to run both recon-all (first) and trac-all (second). One would have to
run recon-all in order to get the cortical parcellation and subcortical
segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all in
the mask creation step.

In my case where I have some preprocessed data, is there a particular
-autorecon# command which only does some of the recon steps that would help
me get the cortical parcellation and subcortical segmentation
(mri/aparc+aseg.mgz) file that I am missing?

I understand I may be asking a lot! Once more thank you very much for your
initial response and your time!

Best,
Nasia Metoki


On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Athanasia - TRACULA expects certains files named a certain
  way to be
  there at the end of each preprocessing step. These are described
  here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfile
  s

  If you are using pre-existing files, you have to make sure that
  they
  follow the same file/directory naming convention.

  You just run recon-all with the default settings. The aparc+aseg
  is
  created in one of the last steps of recon-all, so all the
  previous steps
  have to run as well.

  Hope this helps!

  a.y

  On Sat, 13 Aug 2016, Athanasia Metoki wrote:

  > Dear Freesurfer Developers,
  >
  > I am fairly new to image analysis and this is the first time I
  use
  > Freesurfer.
  >
  > I have some DTI data and I have already preprocessed them and
  ran bedpostX
  > using FSL. I ran probabilistic tractography on FSL as well to
  get the
  > connectivity between two distinct brain areas.
  >
  > I am also interested in getting the probability distribution
  for the
  > uncinate fasciculi so I am trying to use TRACULA.
  > My question is: Can I use TRCULA without doing preprocessing
  and dedpostX
  > again? If so, will I need to do the cortical parcelation and
  subcortical
  > segmentation with recon-all and get the aparc+aseg.mgz file in
  order to use
  > TRACULA? Which argument would I need to use when I run
  recon-all?
  >
  > Thank you!
  >
  > Athanasia Metoki
  > Psychology Doctoral Student - Brain and Cognitive Sciences
  Program
  > Cognitive Neuroscience Laboratory
  > Temple University
  > Department of Psychology
  > 1701 N 13th St.
  > Philadelphia, PA 19122
  > Email: athanasia.met...@temple.edu
  >
  
>___

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  > for the addressee(s) and may contain confidential and/or
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Re: [Freesurfer] How to run part of TRACULA

[Anastasia Yendiki]

Hi Athanasia - TRACULA expects certains files named a certain way to be 
there at the end of each preprocessing step. These are described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles

If you are using pre-existing files, you have to make sure that they 
follow the same file/directory naming convention.

You just run recon-all with the default settings. The aparc+aseg is 
created in one of the last steps of recon-all, so all the previous steps 
have to run as well.

Hope this helps!

a.y

On Sat, 13 Aug 2016, Athanasia Metoki wrote:

> Dear Freesurfer Developers,
> 
> I am fairly new to image analysis and this is the first time I use
> Freesurfer.
> 
> I have some DTI data and I have already preprocessed them and ran bedpostX
> using FSL. I ran probabilistic tractography on FSL as well to get the
> connectivity between two distinct brain areas.
> 
> I am also interested in getting the probability distribution for the
> uncinate fasciculi so I am trying to use TRACULA.
> My question is: Can I use TRCULA without doing preprocessing and dedpostX
> again? If so, will I need to do the cortical parcelation and subcortical
> segmentation with recon-all and get the aparc+aseg.mgz file in order to use
> TRACULA? Which argument would I need to use when I run recon-all?
> 
> Thank you!
> 
> Athanasia Metoki
> Psychology Doctoral Student - Brain and Cognitive Sciences Program
> Cognitive Neuroscience Laboratory
> Temple University
> Department of Psychology
> 1701 N 13th St.
> Philadelphia, PA 19122
> Email: athanasia.met...@temple.edu
> 
> ___
> 
> The contents of this email message and any attachments are intended solely
> for the addressee(s) and may contain confidential and/or privileged
> information and may be legally protected from disclosure. If you are not the
> intended recipient of this message or their agent, or if this message has
> been addressed to you in error, please immediately alert the sender by reply
> email and then delete this message and any attachments. If you are not the
> intended recipient, you are hereby notified that any use, dissemination,
> copying, or storage of this message or its attachments is strictly
> prohibited.
> 
>
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Re: [Freesurfer] FW: TRACULA re-init error

[Anastasia Yendiki]

Hi - Does this directory exist?

ERROR: fio_pushd: 
/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni

I'd have to see the entire trac-all.log file to tell you for sure. The 
first error may show up earlier than the one that causes the crash.

Thanks,

a.y

On Mon, 8 Aug 2016, Song, Daniel wrote:

> 
> 
> Dan
> 
> _
> From: Ostrowski, Lauren
> Sent: Monday, August 08, 2016 4:08 PM
> To: Song, Daniel
> Subject: FW: TRACULA re-init error
> 
> 
> _
> From: Ostrowski, Lauren
> Sent: Monday, August 08, 2016 4:04 PM
> To: Freesurfer@nmr.mgh.harvard.edu
> Subject: TRACULA re-init error
> 
> Hi all,
> 
> I'm running into a problem with TRACULA, when I try to re-initialize tracts 
> that failed to reconstruct during the first
> run. I have set reinit = 1 in the configuration file and specified the 
> particular tracts that I want to reconstruct, but
> when I try to run the "trac-all -prior" step, I keep getting this error 
> message:
> 
> INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects
> INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac
> Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev
> trac-preproc -c 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local
>  -log /cluster/neuromi
> nd/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/
> trac/pBECTS001/scripts/trac-all.cmd
> #-
> /usr/local/freesurfer/dev/bin/trac-preproc 
> #-
> #@# Priors Mon Aug  8 15:53:46 EDT 2016
> /usr/local/freesurfer/dev/bin/dmri_train --outdir 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/m
> ni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt 
> --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/
> mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois 
> dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/m
> ni/fmajor_PP_roi2.bbr.nii.gz --bmask 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain
> _mask.bbr.nii.gz --fa 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz
>  --cptdir /clus
> ter/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg 
> /cluster/neuromind/cat/bects/subjects/pBECTS0
> 01/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc
> ERROR: fio_pushd: 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
> cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni
> cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/
> dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist 
> /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg
>  dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 
> --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz 
> dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lo
> wb_brain_mask.bbr.nii.gz --fa 
> /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz
>  --cptd
> ir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff 
> --reg /cluster/neuromind/cat/bects/subjects
> /pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc 
> sysname  Linux
> hostname truffles
> machine  x86_64
> user lo941
> Output directory: 
> /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
> Output directory in test subject's space: 
> /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/di
> ff
> Output base: fmajor_PP_avg33_mni_bbr
> Training subject directory list: /tmp/subj33.pBECTS001.15581.txt
> Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk
> Location of start ROI files relative to base: 
> dlabel/mni/fmajor_PP_roi1.bbr.nii.gz
> Location of end ROI files relative to base: 
> dlabel/mni/fmajor_PP_roi2.bbr.nii.gz
> Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
> Label ID's from aparc+aseg to add to cortex mask: 0
> Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
> Brain mask for output subject: Segmentation fault (core dumped) 
> Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 
> x86_64 x86_64 x86_64 GNU/Linux
> trac-preproc exited with ERRORS at Mon Aug  8 15:53:46 EDT 2016
> 
> Any help would be very much appreciated. It seems to me that TRACULA can't 
> find the aparc+aseg labels, but when I looked
> at 

Re: [Freesurfer] TRACULA tract endpoints on cortical surface

[Anastasia Yendiki]

Hi Barbara - This can be done with mri_vol2surf. The projection that's 
described in that passage can be done with --projdist-max -6 6 1, and the 
surface smoothing with --surf-fwhm 6. There are other options in 
mri_vol2surf, I'd recommend playing with the settings to see what works 
better for your data.

Best,

a.y


On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:

>
> Dear Freesurfers and TRACULA experts,
>
> Thank you for your help so far. I am trying to map the endpoints of the
> tract probability distributions onto the cortical surface (as mentioned
> in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
>
> I've somehow gathered that I need to do this (example one endpoint):
>
> flirt -ref /mri/orig/T1.nii.gz -in
> dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init
> /dmri/xfms/diff2anat.bbr.mat
>
> I then loaded the images in Freeview and they look reasonable together
> with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv
> dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
>
> What I don't get is how to do this:
>
> "we projected the tract endpoints onto the gray/white matter surface by
> sampling along the surface normal vector, anywhere within 6 mm (3
> DWI-space voxels) of the gray/white junction and then smoothing along
> the surface with a 2D Gaussian kernel of 6mm full width at half max."
> (Solsnes et al. 2016)
>
> Any help would be greatly appreciated.
>
> Best wishes,
> Barbara
>
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

That's correct!

On Wed, 3 Aug 2016, Anri WATANABE wrote:


Hi Anastasia,
Thank you for your kind explanation. I can be understanding how TRACULA tracts 
white matter pathways. 
At each position (in training subjects, not in new subjects of my data) 
probability that next goes for
which direction to every labels in the aparc+aseg (not with setting a certain 
ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects 
(your publication in 2011) and
they are based on manual labeling (the manual labeling tracts are referred to 
Wakana et al. 2007). Then
when white matter pathways are reconstructed in my subjects, TRACULA computes 
anatomical priors in each
subjects in my data in pre-processing and probability distributions from 
anatomical priors and by fitting
ball-and-stick model. 
Is this comprehension ok?

Best Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go
  through, TRACULA uses information like "what is the probability that this 
tract goes
  lateral/anterior/etc to XXX", where XXX any of the labels in the 
aparc+aseg. TRACULA computes
  these prior probabilities from a set of training subjects, where the 
tracts have been labeled
  manually. So it knows how likely a tract is to go through a certain 
aparc+aseg label, or to he
  left, right, anterior, etc of a certain aparc+aseg label. This is 
computed separately at each
  position along the tract. It's computed from the training subjects, and 
then used when
  reconstructing the tract in the new subject that you run TRACULA on.

  Hope this helps,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Thanks, AnastasiaI know that TRACULA use probabilistic tractography 
but if ROIs
are not
set how determine the origin and the end of a certain tract? I 
think that the
first we
have to determine the origin and the end of the tract, the second 
it constructs
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) 
but with the
probabilistic way (considering which direction should be next to). 
Is this
comprehension
wrong?
Thank you.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - TRACULA does not use deterministic ROIs. It uses a 
probabilistic
      model of how likely each tract is to go through or next to 
each of the
labels
      of the freesurfer subcortical segmentation and cortical 
parcellation, as a
      function of position along the trajectory of the tract.

      Best,
      a.y

      On Sun, 31 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,
            Thank you! It seems work well!!
            I have another question. Are ROIs for automatic 
tractography in
            TRACULA the same ROIs
            presented in Wakana et al. 2007?

            Anri



            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
            <ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - The problem is in this line:

                               set cmd = ($cmd

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go through, TRACULA uses information like "what is the 
probability that this tract goes lateral/anterior/etc to XXX", where XXX 
any of the labels in the aparc+aseg. TRACULA computes these prior 
probabilities from a set of training subjects, where the tracts have been 
labeled manually. So it knows how likely a tract is to go through a 
certain aparc+aseg label, or to he left, right, anterior, etc of a certain 
aparc+aseg label. This is computed separately at each position along the 
tract. It's computed from the training subjects, and then used when 
reconstructing the tract in the new subject that you run TRACULA on.


Hope this helps,
a.y

On Sun, 31 Jul 2016, Anri WATANABE wrote:


Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs 
are not
set how determine the origin and the end of a certain tract? I think that the 
first we
have to determine the origin and the end of the tract, the second it constructs 
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) but with the
probabilistic way (considering which direction should be next to). Is this 
comprehension
wrong?
Thank you.

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
  model of how likely each tract is to go through or next to each of the 
labels
  of the freesurfer subcortical segmentation and cortical parcellation, as a
  function of position along the trajectory of the tract.

  Best,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in
TRACULA the same ROIs
presented in Wakana et al. 2007?

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - The problem is in this line:

                   set cmd = ($cmd --ref $cvstempdir/$cvstemp)

      It should be changed to this:

                   set cmd = ($cmd --ref
$cvstempdir/$cvstemp/mri/norm.mgz)

      For this to take effect, you need to run "which trac-all"
and make the change in
      the trac-all file that the which commands shows you.

      Hope this helps,

      a.y

      On Fri, 15 Jul 2016, Anri WATANABE wrote:

            Hi, AnastasiaThis is trac-all.local-copy from 1
subject. Thank you!

            Anri

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of
Medicine
           

**

            2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
            <ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - This may be a bug that was fixed at
some point. Can
                  you send me the scripts/trac-all.local-copy from
one of your
                  subjects? Thanks!

                  a.y

                  On Mon, 11 Jul 2016, Anri WATANABE wrote:

                        Hi Anastasia,There is an error in .log
files of left
                        corticospinal tract in cvs template and I
attached
                        one
      

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic 
model of how likely each tract is to go through or next to each of the 
labels of the freesurfer subcortical segmentation and cortical 
parcellation, as a function of position along the trajectory of the tract.


Best,
a.y

On Sun, 31 Jul 2016, Anri WATANABE wrote:


Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in TRACULA the 
same ROIs
presented in Wakana et al. 2007?

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - The problem is in this line:

               set cmd = ($cmd --ref $cvstempdir/$cvstemp)

  It should be changed to this:

               set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)

  For this to take effect, you need to run "which trac-all" and make the 
change in
  the trac-all file that the which commands shows you.

  Hope this helps,

  a.y

  On Fri, 15 Jul 2016, Anri WATANABE wrote:

Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - This may be a bug that was fixed at some point. Can
      you send me the scripts/trac-all.local-copy from one of your
      subjects? Thanks!

      a.y

      On Mon, 11 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,There is an error in .log files of left
            corticospinal tract in cvs template and I attached
            one
            of file. In addition .log files of right
            corticospinal tract in cvs template doesn't exist. 
            Thanks in advance.

            Anri



           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of
            Medicine
           

**

            2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
            <ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - Is there an error in the stats/*.log
            files for the different tracts?

                  a.y

                  On Tue, 5 Jul 2016, Anri WATANABE wrote:

                        Dear Anastasia, 

                        I use TRACULA to obtain diffusion
            measures at each voxel in a certain pathway for
                        group analysis, but
                        there aren't stats/*.path.mean.txt
            files. I found .log files
                        (_PP.avg33_mni_bbr.log) which
            exist
                        1 file per 1 tract, except corticospinal
            tract which has 2 .log files.

                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

                        Error log: Loading output reference
            volume from
                       
            /Applications/freesurfer/subjects/cvs_avg35

                        corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

                        ERROR: Could not read
            /Applications/freesurfer/subjects/cvs_avg35


 

Re: [Freesurfer] TRACULA: 20% default threshold

[Anastasia Yendiki]

Yes, same thing!

On Wed, 27 Jul 2016, Harms, Michael wrote:



Thanks for clarifying.  Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?

thx,
--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Dillan - Thank you for your support!

Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.

Best,

a.y

On Tue, 26 Jul 2016, Newbold, Dillan wrote:


Hi everyone,

I’m having a little trouble understanding the exact meaning of the 20%
default threshold used in the freeview -tv option and dmri_pathstats
--pthr. I’ve seen multiple threads where Anastasia said that it is 20% of
the maximum value in the probability distribution—which corresponds to
the maximum number of sample paths intersecting a single voxel—but the
default thresholds I’ve seen set by the -tv option are generally lower
than that. For example, I have one subject in whom the right CST has a
maximum value in its path.pd.nii.gz file of 300. I would expect based on
what I’ve read in the mail archives that the threshold would be set at
60, but when I open the merged file with the -tv option the default
threshold for the right CST is 35.

My current best guess is that the default threshold is set to produce a
volume that has a probability sum equal to 20% of the sum of the
pre-threshold volume. (That is, the sum of intensities of all voxels in
the path.pd.nii.gz file should be 5 times the sum of the voxels above the
default threshold.) Is that accurate?

Thanks for all you’ve done to develop this tool. It’s brilliant and I
want to understand as much of it as I can.

-Dillan

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Re: [Freesurfer] TRACULA fornix tractography

[Anastasia Yendiki]

Hopefully soon, as several people have asked for it, but I don't have a 
concrete date unfortunately.

On Wed, 27 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
>
> Thank you that is great! Do you know yet when it will be available?
>
> Best wishes,
>
> Barbara
>
>
> On 27/07/2016 06:25, Anastasia Yendiki wrote:
>> Hi Barbara - We're working on a new atlas for TRACULA that will include
>> the fornix. We've already done the manual labeling for it.
>>
>> Best,
>>
>> a.y
>>
>> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>>
>>> Dear Anastasia,
>>>
>>> As we are analyzing DTI data acquired in patients with epilepsy we are
>>> especially interested in the fornix.
>>> I've come across the mri_cc -f option for fornix segmentation (native space)
>>> but I've also read that manual tracing/labeling of the tracts would be
>>> needed in the 33 controls for TRACULA (training set - trctrain).
>>> In Wakana et al. 2011 I see that the fornix was not included due to low
>>> reproducibility and it further states:
>>>
>>> "the reason for the poor reproducibility is most likely due to not enough
>>> spatial resolution with respect to the diameter"
>>>
>>> I wonder if you could please guide us in how to best add this tract to
>>> TRACULA so that it would be consistent in the methods compared with the
>>> other tract ROI definitions or perhaps state what were the difficulties in
>>> adding this particular tract to TRACULA.
>>>
>>> Thank you very much,
>>> Best wishes,
>>> Barbara
>>>
>>>
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
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>
>
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Re: [Freesurfer] flipping TRACULA tracts

[Anastasia Yendiki]

Hi Barbara - Your hack sounds like the right idea. One option would be to 
switch the FA values between the pathstats.byvoxel.txt files in the lh.* 
and rh.* output directories, by editing the text files without renaming 
the directories.

Hope this helps,

a.y

On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:

> Dear Freesurfers,
>
> I've got data pertaining to patients with left and right-sided temporal
> lobe epilepsy (TLE).
> My aim is to group those tracts according to side of epilepsy for
> waypoint comparisons.
>
> Basically for patients with right TLE I'd like to look at right tracts
> and at the same time for patients with left TLE I'd like to look at left
> tracts (ipsilateral tracts), I need to do the same for the contralateral
> tracts.
> Is there a straightforward way of doing this?
>
> I've already copied the tracts to respective ipsi and contralateral
> byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt;
> do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in
> R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i
> ${i/byvoxel./byvoxel_contraRTLE.}; done
> Now I have to flip the x-coordinates in the patients with right TLE (to
> make them more comparable to the tracts of the patients with left TLE).
> That will not be a problem, but I wonder if I am missing something?
> Can I then just go ahead and run trac-all -stats -c dmrircfile to
> generate the mean waypoint tracts etc.?
>
> Thank you very much,
> Best wishes,
>
> Barbara
>
> ___
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>
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA fornix tractography

[Anastasia Yendiki]

Hi Barbara - We're working on a new atlas for TRACULA that will include 
the fornix. We've already done the manual labeling for it.

Best,

a.y

On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
> 
> As we are analyzing DTI data acquired in patients with epilepsy we are
> especially interested in the fornix.
> I've come across the mri_cc -f option for fornix segmentation (native space)
> but I've also read that manual tracing/labeling of the tracts would be
> needed in the 33 controls for TRACULA (training set - trctrain).
> In Wakana et al. 2011 I see that the fornix was not included due to low
> reproducibility and it further states:
> 
> "the reason for the poor reproducibility is most likely due to not enough
> spatial resolution with respect to the diameter"
> 
> I wonder if you could please guide us in how to best add this tract to
> TRACULA so that it would be consistent in the methods compared with the
> other tract ROI definitions or perhaps state what were the difficulties in
> adding this particular tract to TRACULA.
> 
> Thank you very much,
> Best wishes,
> Barbara
> 
>
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Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Anastasia Yendiki]

Hi Michael - Which build of freesurfer do you use? I can send you the new 
version of dmri_paths so you can try it out.


Best,

a.y

On Wed, 20 Jul 2016, Harms, Michael wrote:



Hi Anastasia,

I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html

It sounds like a new version of dmri_paths was deemed necessary to
appropriately process single time points in the longitudinal TRACULA stream,
but Janosch’s last post seemed to indicate that her issue wasn’t resolved
even with the new build of dmri_paths that you generated.

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington 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

 





The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you
are not the intended recipient, be advised that any unauthorized use,
disclosure, copying or the taking of any action in reliance on the contents
of this information is strictly prohibited. If you have received this email
in error, please immediately notify the sender via telephone or return mail.


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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - Good to know things worked out!

a.y

On Tue, 19 Jul 2016, Derek Pisner wrote:

> Hi Anastasia,
>
> I thought I should let you know that this issue has now been resolved. We 
> specified the base ID's/ subject ID's incorrectly in the config file! Sorry 
> for the confusion. Now our group output looks correct.
>
> Thanks for your help,
> Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner 
> [dpis...@psychiatry.arizona.edu]
> Sent: Tuesday, July 12, 2016 5:06 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Anastasia,
>
> All subjects had both time-points (for DWI and T1-weighted recons). The 
> recons were run following the standard longitudinal pipeline for FS.
>
> Would it matter that I ran the pipeline piecemeal (i.e. separate 
> configuration files for each subject--see attached example)? In case you are 
> wondering, I did it this way in order to run the pipeline in parallel (i.e. 
> by subject) on our cluster...
>
> Another consideration is that we did preprocessing outside of TRACULA (i.e. 
> using FSL's tools directly so that we could apply a fieldmap, use new EDDY 
> with TOPUP, as well as apply a denoising algorithm). We then setup the folder 
> structure and filenames to begin TRACULA at the trac-all -intra stage, which 
> we have done successfully in the past when not using the longitudinal 
> pipeline (i.e. single-subject analyses)
>
> Still, I have a feeling that none of these customizations should have made 
> any difference as our merged outputs look excellent for both timepoints, for 
> all subjects... Any other thoughts about what might be causing this?
>
> Kind regards,
> -Derek
> ____
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 12, 2016 1:45 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't
> been able to replicate the problem in our own longitudinal data. Did you
> by any chance have any subjects that had only a single time point?
>
> a.y
>
> On Thu, 7 Jul 2016, Derek Pisner wrote:
>
>> Sure thing. fmajor mean.txt file is attached.
>>
>>
>> Thanks a bunch,
>> -Derek
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Thursday, July 07, 2016 4:48 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>
>> Hi Derek - this is strange. The dev and 5.3 version of freeview should
>> display them differently. Can you send me one of those mean.txt files?
>>
>> a.y
>>
>> On Wed, 6 Jul 2016, Derek Pisner wrote:
>>
>>> Hi Anastasia,
>>>
>>> This occurs for me on both stable and dev versions of freview and trac-all 
>>> -stat
>>>
>>> -Derek
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>>> [ayend...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 04, 2016 12:47 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>>
>>> Hi Derek - Are you by any chance using the dev version of freeview?
>>>
>>> a.y
>>>
>>> On Fri, 1 Jul 2016, Derek Pisner wrote:
>>>
>>>> Dear Anastasia,
>>>> I am running into an issue with the trac-all -stat option on our 
>>>> longitudinal TRACULA data.
>>>>
>>>> Everything runs smoothly through all earlier stages, and I checked 
>>>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>>>> looks fine.
>>>>
>>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>>>> without error.
>>>>
>>>> But then when I open the results with the command:
>>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>>>
>>>> I get the image seen in the attached .png file. Any idea what migh

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - The problem is in this line:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp)

It should be changed to this:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)

For this to take effect, you need to run "which trac-all" and make the 
change in the trac-all file that the which commands shows you.


Hope this helps,

a.y

On Fri, 15 Jul 2016, Anri WATANABE wrote:


Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!

Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - This may be a bug that was fixed at some point. Can
  you send me the scripts/trac-all.local-copy from one of your
  subjects? Thanks!

  a.y

  On Mon, 11 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,There is an error in .log files of left
corticospinal tract in cvs template and I attached
one
of file. In addition .log files of right
corticospinal tract in cvs template doesn't exist. 
Thanks in advance.

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine

**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - Is there an error in the stats/*.log
files for the different tracts?

      a.y

      On Tue, 5 Jul 2016, Anri WATANABE wrote:

            Dear Anastasia, 

            I use TRACULA to obtain diffusion
measures at each voxel in a certain pathway for
            group analysis, but
            there aren't stats/*.path.mean.txt
files. I found .log files
            (_PP.avg33_mni_bbr.log) which
exist
            1 file per 1 tract, except corticospinal
tract which has 2 .log files.

            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference
volume from
           
/Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            I attached dmrirc.example (configuration
file) and /scripts/trac-all.log.


            Thanks in advance,
            Anri




           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
University of Medicine
           

**

            2016-06-03 9:51 GMT+09:00 Anri WATANABE
<z2aa...@koto.kpu-m.ac.jp>:
                  Hi, Anastasia.
            There aren't any .log files but text
files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
            I guess text
            files complete all pathways and
measures.

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
  

Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Anastasia Yendiki]

Hi Knut Jørgen - Do you get this error only with the dev version of 
freesurfer? The command line causing the error is:


bbregister --s 4_test --init-fsl --dti --mov 
/home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg 
/home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat 
/home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat

Can you please try running this with the 5.3 version?

Thanks!

a.y

On Wed, 13 Jul 2016, Knut J Bjuland wrote:


Hi  Anastasia

Thanks. I am sending my entire trac-all.log

Knut Jøgen


On 07/12/2016 11:19 PM, Anastasia Yendiki wrote:

  Hi Knut Jørgen - Can you please send your entire trac-all.log?
  Thanks!

  a.y

  On Mon, 11 Jul 2016, Knut J Bjuland wrote:


 


flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/ref
vol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/mov
vol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90
-searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fs
l.mat
-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fsl
mat0.trans.mat
-schedule
/usr/local/freesurfer/bin/flirt.newdefault.20080811.sch

terminate called after throwing an instance of
'NEWMAT::SingularException'

Abort (core dumped) 

ERROR: flirt





Fedora 24


glibc-2.23.1-8.fc24.x86_64

gcc-6.1.1-3.fc24.x86_64


libstdc++-6.1.1-3.fc24.x86_64

ldd /usr/local/freesurfer/bin/flirt.fsl 

    linux-vdso.so.1 (0x7ffe8b6c8000)

    libz.so.1 => /lib64/libz.so.1
(0x7feaeba06000)

    libstdc++.so.6 => /lib64/libstdc++.so.6
(0x7feaeb67e000)

    libm.so.6 => /lib64/libm.so.6
(0x7feaeb374000)

    libgcc_s.so.1 => /lib64/libgcc_s.so.1
(0x7feaeb15d000)

    libc.so.6 => /lib64/libc.so.6
(0x7feaead9a000)

    /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)







Knut Jørgen Bjuland





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Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Anastasia Yendiki]

Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks!

a.y

On Mon, 11 Jul 2016, Knut J Bjuland wrote:



 


flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat
-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat
-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch

terminate called after throwing an instance of
'NEWMAT::SingularException'

Abort (core dumped) 

ERROR: flirt





Fedora 24


glibc-2.23.1-8.fc24.x86_64

gcc-6.1.1-3.fc24.x86_64


libstdc++-6.1.1-3.fc24.x86_64

ldd /usr/local/freesurfer/bin/flirt.fsl 

    linux-vdso.so.1 (0x7ffe8b6c8000)

    libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)

    libstdc++.so.6 => /lib64/libstdc++.so.6
(0x7feaeb67e000)

    libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000)

    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000)

    libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000)

    /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)







Knut Jørgen Bjuland


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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - This may be a bug that was fixed at some point. Can you send me 
the scripts/trac-all.local-copy from one of your subjects? Thanks!


a.y

On Mon, 11 Jul 2016, Anri WATANABE wrote:


Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs 
template and I attached one
of file. In addition .log files of right corticospinal tract in cvs template 
doesn't exist. 
Thanks in advance.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?

  a.y

  On Tue, 5 Jul 2016, Anri WATANABE wrote:

Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a 
certain pathway for
group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log 
files.

Command: trac-all –stat –c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file 
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and 
/scripts/trac-all.log.


Thanks in advance,
Anri





**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-03 9:51 GMT+09:00 Anri WATANABE <z2aa...@koto.kpu-m.ac.jp>:
      Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
I guess text
files complete all pathways and measures.


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu>:

      Thanks, Anri. So the previous steps seem to have run fine. 
Are there any .log
files
      created in the stats/ folder, which is created by trac-all 
-stat?

      On Wed, 1 Jun 2016, Anri WATANABE wrote:

            Hi Anastasia, This is a /scripts/trac-all.log 
of one subject of
            the group.

            Thanks,
            Anri

            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
            <ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
            I'll need to see what
                  exactly was running when the error occurred. 
Thanks!

                  a.y

                  On Sat, 28 May 2016, Anri WATANABE wrote:

                        Hello Anastasia,sorry for few information 
and let me tell
you
            command and
                        error log.
                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion

Re: [Freesurfer] TRACULA tract group comparison p-values

[Anastasia Yendiki]

Hi Barbara - Unfortunately we are very limited right now in our options 
for point set overlay display. I guess there's nothing that would be more 
suitable for displaying values that go all the way from negative to 
positive (which is what I suspect you have).

I'll submit this request to freeview headquarters :) Hopefully we can get 
it in there quickly. Thanks for your patience!

a.y

On Sun, 10 Jul 2016, Barbara Kreilkamp wrote:

> Dear Anastasia,
>
> Thank you, yes that was exactly what I was attempting to do. Would you
> be able to assist me with this following question as well please?
>
> How would I be able to use a different colormap under point sets please?
> I can only find "solid color" and "heatmap" but for example a
> blue-yellow-to-red colormap would suit my needs more.
>
> Thank you,
>
> Best wishes,
>
> Barbara
>
>
> On 07/07/2016 13:52, Anastasia Yendiki wrote:
>> Hi Barbara - I don't believe that freeview has an option to show colorbars
>> for heat maps that are loaded onto waypoints (if that's what you're
>> trying to display). We should definitely add it in the future.
>>
>> Best,
>> a.y
>>
>> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
>>
>>> Dear Freesurfers,
>>>
>>> I am looking for a way to add a colorbar to my p-value tract cores
>>> generated through TRACULA.
>>>
>>> When I load up the images as described in the tutorial here
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>>>
>>> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
>>> there is no option to select my textfile with the p-values unfortunately.
>>>
>>> Would you please help?
>>>
>>> Thanks ever so,
>>>
>>> Barbara
>>>
>>> ___
>>> Freesurfer mailing list
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>>>
>>>
>>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
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>
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Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Anastasia Yendiki]

Hi Shashwath - Unfortunately this is not possible right now, so you'd have 
to add those extra columns after you run it.


a.y

On Fri, 8 Jul 2016, Shashwath Meda wrote:


Hi Anastasia - Yes thats what i figured, however the way our pipeline system is 
setup this was the most
straightfoward way of doing it. Anyways i did figure out how to extract the 
average values in a more
convoluted fashion so we are all set with that. However,  im trying to do the 
same with the trac-all -stat
command now to extract pathbyvoxel stats and am having issues. I see that while 
assimilating group level
info, the program automatically rejects or doesnt ouput a column for the 
subject that has failed, is there
a quick and dirty fix to the code that will enable me to output all subjects 
data even if its failed (maybe
replace the values with NaN or somethign similar for failed subjects?). Please 
let me know.
Thanks
Shashwath

On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Shashwath - It looks like you have modified the directory structure of 
the output files.
  Normally the dpath/ directory is right under the directory with subject's 
name. From your file
  of inputs, it looks like you've created some other subdirectories and now 
dpath/ is a few
  levels down the hierarchy. I'd recommend reverting to the original 
structure that the commands
  expect.

  Best,
  a.y

  On Fri, 10 Jun 2016, Shashwath Meda wrote:

Dear Group -  I seem to have run into an issue when attempting to 
assimilate the
averaged pathway information from TRACULA into a group table. I have
attached my input list of paths and my output table for one of the 
tracts.
The below is the command that i have used but as you can see the 
values in my final
table are all from one subject (just replicated) despite my input 
list
having paths from different subjects, Has anyone encountered a 
similar situation?

tractstats2table --load-pathstats-from-file 
fmajor_PP_avg33_mni_bbr.txt --overall
--tablefile fmajor_PP_avg33_mni_bbr.table


--
Best,
Shashwath



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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't 
been able to replicate the problem in our own longitudinal data. Did you 
by any chance have any subjects that had only a single time point?

a.y

On Thu, 7 Jul 2016, Derek Pisner wrote:

> Sure thing. fmajor mean.txt file is attached.
>
>
> Thanks a bunch,
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 07, 2016 4:48 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - this is strange. The dev and 5.3 version of freeview should
> display them differently. Can you send me one of those mean.txt files?
>
> a.y
>
> On Wed, 6 Jul 2016, Derek Pisner wrote:
>
>> Hi Anastasia,
>>
>> This occurs for me on both stable and dev versions of freview and trac-all 
>> -stat
>>
>> -Derek
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 04, 2016 12:47 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA group stats visualization
>>
>> Hi Derek - Are you by any chance using the dev version of freeview?
>>
>> a.y
>>
>> On Fri, 1 Jul 2016, Derek Pisner wrote:
>>
>>> Dear Anastasia,
>>> I am running into an issue with the trac-all -stat option on our 
>>> longitudinal TRACULA data.
>>>
>>> Everything runs smoothly through all earlier stages, and I checked 
>>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>>> looks fine.
>>>
>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>>> without error.
>>>
>>> But then when I open the results with the command:
>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>>
>>> I get the image seen in the attached .png file. Any idea what might be 
>>> causing this?
>>>
>>> Many thanks in advance for you help.
>>>
>>> Best,
>>> Derek
>>>
>>>
>>>
>>>
>>
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>>
>>
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Re: [Freesurfer] TRACULA tract group comparison p-values

[Anastasia Yendiki]

Hi Barbara - I don't believe that freeview has an option to show colorbars 
for heat maps that are loaded onto waypoints (if that's what you're 
trying to display). We should definitely add it in the future.

Best,
a.y

On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:

> Dear Freesurfers,
>
> I am looking for a way to add a colorbar to my p-value tract cores
> generated through TRACULA.
>
> When I load up the images as described in the tutorial here
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>
> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
> there is no option to select my textfile with the p-values unfortunately.
>
> Would you please help?
>
> Thanks ever so,
>
> Barbara
>
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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - this is strange. The dev and 5.3 version of freeview should 
display them differently. Can you send me one of those mean.txt files?

a.y

On Wed, 6 Jul 2016, Derek Pisner wrote:

> Hi Anastasia,
>
> This occurs for me on both stable and dev versions of freview and trac-all 
> -stat
>
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 04, 2016 12:47 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - Are you by any chance using the dev version of freeview?
>
> a.y
>
> On Fri, 1 Jul 2016, Derek Pisner wrote:
>
>> Dear Anastasia,
>> I am running into an issue with the trac-all -stat option on our 
>> longitudinal TRACULA data.
>>
>> Everything runs smoothly through all earlier stages, and I checked 
>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>> looks fine.
>>
>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>> without error.
>>
>> But then when I open the results with the command:
>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>
>> I get the image seen in the attached .png file. Any idea what might be 
>> causing this?
>>
>> Many thanks in advance for you help.
>>
>> Best,
>> Derek
>>
>>
>>
>>
>
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?


a.y

On Tue, 5 Jul 2016, Anri WATANABE wrote:


Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a certain pathway 
for group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files 
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log files.

Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from 
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and /scripts/trac-all.log.


Thanks in advance,
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-03 9:51 GMT+09:00 Anri WATANABE <z2aa...@koto.kpu-m.ac.jp>:
  Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
files complete all pathways and measures.

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Thanks, Anri. So the previous steps seem to have run fine. Are there any 
.log files
  created in the stats/ folder, which is created by trac-all -stat?

  On Wed, 1 Jun 2016, Anri WATANABE wrote:

Hi Anastasia, This is a /scripts/trac-all.log of one 
subject of
the group.

Thanks,
Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
I'll need to see what
      exactly was running when the error occurred. Thanks!

      a.y

      On Sat, 28 May 2016, Anri WATANABE wrote:

            Hello Anastasia,sorry for few information and let me 
tell you
command and
            error log.
            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference volume from
            /Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            dmrirc.example (configuration file) is attached to this
e-mail.

            Thanks in advance,
            Anri



           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
           

**

            2016-05-27 22:57 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - I do not know what command line you ran 
and
what your
            configuration file looks like, so it is very
                  hard for me to suggest solutions.

                  Best,
                  a.y

                  On Fri, 27 May 2016, Anri WATANABE wrote:

  

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi there - I think I know what it is, but it's a problem that should be 
solved if you have the last tracula update. It means that your LANG 
environment variable needs to be set to en_US.UTF-8, which the update does 
for you.


a.y

On Tue, 5 Jul 2016, Lars M. Rimol wrote:



Hi Anastasia,

I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the
dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the
generated bvec file has commas instead of full stop (0,832 instead of
0.832). The input file (attached: "bvec_rows") has full stop. Another thing
is that the generated bvals file has an empty space at the end of the row,
which is not there in the input file ("bvals_rows").



thank you!

LMR

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?

a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:

Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I do

n't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).



Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n

ii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o

/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U
TC 
2015 x86_64 x86_64 x86_64 GNU/Linux


trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula

version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway










sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

You get the same error as trac-all because trac-all runs mri_convert. I'd 
send the mri_convert error in a new email with mri_convert somewhere in 
the title, so that someone else can help you.


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Also when I run mir_convert on the DICOMs I get the same error as the one I
got when I used DICOMs :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.
45306.2014091812330393354083931 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea what this could be ?

Thanks,

Ismail

  On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
  <ikoub...@bwh.harvard.edu> wrote:

It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …

Ismail

  On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
  <ayend...@nmr.mgh.harvard.edu> wrote:


  I do not know why the dicoms do not work. When you run
  mri_info on your nifti, what is the number of frames that
  shows up?

  On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:

Hi Anastasia,

This is what’s weird, my nifti volume contains
64 frames as my bvecs/bvals. So this shouldn’t
be the reason.
Also why the DICOMs wouldn’t work at the
beginning ?

Thanks,
Ismail

  On Jul 4, 2016, at 2:41 PM,
      Anastasia Yendiki
  <ayend...@nmr.mgh.harvard.edu>
  wrote:


  Hi Ismail - You can see from the
  log file that the command that
  causes the error is this:

  mri_convert --frame 31
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
  
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

  It's trying to extract the 32nd
  frame of your nifti file, but from
  the error message it looks like
  your nifti file doesn't have a
  32nd frame. So either the nifti
  file has too few volumes, or the
  bvecs/bvals have too many lines.
  You'll have to figure that out.

  a.y

  On Mon, 4 Jul 2016, Koubiyr,
  Ismail wrote:

Hi Anastasia,
Here it is.
But how could the
problem be related to
the nifti volume since
I have errors
when using the DICOMs
too ?
Thanks again,
Ismail
  On Jul 4,
  2016, at
  1:44 PM,
  Anastasia
      Yendiki

<ayend...@nmr.mgh.harvard.edu>
wrote:


  Hi Ismail
  - It
  sounds
  like the
  error has
  to do with
  the nifti
  volume,
  not

the bvecs/bvals. Can
you send the log file
from
scripts/trac-all.log?

  Thanks,
  a.y

  On Mon, 4
  Jul 2016,
  Koubiyr,
  Ismail
  wrote:

Hi
Anastasia,
Thank
you
for
getting
back
to
me.
Here
are
more
details
about
my
problem,
I
think
it
should
help
you
understand
more.
I
   

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

I do not know why the dicoms do not work. When you run mri_info on your 
nifti, what is the number of frames that shows up?


On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So 
this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?

Thanks,
Ismail


On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 
wrote:


Hi Ismail - You can see from the log file that the command that causes the 
error is this:

mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the error 
message it looks like your nifti file doesn't have a 32nd frame. So either the 
nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll 
have to figure that out.

a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail

On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki

<ayend...@nmr.mgh.harvard.edu> wrote:



Hi Ismail - It sounds like the error has to do with the nifti volume, not

the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error

:

WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368

0043

.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional

space,

but when the new bvecs  and bvals are created, they seem messed up. I

will

attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

 On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
 <ayend...@nmr.mgh.harvard.edu> wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

 Hi everyone,

 I have some problems trying to run TRACULA on some DWI
 data. It is a mosaic Siemens DWI. I first converted the
 DICOM files with dcm2nii to get the bvec and bval files.
 Then I run the trac-all -prep -c command and I get the
 following error :

 WARNING: file /My/path/to/dicom does not contain a Siemens
 ASCII header
 has this file been anonymized?
 ERROR: cannot unpack mosiacs without ASCII header

 I tried to unpack the mosaics with gdcmtar, but I got the
 same error.

 Thank you in advance for your help,

 Ismail
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - You can see from the log file that the command that causes the 
error is this:


mri_convert --frame 31 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz 
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz

It's trying to extract the 32nd frame of your nifti file, but from the 
error message it looks like your nifti file doesn't have a 32nd frame. So 
either the nifti file has too few volumes, or the bvecs/bvals have too 
many lines. You'll have to figure that out.


a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,

Ismail



> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
>
> Thanks,
> a.y
>
> On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
>
>> Hi Anastasia,
>> Thank you for getting back to me.
>> Here are more details about my problem, I think it should help you
>> understand more.
>> I run trac-all -prep -c on some DICOM files but I had the following error
:
>> 
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
>> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
>> header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>> I also tried to de-mosiac the DICOMs, it gave me the same error.
>> Then I converted the DICOMs into NIFTI, which allowed me not to get the
>> previous error but something else weird happened. Now I get :
>> ERROR: fMRIframe: frame >= nframes
>> I checked the bvecs and bvals files, they seem normal, no additional
space,
>> but when the new bvecs  and bvals are created, they seem messed up. I
will
>> attach you all the bvecs and bvals I used and the ones I get too.
>> Ideally, the DICOMs should work fine but I have no idea why I get these
>> errors.
>> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
>> any additional space.
>> Thank you in advance for your help.
>> Best,
>> Ismail
>> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
>>
>>  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
>>  <ayend...@nmr.mgh.harvard.edu> wrote:
>> Hi Ismail - Are you passing the nifti volume as input to trac-all?
>> It's
>> hard to tell without looking at your configuration file.
>> Best,
>> a.y
>> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
>>
>>  Hi everyone,
>>
>>  I have some problems trying to run TRACULA on some DWI
>>  data. It is a mosaic Siemens DWI. I first converted the
>>  DICOM files with dcm2nii to get the bvec and bval files.
>>  Then I run the trac-all -prep -c command and I get the
>>  following error :
>>
>>  WARNING: file /My/path/to/dicom does not contain a Siemens
>>  ASCII header
>>  has this file been anonymized?
>>  ERROR: cannot unpack mosiacs without ASCII header
>>
>>  I tried to unpack the mosaics with gdcmtar, but I got the
>>  same error.
>>
>>  Thank you in advance for your help,
>>
>>  Ismail
>>  ___
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - It sounds like the error has to do with the nifti volume, not 
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?


Thanks,
a.y

On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:


Hi Anastasia,

Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.

I run trac-all -prep -c on some DICOM files but I had the following error :
WARNING: 
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.

Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional space,
but when the new bvecs  and bvals are created, they seem messed up. I will
attach you all the bvecs and bvals I used and the ones I get too.

Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.

Thank you in advance for your help.

Best,

Ismail

P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.


  On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
  <ayend...@nmr.mgh.harvard.edu> wrote:


Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

  Hi everyone,

  I have some problems trying to run TRACULA on some DWI
  data. It is a mosaic Siemens DWI. I first converted the
  DICOM files with dcm2nii to get the bvec and bval files.
  Then I run the trac-all -prep -c command and I get the
  following error :

  WARNING: file /My/path/to/dicom does not contain a Siemens
  ASCII header
  has this file been anonymized?
  ERROR: cannot unpack mosiacs without ASCII header

  I tried to unpack the mosaics with gdcmtar, but I got the
  same error.

  Thank you in advance for your help,

  Ismail
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Re: [Freesurfer] longitudinal tracula

[Anastasia Yendiki]

Hi Michael - There is no bvec file associated with the base template. The 
base template is a structural (the median of a subject's structural time 
points) and not a diffusion scan.


The way you'd want to account for different amounts of motion across 
subjects in a cross-sectional analysis, you'd probably want to account for 
different changes in motion in a longitudinal study. Whether you'd also 
want to discard data is an open question.


a.y

On Mon, 4 Jul 2016, Harms, Michael wrote:



So, what bvec/bvec file should be associated with the BASE scan?  It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.

I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study, the same issue applies, even if you use all frames “as is”.  In
that case, the potential bias would be due to using data of differing
quality across sessions.  In a sense, we are just making the issue
explicit by discarding bad frames as part of a QC step.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.

However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent as possible
across time points. If you find that there's a longitudinal change, would
this be because there were different directions/b-values in each time
point or because of an actual change in the brain? I suppose that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.

Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:



Hi Anastasia,
Looking through the trac-preproc and trac-paths scripts, it is now clear
to me that all the time points for a given subject have to be
contained/specified
within the same dmrirc configuration file in order to implement a
longitudinal TRACULA analysis.  So, I've answered my previous question in
that regard.

The challenge in our case is that we have separately pre-processed the
dMRI data for each subject and time point, removing bad frames/volumes
(using the
DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the
time points of a given subject.  We can specify the bvec file for each
subject/time
point using the bveclist configuration parameter.  But there is no
analog available for bvals, since only a single bvalfile can be
specified.

I see that this issue has been raised in a couple other posts relatively
recently (2015):
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
but no working solution was provided at that time.

I’m wondering if there is perhaps now a development version of TRACULA
that supports a “bvallist” capability?  If not, it doesn’t look like it
would be too
difficult to modify trac-all  to include that capability (modeling after
what is already in trac-all for the bveclist/bvecfile stuff).  But, in
that case,
it isn’t immediately clear to me if there are other downstream “gotchas”
in the preproc, paths, or stats stage specific scripts/binaries that
would need
modifications as well.  [I don’t see anything in the sections related to
the BASE-specific processing in trac-preproc involving bvals/bvecs, so
think we are
fine there.  But it is harder for me to tell what is going on in
trac-paths].

thanks,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington 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: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms,
Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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 single dmrirc file?  My
initial
thought was “no”, that it would be fine to run one scan wave per subject
per dmrirc file (as lo

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

[Anastasia Yendiki]

Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals 
and dmri/bvecs files that get generated look fine too?


a.y

On Sat, 2 Jul 2016, Lars M. Rimol wrote:


Hi,

Trying to run trac-all -c dmric_file -prep,  I get an error message stating 
that there are different numbers of entries in the bval and bvec files. I don't
understand why, since both have the same number of rows (64).

OS = Ubuntu 14.04.4
Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated 
Tracula and FSL (v 5.0.9).


Error message:

#@# Tensor fit fr. 01. juli 19:20:29 +0200 2016
dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
 -r
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b 
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o
/media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit
Error: bvecs and bvals don't have the same number of entries
Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016

--
I also tried flipping the bvec/bval files, but got the same error.
I don't know if there's anything wrong with the bval/bvec files, or if this 
error message is indicative of some other problem. Is the updated Tracula
version only compatible with the dev version of FS?

I have attached the bval/bvec files and the trac-all.log.

---
The contents of the dmric file is:

setenv SUBJECTS_DIR  /media/lmr2/subjects/DTI
set dtroot =  /media/lmr2/subjects/DTI/tracula_2016_nativerows
set subjlist = (4_FS)
set dcmroot =  /media/lmr2/subjects/DTI
set dcmlist =   ( 4/5/1.dcm )
set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv
set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv



Thank you!


yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - Are you by any chance using the dev version of freeview?

a.y

On Fri, 1 Jul 2016, Derek Pisner wrote:


Dear Anastasia,
I am running into an issue with the trac-all -stat option on our longitudinal 
TRACULA data. 

Everything runs smoothly through all earlier stages, and I checked individual 
subjects' merged outputs in freeview with -tv mode. Everything looks fine.

Also, then when I run trac-all -c dmric_config -stat, everything finishes 
without error.
 
But then when I open the results with the command:
freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
/data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt

I get the image seen in the attached .png file. Any idea what might be causing 
this?

Many thanks in advance for you help.

Best,
Derek



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Re: [Freesurfer] longitudinal tracula

[Anastasia Yendiki]

Hi Michael - Indeed it should not be too difficult to add the feature of 
specifying the b-value table for each scan and I can add this in the next 
version.


However, I would be a bit careful with removing different DWI volumes for 
different time points. The acquisition should be as consistent as possible 
across time points. If you find that there's a longitudinal change, would 
this be because there were different directions/b-values in each time 
point or because of an actual change in the brain? I suppose that, unless 
there's a systematic bias, you might expect that these changes will be in 
different directions for different subjects and would then average out. 
But it's a tricky issue.


Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:



Hi Anastasia,
Looking through the trac-preproc and trac-paths scripts, it is now clear to me 
that all the time points for a given subject have to be contained/specified
within the same dmrirc configuration file in order to implement a longitudinal 
TRACULA analysis.  So, I've answered my previous question in that regard.

The challenge in our case is that we have separately pre-processed the dMRI 
data for each subject and time point, removing bad frames/volumes (using the
DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the time 
points of a given subject.  We can specify the bvec file for each subject/time
point using the bveclist configuration parameter.  But there is no analog 
available for bvals, since only a single bvalfile can be specified.  

I see that this issue has been raised in a couple other posts relatively 
recently (2015):
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
but no working solution was provided at that time.

I’m wondering if there is perhaps now a development version of TRACULA that 
supports a “bvallist” capability?  If not, it doesn’t look like it would be too
difficult to modify trac-all  to include that capability (modeling after what 
is already in trac-all for the bveclist/bvecfile stuff).  But, in that case,
it isn’t immediately clear to me if there are other downstream “gotchas” in the 
preproc, paths, or stats stage specific scripts/binaries that would need
modifications as well.  [I don’t see anything in the sections related to the 
BASE-specific processing in trac-preproc involving bvals/bvecs, so think we are
fine there.  But it is harder for me to tell what is going on in trac-paths].

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington 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 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 per subject per 
dmrirc file (as long as the “baselist” variable is set appropriately for each
scan wave and subject).

But looking at the ‘trac-all’ script, I see

if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…

So, I’m wondering why different sections in the code would be necessary if in 
fact it is ok to process a single scan wave per dmrirc file.

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington 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

 





The materials in this message are private and may contain Protected Healthcare 
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or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

[Anastasia Yendiki]

Hi Ismail - Are you passing the nifti volume as input to trac-all? It's 
hard to tell without looking at your configuration file.

Best,
a.y

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:

> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
> Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec 
> and bval files.
> Then I run the trac-all -prep -c command and I get the following error :
>
> WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
> has this file been anonymized?
> ERROR: cannot unpack mosiacs without ASCII header
>
> I tried to unpack the mosaics with gdcmtar, but I got the same error.
>
> Thank you in advance for your help,
>
> Ismail
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula not work

[Anastasia Yendiki]

Hi Yang - Have you followed the instructions on how to set up the 
freesurfer environment?


https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration

Best,
a.y

On Mon, 13 Jun 2016, yangfuxing wrote:


Hi professor??   When I finished setting up the configuration file "dmrirc", type 
"trac-all -c dmrirc"in the terminal ,it return "FSLDIR: Undefined
variable", how can I solve it?Thank you.
Best,
yang

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Fwd: TRACULA stat extraction issue

[Anastasia Yendiki]

Hi Shashwath - It looks like you have modified the directory structure of 
the output files. Normally the dpath/ directory is right under the 
directory with subject's name. From your file of inputs, it looks like 
you've created some other subdirectories and now dpath/ is a few levels 
down the hierarchy. I'd recommend reverting to the original structure that 
the commands expect.


Best,
a.y

On Fri, 10 Jun 2016, Shashwath Meda wrote:


Dear Group -  I seem to have run into an issue when attempting to assimilate 
the averaged pathway information from TRACULA into a group table. I have
attached my input list of paths and my output table for one of the tracts.
The below is the command that i have used but as you can see the values in my 
final table are all from one subject (just replicated) despite my input list
having paths from different subjects, Has anyone encountered a similar 
situation?

tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt 
--overall --tablefile fmajor_PP_avg33_mni_bbr.table


--
Best,
Shashwath


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Re: [Freesurfer] About TRACULA

[Anastasia Yendiki]

Hi Yang - TRACULA does not assume that the shape, size, or integrity of 
the tracts is the same in the study subjects as in the atlas subjects. It 
just assumes that the relative position of the tracts with respect to the 
cortical and subcortical segmentation labels from freesurfer. For example, 
does tract X go lateral to the thalamus or superior to the thalamus, and 
does this happen in the beginning, end, or 2/3 along the length of tract 
X? If these general relationships are preserved, and if the cortical and 
subcortical segmentation can be reconstructed in the study subjects, then 
TRACULA should work.


Again, the best way to know if TRACULA will work is to run it on a couple 
of representative subjects. I may have written every line of code in it, I 
can explain how it works, but even I can't predict how it'll do on every 
single data set out there that I haven't even seen :)


Best,

a.y

On Thu, 2 Jun 2016, ?? wrote:


Hi,
    To be specific, I'm trying to reconstruct arcuate fasciculus (refer to SLFT 
according to your paper 2011) in patients who suffered from frontal or temporal 
or parietal gliomas. I noticed that
TRACULA was used to study neuropsychiatry and neurodegeneration diseases, such 
as schizophrenia, autism etc. When it comes to organic diseases, like brain 
tumor, white matter structures may be pushed or
deformed due to mass effect. So my question is should I involve the patients in 
the training set? What can I do to succeed in reconstruction of arcuate 
fasciculus using TRACULA in my research? Thanks
for your time.
BW,
yang

 



-- Original --
From:  "ayendiki";;
Date:  Jun 2, 2016
To:  "Freesurfer support list";
Subject:  Re: [Freesurfer] About TRACULA


Hi - It's hard to predict in advance what will happen without trying it
out. A lot will depend on the size/position/nature of the tumor. Some
tumor patients will go through just fine, other will have issues. If the
freesurfer segmentation works, then tracula will work too.

Best,
a.y

On Thu, 2 Jun 2016, yangfuxing wrote:

> Dear professor,
>     I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical
> parcellation and subcortical segmentation using freesurfer. In my study, all
> patients have brain tumors. So I begin to wonder if "recon-all" can still be
> applied to these subjects, or in other word, is it possible that
> freesurfer's automated brain segmentation could be applied to brain tumor
> patients because their normal structures were changed? If I just run it
> regularly according to fswiki, would the outcome be accurate?
>     Second question is about automatic tractography using TRACULA.
> Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in
> patients with brain tumor, is it possible? How can I set up the
> configuration? Hope to hear from you soon. Best wishes!
> Sincerely
>
>
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dispose of the e-mail.

Re: [Freesurfer] About TRACULA

[Anastasia Yendiki]

Hi - It's hard to predict in advance what will happen without trying it 
out. A lot will depend on the size/position/nature of the tumor. Some 
tumor patients will go through just fine, other will have issues. If the 
freesurfer segmentation works, then tracula will work too.


Best,
a.y

On Thu, 2 Jun 2016, yangfuxing wrote:


Dear professor,
    I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical
parcellation and subcortical segmentation using freesurfer. In my study, all
patients have brain tumors. So I begin to wonder if "recon-all" can still be
applied to these subjects, or in other word, is it possible that
freesurfer's automated brain segmentation could be applied to brain tumor
patients because their normal structures were changed? If I just run it
regularly according to fswiki, would the outcome be accurate?
    Second question is about automatic tractography using TRACULA.
Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in
patients with brain tumor, is it possible? How can I set up the
configuration? Hope to hear from you soon. Best wishes!
Sincerely

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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Thanks, Anri. So the previous steps seem to have run fine. Are there any 
.log files created in the stats/ folder, which is created by trac-all 
-stat?


On Wed, 1 Jun 2016, Anri WATANABE wrote:


Hi Anastasia, This is a /scripts/trac-all.log of one subject of the 
group.

Thanks,
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-31 22:55 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll 
need to see what
  exactly was running when the error occurred. Thanks!

  a.y

  On Sat, 28 May 2016, Anri WATANABE wrote:

Hello Anastasia,sorry for few information and let me tell you 
command and
error log.
Command: trac-all –stat –c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


dmrirc.example (configuration file) is attached to this e-mail.

Thanks in advance,
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-27 22:57 GMT+09:00 Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu>:

      Hi Anri - I do not know what command line you ran and what 
your
configuration file looks like, so it is very
      hard for me to suggest solutions.

      Best,
      a.y

      On Fri, 27 May 2016, Anri WATANABE wrote:

            Hi Anastasia, 
            Thank you for your answer.
            There aren't stats/*.path.mean.txt files and terminal 
says 'Could
not read
            /Applications/freesurfer/subjects/cvs_avg35.' I
            checked /Application/freesurfer/subjects/cvs_avg35 
folder and
couldn't find COR-.info file.
            Could you tell me any resolutions, please?

            Thanks, 
            Anri

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
           

**

            2016-05-21 6:48 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:

                  Hi Anri - The FA values are extracted in the 
native space
of each subject, which is why
            those are the only
                  coordinates that you see. If you want to display 
the
results of your analysis on an average
            path, after
                  running trac-all -stat, you can use the
stats/*.path.mean.txt files (see also the last part
            of the TRACULA
                  tutorial).

                  Best,
                  a.y

                  On Wed, 18 May 2016, Anri WATANABE wrote:

                        Dear experts, 
                        I use TRACULA to examine a measure (FA) at 
each voxel
in one pathway.
                        pathstats.byvoxel.txt files show 
coordinates in
native space and after converting
            those the new
                        files don't show any coordinates which are 
in MNI
space.
                        Could you tell me how can I know MNI 
coordinate
values?

               

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

The input needs to be the diffusion-weighted images, not the FA, MD, etc. 
There should be as many volumes in this input nifti as there are b-values 
in bval file and gradient vectors in the bvec file. The image 
registration, tractography, etc etc is performed on the diffusion-weighted 
images, not on the FA, MD, etc. The FA, MD, etc are used only in the very 
end, to extract FA, MD, etc for each tract. But to get the tracts in the 
first place, you need the images.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu>
wrote:



Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's
from
SUBJECTS_DIR (see example config file). Based on your log file, it
looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so
that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
ayend...@nmr.mgh.harvard.edu> wrote:



No, it should be pointed to the DWI data, which can be corrected
niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to
be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in
a
different folder.
Enclosed is the log file (of one subject) and the configuration
file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - The intra-subject registration step that you're trying
to
run
registers your subject's DWI and T1 images. It expects to find
those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can
you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics
(FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out
of
range

I do not have the original filesŠ is there a way that I can get
the
script working?

Many thanks.
Heidi










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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Some of the errors make me suspect that your input DWI files contain only 
one volume. Could this be the case?


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi







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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks 
like you haven't turned off the eddy current compensation, because it's 
trying to run it. If you attach your config file, I'll take a look.


Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi





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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

No, it should be pointed to the DWI data, which can be corrected niftis 
instead of the original dicoms. I would recommend turning off all the 
corrections in the configuration file, and then running everything without 
skipping steps. This will create all the files that are expected to be 
there for the registration.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:



Hi Heidi - The intra-subject registration step that you're trying to run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi



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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Hi Heidi - The intra-subject registration step that you're trying to run 
registers your subject's DWI and T1 images. It expects to find those 
images. It doesn't use the FA, MD, etc in any way.


Did the log file get created in scripts/trac-all.log? If so, can you 
please send that file and your configuration file? Thanks!


a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, 
L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3. 

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things I don’t 
need and then I tried to run:
Trac-all –intra –c 

Unfortunately, it does not work, it says: dcmlist: subscript out of range

I do not have the original files… is there a way that I can get the script 
working?

Many thanks.
Heidi

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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - I do not know what command line you ran and what your 
configuration file looks like, so it is very hard for me to suggest 
solutions.


Best,
a.y

On Fri, 27 May 2016, Anri WATANABE wrote:


Hi Anastasia, 
Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal says 'Could not read 
/Applications/freesurfer/subjects/cvs_avg35.' I
checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find 
COR-.info file.
Could you tell me any resolutions, please?

Thanks, 
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-21 6:48 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:

  Hi Anri - The FA values are extracted in the native space of each 
subject, which is why those are the only
  coordinates that you see. If you want to display the results of your 
analysis on an average path, after
  running trac-all -stat, you can use the stats/*.path.mean.txt files (see 
also the last part of the TRACULA
  tutorial).

  Best,
  a.y

  On Wed, 18 May 2016, Anri WATANABE wrote:

Dear experts, 
I use TRACULA to examine a measure (FA) at each voxel in one 
pathway.
pathstats.byvoxel.txt files show coordinates in native space and 
after converting those the new
files don't show any coordinates which are in MNI space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards, 
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**


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Re: [Freesurfer] DTI error

[Anastasia Yendiki]

Hi Jasmin - On my screen the dash "-" symbol before the "c" looks 
different than the one before "path". I'd check if you are indeed typing a 
plain "-c".


Best,
a.y

On Wed, 25 May 2016, Jasmin Alves wrote:


Hi Anastasia,
 I am still receiving the following error message when I run a different 
participant doing, trac-all -path –c
dmrirc1_sim.txt: 

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


If you have any ideas for what i can try it would be very appreciated!  


Thanks!

Jasmin 


On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves <jal...@usc.edu> wrote:
  Correct. 

  On Sunday, May 22, 2016, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 
wrote:

No idea, sorry. You used the -c option with the previous steps of 
trac-all and didn't see this
error, correct?

On Sun, 22 May 2016, Jasmin Alves wrote:

  Hi Anastasia,
  Perhaps I was asking for advice regarding the wrong step in 
trac-all, do you
  have any ideas why I am still receiving the following error:

  ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt

  This occurs when I do trac-all -path –c dmrirc1_sim.txt

  I tried looking at posts from previous mailing lists, and 
found no match to
  this problem.


  Thank you,

  Jasmin


      On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
  <ayend...@nmr.mgh.harvard.edu> wrote:

        Ok, then you can ignore the error that you see when you 
run the
        bedpost step.

        `On Sun, 22 May 2016, Jasmin Alves wrote:

        Sorry for the mix-up. All of the bedpost output files 
are
        generated as well
        both 1 and 2 of each file. 

            On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
        <ayend...@nmr.mgh.harvard.edu> wrote:

              These are output files from the -prep step. I'm
        asking about
              output files from the bedpost step, since that's
        where you're
              encountering the error.

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

  
.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt

  
AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D

  
f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA

              =
              What's in the dmri.bedpostX/ directory?

              On Sun, 22 May 2016, Jasmin Alves wrote:

                    Output files are being generated, ie.
                     1. dtifit_FA.nii.gz - Fractional Anisotropy
                     2. dtifit_MD.nii.gz - Mean Diffusivity
                     3. dtifit_MO.nii.gz - Mode of the 
Anisotropy
                     4. dtifit_S0.nii.gz - Non-Diffusion 
weighted
        image
                     5. dtifit_L1.nii.gz - Primary Eigenvalue
                     6. dtifit_L2.nii.gz - Secondary Eigenvalue
                     7. dtifit_L3.nii.gz - Tertiary Eigenvalue
                     8. dtifit_V1.nii.gz - Primary Eigenvector
                     9. dtifit_V2.nii.gz - Secondary Eigenvector
                    10. dtifit_V3.nii.gz - Tertiary Eigenvector
                    But it seems the bedpost process gets cut
        short and
                    then,  the trac-all path
                    step won't work. I have ran it a few times 
and
        the
                    bedpost step ends at the
                    same point. 


                    On Sun, May 22, 2016 at 3:24 PM, Anastasia
        Yendiki
                    <ayend...@nmr.mgh.harvard.edu> wrote:

                          But do you see the output files from 
the
                    previous step? The
                          outputs from each step are described 
on
        the
                    wiki.

                          On Sun, 22 May 2016, Jasmin Alves 
wrote:

                                Hi Anastasia,
                                Thank you for the reply, when I 
do
 

Re: [Freesurfer] DTI error

[Anastasia Yendiki]

No idea, sorry. You used the -c option with the previous steps of trac-all 
and didn't see this error, correct?


On Sun, 22 May 2016, Jasmin Alves wrote:


Hi Anastasia,
Perhaps I was asking for advice regarding the wrong step in trac-all, do you
have any ideas why I am still receiving the following error:

ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt

This occurs when I do trac-all -path –c dmrirc1_sim.txt

I tried looking at posts from previous mailing lists, and found no match to
this problem.


Thank you,

Jasmin


On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  Ok, then you can ignore the error that you see when you run the
  bedpost step.

  `On Sun, 22 May 2016, Jasmin Alves wrote:

  Sorry for the mix-up. All of the bedpost output files are
  generated as well
  both 1 and 2 of each file. 

  On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
  <ayend...@nmr.mgh.harvard.edu> wrote:

        These are output files from the -prep step. I'm
  asking about
        output files from the bedpost step, since that's
  where you're
        encountering the error.

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard

.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt

AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D

f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA

        =
        What's in the dmri.bedpostX/ directory?

        On Sun, 22 May 2016, Jasmin Alves wrote:

              Output files are being generated, ie.
               1. dtifit_FA.nii.gz - Fractional Anisotropy
               2. dtifit_MD.nii.gz - Mean Diffusivity
               3. dtifit_MO.nii.gz - Mode of the Anisotropy
               4. dtifit_S0.nii.gz - Non-Diffusion weighted
  image
               5. dtifit_L1.nii.gz - Primary Eigenvalue
               6. dtifit_L2.nii.gz - Secondary Eigenvalue
               7. dtifit_L3.nii.gz - Tertiary Eigenvalue
               8. dtifit_V1.nii.gz - Primary Eigenvector
               9. dtifit_V2.nii.gz - Secondary Eigenvector
              10. dtifit_V3.nii.gz - Tertiary Eigenvector
              But it seems the bedpost process gets cut
  short and
              then,  the trac-all path
              step won't work. I have ran it a few times and
  the
              bedpost step ends at the
              same point. 


              On Sun, May 22, 2016 at 3:24 PM, Anastasia
  Yendiki
              <ayend...@nmr.mgh.harvard.edu> wrote:

                    But do you see the output files from the
              previous step? The
                    outputs from each step are described on
  the
              wiki.

                    On Sun, 22 May 2016, Jasmin Alves wrote:

                          Hi Anastasia,
                          Thank you for the reply, when I do
  just
              let it run,
                          I get the following
                          error when I try to do trac-all
  -path –c
                          dmrirc1_sim.txt

                          I get the following error:

                          ERROR: flag –c unrecognized

                          -path –c dmrirc1_sim.txt


                          Thanks,

                          Jasmin 


                          On Sun, May 22, 2016 at 1:51 AM,
              Anastasia Yendiki
                          <ayend...@nmr.mgh.harvard.edu>
  wrote:

                                Hi Jasmin - Check if things
  are
              running
                          despite that error. Are
                                output files being
  generated?

                                a.y

                                On Sat, 21 May 2016, Jasmin
  Alves
              wrote:


                                      Dear Freesurfer,

                                      While doing the
  bedpost step
              for
                          TRAC-all ( trac-all
                                      -bedp -c
                                      dmrirc1_sim.txt) I
  received
              the
                          following error:

                                     
                         
              /Applications/freesurfer/bin/bedpostx_mgh:
  line 345:
                                      kill: (51042) - No
  such
                                      process

                                      Any ideas?

                                      Thank you,
                                      Jasmin 

                                      Jasmi

Re: [Freesurfer] DTI error

[Anastasia Yendiki]

Ok, then you can ignore the error that you see when you run the bedpost 
step.


`On Sun, 22 May 2016, Jasmin Alves wrote:


Sorry for the mix-up. All of the bedpost output files are generated as well
both 1 and 2 of each file. 

On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  These are output files from the -prep step. I'm asking about
  output files from the bedpost step, since that's where you're
  encountering the error.

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
.edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp=DQIDaQ=clK7kQUTWt
AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=7c1gaW5UpDUs-D
f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA
  =
  What's in the dmri.bedpostX/ directory?

  On Sun, 22 May 2016, Jasmin Alves wrote:

Output files are being generated, ie.
 1. dtifit_FA.nii.gz - Fractional Anisotropy
 2. dtifit_MD.nii.gz - Mean Diffusivity
 3. dtifit_MO.nii.gz - Mode of the Anisotropy
 4. dtifit_S0.nii.gz - Non-Diffusion weighted image
 5. dtifit_L1.nii.gz - Primary Eigenvalue
 6. dtifit_L2.nii.gz - Secondary Eigenvalue
 7. dtifit_L3.nii.gz - Tertiary Eigenvalue
 8. dtifit_V1.nii.gz - Primary Eigenvector
 9. dtifit_V2.nii.gz - Secondary Eigenvector
10. dtifit_V3.nii.gz - Tertiary Eigenvector
But it seems the bedpost process gets cut short and
then,  the trac-all path
step won't work. I have ran it a few times and the
bedpost step ends at the
same point. 


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

      But do you see the output files from the
previous step? The
      outputs from each step are described on the
wiki.

      On Sun, 22 May 2016, Jasmin Alves wrote:

            Hi Anastasia,
            Thank you for the reply, when I do just
let it run,
            I get the following
            error when I try to do trac-all -path –c
            dmrirc1_sim.txt

            I get the following error:

            ERROR: flag –c unrecognized

            -path –c dmrirc1_sim.txt


            Thanks,

            Jasmin 


            On Sun, May 22, 2016 at 1:51 AM,
    Anastasia Yendiki
            <ayend...@nmr.mgh.harvard.edu> wrote:

                  Hi Jasmin - Check if things are
running
            despite that error. Are
                  output files being generated?

                  a.y

                  On Sat, 21 May 2016, Jasmin Alves
wrote:


                        Dear Freesurfer,

                        While doing the bedpost step
for
            TRAC-all ( trac-all
                        -bedp -c
                        dmrirc1_sim.txt) I received
the
            following error:

                       
           
/Applications/freesurfer/bin/bedpostx_mgh: line 345:
                        kill: (51042) - No such
                        process

                        Any ideas?

                        Thank you,
                        Jasmin 

                        Jasmin AlvesPredoctoral
Student 
                        Medical Biology Graduate
Program 
                        University of Southern
California
                        jal...@usc.edu 



                 
           
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                  The information in this e-mail is
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            only for the person
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            to you in error
              

Re: [Freesurfer] DTI error

[Anastasia Yendiki]

These are output files from the -prep step. I'm asking about output files 
from the bedpost step, since that's where you're encountering the error.


https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputsfromtrac-all-bedp

What's in the dmri.bedpostX/ directory?

On Sun, 22 May 2016, Jasmin Alves wrote:


Output files are being generated, ie.
 1. dtifit_FA.nii.gz - Fractional Anisotropy
 2. dtifit_MD.nii.gz - Mean Diffusivity
 3. dtifit_MO.nii.gz - Mode of the Anisotropy
 4. dtifit_S0.nii.gz - Non-Diffusion weighted image
 5. dtifit_L1.nii.gz - Primary Eigenvalue
 6. dtifit_L2.nii.gz - Secondary Eigenvalue
 7. dtifit_L3.nii.gz - Tertiary Eigenvalue
 8. dtifit_V1.nii.gz - Primary Eigenvector
 9. dtifit_V2.nii.gz - Secondary Eigenvector
10. dtifit_V3.nii.gz - Tertiary Eigenvector
But it seems the bedpost process gets cut short and then,  the trac-all path
step won't work. I have ran it a few times and the bedpost step ends at the
same point. 


On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  But do you see the output files from the previous step? The
  outputs from each step are described on the wiki.

  On Sun, 22 May 2016, Jasmin Alves wrote:

Hi Anastasia,
Thank you for the reply, when I do just let it run,
I get the following
error when I try to do trac-all -path –c
dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin 


On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

      Hi Jasmin - Check if things are running
despite that error. Are
      output files being generated?

      a.y

      On Sat, 21 May 2016, Jasmin Alves wrote:


            Dear Freesurfer,

            While doing the bedpost step for
TRAC-all ( trac-all
            -bedp -c
            dmrirc1_sim.txt) I received the
following error:

           
/Applications/freesurfer/bin/bedpostx_mgh: line 345:
            kill: (51042) - No such
            process

            Any ideas?

            Thank you,
            Jasmin 

            Jasmin AlvesPredoctoral Student 
            Medical Biology Graduate Program 
            University of Southern California
            jal...@usc.edu 



     
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Re: [Freesurfer] DTI error

[Anastasia Yendiki]

But do you see the output files from the previous step? The outputs from 
each step are described on the wiki.


On Sun, 22 May 2016, Jasmin Alves wrote:


Hi Anastasia,
Thank you for the reply, when I do just let it run, I get the following
error when I try to do trac-all -path –c dmrirc1_sim.txt

I get the following error:

ERROR: flag –c unrecognized

-path –c dmrirc1_sim.txt


Thanks,

Jasmin 


On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Jasmin - Check if things are running despite that error. Are
  output files being generated?

  a.y

  On Sat, 21 May 2016, Jasmin Alves wrote:


Dear Freesurfer,

While doing the bedpost step for TRAC-all ( trac-all
-bedp -c
dmrirc1_sim.txt) I received the following error:

/Applications/freesurfer/bin/bedpostx_mgh: line 345:
kill: (51042) - No such
process

Any ideas?

Thank you,
Jasmin 

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 



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Re: [Freesurfer] DTI error

[Anastasia Yendiki]

Hi Jasmin - Check if things are running despite that error. Are output 
files being generated?


a.y

On Sat, 21 May 2016, Jasmin Alves wrote:



Dear Freesurfer,

While doing the bedpost step for TRAC-all ( trac-all -bedp -c
dmrirc1_sim.txt) I received the following error:

/Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such
process

Any ideas?

Thank you,
Jasmin 

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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Re: [Freesurfer] Mult-Shell Tracula Help

[Anastasia Yendiki]

Hi Kristina - You can enter nifti DWI volumes in the configuration file 
(or any other format that mri_convert can recognize). You should do the 
entire processing from scratch (including bedpost) using the concatenated 
data.

Best,
a.y

On Fri, 20 May 2016, Kristina Jelinkova wrote:

> Hi Anastasia,
>
> Thank you for your response. Yes, we have created the concatenated DWIs and 
> bvec/bval files that we have gotten after running each of the sequences 
> separately from trac-all. How can we run these concatenated nii.gz mages 
> through the ball-and-stick model fit (I'm assuming the configuration file 
> only looks for dcm images)? Would we also need to run bedpostX again 
> separately with the concatenated images?
>
> Thanks again for your help!
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki 
> <ayend...@nmr.mgh.harvard.edu>
> Sent: Friday, May 20, 2016 3:52:02 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Mult-Shell Tracula Help
>
> Hi Kristina - I'm assuming the 2 data sets were acquired in the same
> session and with the same acquisition parameters, other than the b-values?
> Then you can just concatenate the DWIs from the 2 runs (e.g. with
> mri_concat) and also concatenate the b-value and gradient vector tables
> (and make sure the 2 runs are concatenated in the same order for each type
> of file!)
>
> Best,
> a.y
>
> On Fri, 20 May 2016, Kristina Jelinkova wrote:
>
>>
>> Hello all,
>>
>>
>> I had a question regarding the program Tracula. I have two different DTI 
>> sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
>> am suppose to merge the two sequences together.
>>
>>
>> At this point, I have pre-processed each of the sequences separately using 
>> trac-all. Should I take each of the separate trac-all output
>> data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick 
>> model fit on the new bedpostX output? Also, is there a way  to use nii.gz
>> files in the configuration file rather than a dcm list?
>>
>>
>> Thank you in advance for your help!
>>
>>
>>
>
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Re: [Freesurfer] Mult-Shell Tracula Help

[Anastasia Yendiki]

Hi Kristina - I'm assuming the 2 data sets were acquired in the same 
session and with the same acquisition parameters, other than the b-values? 
Then you can just concatenate the DWIs from the 2 runs (e.g. with 
mri_concat) and also concatenate the b-value and gradient vector tables 
(and make sure the 2 runs are concatenated in the same order for each type 
of file!)


Best,
a.y

On Fri, 20 May 2016, Kristina Jelinkova wrote:



Hello all, 


I had a question regarding the program Tracula. I have two different DTI 
sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
am suppose to merge the two sequences together. 


At this point, I have pre-processed each of the sequences separately using 
trac-all. Should I take each of the separate trac-all output
data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick 
model fit on the new bedpostX output? Also, is there a way  to use nii.gz
files in the configuration file rather than a dcm list?


Thank you in advance for your help! 


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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - The FA values are extracted in the native space of each subject, 
which is why those are the only coordinates that you see. If you want to 
display the results of your analysis on an average path, after running 
trac-all -stat, you can use the stats/*.path.mean.txt files (see also the 
last part of the TRACULA tutorial).


Best,
a.y

On Wed, 18 May 2016, Anri WATANABE wrote:


Dear experts, 
I use TRACULA to examine a measure (FA) at each voxel in one pathway.
pathstats.byvoxel.txt files show coordinates in native space and after 
converting those the new files don't show any coordinates which are in MNI 
space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

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Re: [Freesurfer] trac-all problem

[Anastasia Yendiki]

Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files? 
What are the contents of that file?


a.y

On Fri, 6 May 2016, Zeng, Qi wrote:



Hi, 

I am running dti data with trac-all. I followed the command:

trac-all -prep -c /Studies/*/DTI/dmrirc_subject

but it exited with error "Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for 
that dimension." 


Before. there is another post about similar problem

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html

Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but 
new version wouldn't need this (5.3, a new version?). If so, where can I
 obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec?

Best, 

Qi 


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Re: [Freesurfer] Fwd: trac-all -path error

[Anastasia Yendiki]

Hi Elijah - Since the error occurs in the CST, is any of the brainstem cut 
off for this subject? It's hard to tell from the screenshot, but the field 
of view seems a bit cropped inferiorly.

Best,
a.y

On Thu, 5 May 2016, Elijah Mak wrote:

> Dear Anastasia Yendiki,
> I ran into a hitch while running trac-all -path and came across an identical 
> problem where there was a segmentation fault. I have attached my error and
> log files.
> 
> Loading initial proposal SD's from 
> /subject/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt
> 
> Processing pathway 2 of 18...
> 
> Initializing MCMC
> 
> I have also checked the aparc+aseg and aparc+aseg_mask (overlaid on FA; 
> screenshot attached) as you have suggested, but I can't seem to find anything
> that would have compromised the -path process.
> 
> What else could have gone wrong? trac-all -path works for other subjects.
> 
> Thanks for your help.
> 
> Best Wishes,
> Elijah
> 
> 
> 
>
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Re: [Freesurfer] Inquiry a single curve problem for Tracula outputs

[Anastasia Yendiki]

Hi Xiaofu - It's hard to tell but it looks like the brain mask (which 
comes from the structural data) is a bit too large in the temporal lobe, 
so it's possible that the structural-to-diffusion registration didn't go 
so well for this subject. You can check on this by overlaying the 
structural segmentation transformed into diffusion space (from 
dlabel/diff/aparc+aseg...) onto the FA map.


Best,
a.y

On Sun, 1 May 2016, Xiaofu wrote:


Dear Anastasia or Tracula-group,
   I have run Tracula and found there was only one single curve for some 
tracts. But others went well. I tried setting reinit parameter to 1 and
rerunning
"trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right 
UNC was a single curve (see attached). I also checked the two end point
set of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) (see attached) 
and found those end points were visually not correct when loaded to FA
image. I guess that may be the reason of the single curve problem. Is there 
anyway to fix this problem? Moreover, do you have any suggestions on the
tract statistics for those single curve tracts. I'd appreciate it if could take 
a look at it for me. If you need more files for the diagnosis please let
me know. 
  Looking forward to hearing from you. Thank you very much.

Best,
Xiaofu

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Re: [Freesurfer] Tracula Pathway reconstruction

[Anastasia Yendiki]

Hi Peggy - If it looks like a single path, it definitely is an 
initialization error. If you reinitialize repeatedly and it doesn't get 
fixed, it might be that something went wrong earlier in the processing 
(for example some part of brain that the tract goes through is missing 
from the brain mask).


Best,
a.y

On Mon, 25 Apr 2016, Peggy Skelly wrote:


Hi Tracula Experts,
How do you determine if a pathway reconstructed well? I've been examining the merged 
pathways (/dpath/merged_avg33_mni_bbr.mgz) in freeview, and
if the pathway looked too small when viewing with the default threshold, I 
would reinitialize those pathways. Most of the time, the new pathway would
look ok upon re-inspection. A few pathways, however, still appear too small 
when viewed at the default threshold in Freeview, but at lower thresholds,
they begin to look ok. 

I've encountered 1 pathway that still appears too small in Freeview, but the 
output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable.
On the other hand, its path distribution (path.pd.nii.gz) does not look like a 
distribution, but a single path -- there are a 38 voxels with values of
4000, and all others are 0. This doesn't seem right. What could cause this to 
happen?

What objective measure can I use to determine if a pathway is reconstructed 
well enough?

Thanks,
Peggy

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Re: [Freesurfer] bvals bvecs Error

[Anastasia Yendiki]

Hi Marissa - If your bvecs/bvals files are in row format, you need to make 
sure that you have the most recent update that supports this. It was a 
feature that was added later on:


http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Best,
a.y

On Fri, 15 Apr 2016, Marissa Pifer wrote:


Hi freesurfers,
I'm having a problem the bvals and bvecs for one of my subject's DTI data. When 
I try to run the first step of tracula I get this error message:

"Error: data and bvals/bvecs do not contain the same number of entries"

I have checked, the bvals and bvecs do contain the same amount of entries (42), 
and they are in the proper format (bvals one line, bvecs three lines).
The entries in the bvals/bvecs matches the number of images within the DTI file 
as well. Looking online, I saw that this was part of the FAQs on
tracula. It suggested making sure the locale settings were correct, which it is 
(en_US.UTF-8). 

I've run tracula on every other subject and have not run into this problem, but 
the same subject had an error with multiple frames when we were
processing the T2 images. Could this be related? Any idea about what is going 
on, or how I can fix it?

Thanks in advance,

Marissa

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Re: [Freesurfer] REPOST: TRACULA dev version: Error message

[Anastasia Yendiki]

Hi Elijah - Are the bvec/bval files located in the current directory from 
where you are running trac-all? This is where it seems to be looking for 
them:


cp 16084.bvec 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
cp 16084.bval 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

If they're in a different location, you need to specify the full path to 
that location, as shown in the sample configuration file.


Best,
a.y

On Fri, 15 Apr 2016, Elijah Mak wrote:


Hi Freesurfer,
Sorry about reposting this email from earlier:

I can't seem to get the TRACULA in the dev version of FS6 to run. 

mv -f 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs

mv: rename 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs to 
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such
file or directory

The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs 
dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms

The full error message is enclosed with this email.

Thanks!

Best Wishes,
Elijah



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Re: [Freesurfer] dt_recon image inputs -i flag

[Anastasia Yendiki]

Hi Bryan - It'll convert whatever input you give it to nifti, so it's fine 
if your input is already nifti.


Best,
a.y

On Wed, 6 Apr 2016, Chiu, Bryan (PHTH) wrote:


Hi,

I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI 
images in par/rec. I ran dcm2nii
and have retrieved the associated *bval, *bvec and *nii.gz files that come out.

In the tutorial it mentions the -i flag requiring a dcm image. Is it possible 
to pass a *.nii.gz file ?

Regards,

___
Bryan Chiu
Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia


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Re: [Freesurfer] Tracula problems (creating symbolic link)

[Anastasia Yendiki]

Hi Efrat - You could just use cp instead of ln -s. This will duplicate the 
file, instead of creating a link to it.


a.y

On Tue, 5 Apr 2016, Efrat Kliper wrote:



Dear Anastasia,

 

Thank you for the fast replay.

I have tried both suggestions, however it still reports:  Operation not 
supported

Also, I have used the links that you have sent me but non work. This time 
(after changing according to the
links), I got the message: operation denied


I don’t know how to resolve the issue of virtual machine, as not much is 
written about that and the links are
not helping with that issue.


Do you have other suggestions regarding how to change the script, so it will 
create the data.nii without the
symbolic link (there are plenty "ln" commands uses in the script)?


Many thanks,

Efrat


On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki 
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Efrat - This appears to be a virtual machine problem:

  https://communities.vmware.com/thread/312591?tstart=0

  There are some solutions suggested in that thread. I'm wondering if using 
a relative instead of an
  absolute path for the symlink works, i.e.,

  ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  instead of:

  ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
  /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  Can you please try it both ways and let me know if the former works on a 
computer where the latter
  doesn't?

  And yes, if you fix error #1 it'll fix error #2 as well.

  Thanks,
  a.y


  On Tue, 29 Mar 2016, Efrat Kliper wrote:


Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the 
preprocessing has already
been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64

 

 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message: ln -sf
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

 

ln: creating symbolic link 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation 
not
supported

 

2.  If I run the trac-all –bedp command of Tracula (on already 
trac-all data which
was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message:

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  
ProgramVersion: $Name:  $ 
TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014 
05:13:24 
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  
User: fsl  Machine:
localhost.localdomain  Platform: Linux  PlatformVersion:
2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 

Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

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 2016, Emad Ahmadi wrote:


Hi Anastasia,

I’ve attached the log files. The cases are:

1. Case #2; time points: 2a, 2b; base template: 2tem
2. Case #3; time points: 3a, 3b; base template: 3tem

Thank you again for your help,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu



On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 
wrote:


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 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 cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

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 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 cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula problems (creating symbolic link)

[Anastasia Yendiki]

Hi Efrat - This appears to be a virtual machine problem:

https://communities.vmware.com/thread/312591?tstart=0

There are some solutions suggested in that thread. I'm wondering if using 
a relative instead of an absolute path for the symlink works, i.e.,


ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

instead of:

ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

Can you please try it both ways and let me know if the former works on a 
computer where the latter doesn't?


And yes, if you fix error #1 it'll fix error #2 as well.

Thanks,
a.y


On Tue, 29 Mar 2016, Efrat Kliper wrote:



Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has 
already been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update 
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64

 

 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c 
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 
2009 x86_64 x86_64 x86_64 GNU/Linux

 

I am getting the following message: ln -sf 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz 
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

 

ln: creating symbolic link 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
supported

 

2.  If I run the trac-all –bedp command of Tracula (on already trac-all 
data which was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 
2009 x86_64 x86_64 x86_64 GNU/Linux

 

I am getting the following message:

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014 05:13:24 
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User: fsl  
Machine: localhost.localdomain  Platform: Linux  PlatformVersion:
2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $

ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013 22:46:06 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014 05:15:35 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014 05:15:35 
CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
22:46:06  CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
05:15:35  CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux  
PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  
$  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: 

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Anastasia Yendiki]

Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial 
diffusivity (RD) to help you interpret these results. These are the 
diffusivity parallel and perpendicular to the main budnle going through a 
voxel, respectively. Essentially, FA tells you how different the AD and RD 
are from each other, and MD tells you how big AD and RD are in aggregate.


Here are just a couple of all the possible scenarios that can lead to 
opposite FA/MD relationships:


AD increases, RD stays the same => MD increases, FA increases
AD stays the same, RD increases => MD increases, FA decreases

Hope this helps,

a.y

On Thu, 24 Mar 2016, Elijah Mak wrote:


Hi Freesurfer Community,
I recently used mri_segstats to extract FA and MD as suggested
here: http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001 

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah


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Re: [Freesurfer] Trac-all -path Segmentation error

[Anastasia Yendiki]

Hi Katherine - The dlabel/ directory is created during the -prep step, 
when the structural segmentation gets mapped from T1 to diffusion space. 
However bedpost may still run fine without the dlabel/ directory. It seems 
that the problem is fairly early in the -prep step. Any errors there?


Best,

a.y

On Wed, 23 Mar 2016, Katherine Damme wrote:


Hey Anastasia,


Although the bedpost appears to complete properly the dlabel/diff is not
being created during the bedp step. I am not sure how or why this error is
occurring. That would, it appears, definitely be the cause of the failure.
However, I am not getting an error during the prep or the bedpost stage, and
so I am still completely lost any advice would be deeply appreciated!

Thank you,

KD

On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

  Hi Katherine - Do the freesurfer segmentations look ok? What
  about the registration from structural to diffusion? You can
  inspect those quickly with:

  freeview dmri/dtifit_FA.nii.gz
  dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3

  Hope this helps,
  a.y

  On Sun, 3 Jan 2016, Katherine Damme wrote:

First I should note that using the same scripts I
completed 52 participants successfully and am
currently trying to
batch process the newest 42 participants that are
only failing at the path level. Upon Visual
Inspection they all
appear normal (with the exception of the one
attached). After carefully comparing a random sample
of 5 from each
group images from the files that failed versus the
files that were successful, I found:

1. The range of values in the mean_ph1samples in the
successful ( i.e. -3.00 to 87.30 ) differed from the
failures
(i.e. -2 to 17) (the successful samples varied on
their high end from 50-114 but the failures were on
the 5-24
range)
2. The range of values in the mean_th1samples in the
successful ( -0.02 to 19.12) differed from the
failures
(-0.00267 to 7.176) (the successful samples varied
on their high end from 19-17 but the failures were
on the 3-10
range)
3. Some, but not all (2/5), mean_S0samples, had a
abnormal range in successful (0 to 19998.4) compared
to the
unsuccessful (0 to 709.96)

However, I understand that the diffusion units are
likely arbitrary and not sure these patterns will
hold in a
larger sample.

I know this is a lot of confusing information and so
in response to your question. After an initial
inspection
there are two types of output:
1. data that appears visually normal with a slightly
altered range.
  Should I be concerned about the range if all other
data looks fine?

2. data that appears visually normal with a normal
range and bizarre merged files.
  What do you think could be a cause of these odd
merged files?




On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:

      Hi Katherine - Have you looked at any of the
intermediate images? Do they look normal?

      a.y

      On Mon, 21 Dec 2015, Katherine Damme wrote:

            Hello Everyone!

            It looks as though my prep and bedp
stages completed properly, but the prep stage ends
in a
            segmentation
            errror.

            See attached and let me know your
thoughts. I would prefer not to have to redo all
steps if
            possible!
            Thank you!




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Re: [Freesurfer] Tracula bedpostx error

[Anastasia Yendiki]

Hi Prad - I'm guessing the tutorial was generated with an earlier version 
of bedpostx, tracula, or a combination of both. So I wouldn't expect to 
find the exact same values. As long as things run and the files are 
generated, it looks like you're fine.

Best,

a.y

On Mon, 7 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:

> Hi Anastasia,
>
> Thank you for clarifying that. I have a follow up question.
>
> To avoid this error while running the ball and stick model fit( Syntax error: 
> "(" unexpected), I ran it locally using "bedpostx $path_to_dmri". 
>
> The results of the overall path statistics differ from those in the tutorial. 
> I've attached my results for the left ILF (pathstats.overall_redone.txt) and 
> the tutorial results (pathstats.overall_original.txt)
>
> Is this difference due to running them on different machines or is because I 
> had to run the bedpostx command directly ?
>
> Thanks!
> -Prad
> ___
>
> _
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki 
> <ayend...@nmr.mgh.harvard.edu>
> Sent: Monday, March 7, 2016 10:19 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula bedpostx error
>
> Hi Prad - What will affect the speed is whether you run it locally on your
> computer (in which case it'll process one slice after the other) or on a
> cluster (in which case all the slices will be processed in parallel on
> different nodes of the cluster). This is the case regardless of the
> version that you use.
>
> Best,
>
> a.y
>
> On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
>
>>
>>
>> Hello Anastasia,
>>
>> I have been trying to run through the tutorial with one of the subjects from 
>> the tutorial(elmo.2008) to familiarize myself with Tracula.
>> The preprocessing step seems to have been completed without any errors (Log 
>> file attached).However, when I proceed with the ball and stick model fit
>> step, I get the following error
>>
>> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
>> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: 
>> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu
>> 12.04 with FSL 5.0.9.
>>
>> In an earlier post where the same error was 
>> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
>>  you recommended
>> running bedpostx directly.
>>
>> Would this impact the results or run time in any way? and is there something 
>> I can do to fix this error if it is likely to take much longer?
>>
>>
>> Thanks!
>>
>> -Prad
>>
>>
>>
>>
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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

Anatorig will take you to freesurfer space. I's suggest smoothing these to 
make them more presentable, and potentially also thresholding them based 
on the probability map (which is the sum of these streamlines).

On Mon, 7 Mar 2016, Peled, Noam wrote:

> I want to display it in my new 3d visualization tool, along the hemispheres 
> and the subcortical regions.
> The hemispheres and the subcortical regions I import from freesurfer.
>
> Thanks,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:20 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> What to you want to display it on? If you want to display in on the FA
> map, or anything that's in diffusion space, you don't need any transform.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> So for plotting the fibers, like in freeview, should I just use the 
>> /dmri/xfms/diff2anatorig..mat or 
>> /dmri/xfms/diff2anat..mat transformation matrices?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, March 07, 2016 12:09 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Yes, native diffusion space.
>>
>> On Mon, 7 Mar 2016, Peled, Noam wrote:
>>
>>> Thanks!
>>> Do you in which space are the voxel coordinates coordinates? Are they in 
>>> the diffusion space?
>>>
>>> Thanks again,
>>> Noam
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>>> [ayend...@nmr.mgh.harvard.edu]
>>> Sent: Saturday, March 05, 2016 5:10 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] path.pd.trk format
>>>
>>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>>> path samples that are added up to created the probability distribution of
>>> the path. Please keep in mind, however, that this .trk file is just meant
>>> for generating stats and not for visualization, so these are not the usual
>>> smoothed kind of streamlines that you get from deterministic tractography.
>>> It contains only integer voxel coordinates, so the streamlines will look
>>> sort of like step ladders if you visualize them.
>>>
>>> Best,
>>>
>>> a.y
>>>
>>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>>
>>>> Hello,
>>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>>>> output directory.
>>>> How can I read this file? I would like to read the actual splines and not 
>>>> the probabilistic distribution in path.pd.nii.gz.
>>>>
>>>> Thanks,
>>>> Noam Peled
>>>>
>>>>
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>>>
>>>
>>>
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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

What to you want to display it on? If you want to display in on the FA 
map, or anything that's in diffusion space, you don't need any transform.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> So for plotting the fibers, like in freeview, should I just use the 
> /dmri/xfms/diff2anatorig..mat or 
> /dmri/xfms/diff2anat..mat transformation matrices?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:09 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Yes, native diffusion space.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> Thanks!
>> Do you in which space are the voxel coordinates coordinates? Are they in the 
>> diffusion space?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Saturday, March 05, 2016 5:10 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>> path samples that are added up to created the probability distribution of
>> the path. Please keep in mind, however, that this .trk file is just meant
>> for generating stats and not for visualization, so these are not the usual
>> smoothed kind of streamlines that you get from deterministic tractography.
>> It contains only integer voxel coordinates, so the streamlines will look
>> sort of like step ladders if you visualize them.
>>
>> Best,
>>
>> a.y
>>
>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>
>>> Hello,
>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>>> output directory.
>>> How can I read this file? I would like to read the actual splines and not 
>>> the probabilistic distribution in path.pd.nii.gz.
>>>
>>> Thanks,
>>> Noam Peled
>>>
>>>
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>>
>>
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Re: [Freesurfer] Tracula bedpostx error

[Anastasia Yendiki]

Hi Prad - What will affect the speed is whether you run it locally on your 
computer (in which case it'll process one slice after the other) or on a 
cluster (in which case all the slices will be processed in parallel on 
different nodes of the cluster). This is the case regardless of the 
version that you use.


Best,

a.y

On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:




Hello Anastasia,

I have been trying to run through the tutorial with one of the subjects from 
the tutorial(elmo.2008) to familiarize myself with Tracula.
The preprocessing step seems to have been completed without any errors (Log 
file attached).However, when I proceed with the ball and stick model fit
step, I get the following error

bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
/apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: 
"(" unexpected. I'm running the tutorial locally on Ubuntu
12.04 with FSL 5.0.9.

In an earlier post where the same error was 
encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
 you recommended
running bedpostx directly.

Would this impact the results or run time in any way? and is there something I 
can do to fix this error if it is likely to take much longer?


Thanks!

-Prad



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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

Yes, native diffusion space.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> Thanks!
> Do you in which space are the voxel coordinates coordinates? Are they in the 
> diffusion space?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Saturday, March 05, 2016 5:10 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Hi Noam - You can read the .trk file with trackvis. It contains all the
> path samples that are added up to created the probability distribution of
> the path. Please keep in mind, however, that this .trk file is just meant
> for generating stats and not for visualization, so these are not the usual
> smoothed kind of streamlines that you get from deterministic tractography.
> It contains only integer voxel coordinates, so the streamlines will look
> sort of like step ladders if you visualize them.
>
> Best,
>
> a.y
>
> On Tue, 16 Feb 2016, Peled, Noam wrote:
>
>> Hello,
>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>> output directory.
>> How can I read this file? I would like to read the actual splines and not 
>> the probabilistic distribution in path.pd.nii.gz.
>>
>> Thanks,
>> Noam Peled
>>
>>
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Re: [Freesurfer] TRACULA messy tracts

[Anastasia Yendiki]

Hi Jacek - I looked at the data that you uploaded. The problem is that 
both the b-value table and the gradient table that you were using were 
assuming that the b=0 images were interspersed throughout your scan, when 
in fact based on your dicoms they are all in the begining of the scan. So 
the 10 entries of 0.000 need to be in the beginning of the b-value table, 
not one every 7th image. Same with the gradient table. The gradient table 
also had some flipped coordinates that would cause a different problem 
down the line.


I was able to get the right tables by using mri_convert from the 
development version of freesurfer. The 5.3 version doesn't have the 
capability to read these tables from the dicoms but the 6.0 version will. 
In the meantime you can download the dev version and use mri_convert from 
that version.


Best,

a.y

On Sun, 14 Feb 2016, Jacek Manko wrote:



Dear Freesurfer experts,

 

I have also noticed something wrong with the tracts I reconctructed. There were 
no erroors during the processing, but when I visualized all tracts in
Freeview according to your command "freeview -tv 
my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say 
the least. Please
have a look at the attached image.

 

I have also notice abnormal volumes of these tracts in comparison to your 
elmo-subjects. For example the volume of left uncinate for your tutorial
subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy seems 
to coincide with with what you can spot in my screen, because it was my
first impression that these tracts are extremely large.

 

I run tracula with default commands as you stated in your tutorial, no major 
changes were made. If there is anything you could advise me, I will very
grateful. Are these results ok or I should udertake some steps? If you perhaps 
need some additional information I will be pleased to provide you with
that as well.

 

Cheers,

Jacek

 

 

Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):

  Dear Anastasia and Tracula users,
 
I succesfully ran the longitudinal Tracula procedure for one subject. However, 
when I visualized the tracts, they look a bit weird (not smooth).
Even if I played with the threshold on freeview, I couldn't make them look nice 
as in the wiki page. I checked the registration and it looks
accurate, so I am not sure what could be wrong. I am attaching the messy 
looking tracts for your reference.
 
Could you tell me if I should run again with reinit=1 for these tracts?
 
Thank you very much for your time.
Best regards,
 
 
--
D.





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