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: [email protected]
[[email protected]] on behalf of Anastasia Yendiki
[[email protected]]
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: [email protected]
> [[email protected]] on behalf of Anastasia Yendiki
> [[email protected]]
> 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: [email protected]
>> [[email protected]] on behalf of Anastasia Yendiki
>> [[email protected]]
>> 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
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> [email protected]
> 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.
>
>
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
#!/bin/tcsh
set workingDIR = "/data/blt/TRACULA"
set SUBJECTS_DIR = $workingDIR/diffusion_recons
setenv SUBJECTS_DIR $workingDIR/diffusion_recons
setenv FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
set dtroot = $workingDIR/tractography_output
set subjlist = ( BL01_1 \
BL01_2 )
set baselist= ( BL01_1 \
BL01_2 )
set dcmlist = ( $dcmroot/BL01_1.long.BL01_1/dmri/dwi.nii.gz \
$dcmroot/BL01_2.long.BL01_2/dmri/dwi.nii.gz )
set bveclist = (
/data/blt/TRACULA/tractography_output/BL01_1.long.BL01_1/dmri/bvecs \
/data/blt/TRACULA/tractography_output/BL01_2.long.BL01_2/dmri/bvecs )
set bvalfile =
/data/blt/TRACULA/tractography_output/BL01_1.long.BL01_1/dmri/bvals
# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 1
# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
set doregmni = 1
# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Perform registration of T1 to CVS template?
# Default: 0 (no)
#
set doregcvs = 0
# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
# Paths to reconstruct
# Default: All paths in the atlas
#
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.unc_AS rh.unc_AS \
lh.ilf_AS rh.ilf_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
# Number of path control points
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist
# Default: 7 for the forceps major, 6 for the corticospinal tract,
# 4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2
# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 200
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
#
set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0
_______________________________________________
Freesurfer mailing list
[email protected]
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.
