Ok, got it.

So for the first 3 steps (prep, bedp, and path) I included the base list.

Just for the stat I didn't.

I am sending one of the scripts that I used.

Gabriela

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

setenv SUBJECTS_DIR /fsrecon

set dtroot = /tracula/Output

set subjlist = (038_s2_170326 \ 038_s3_170702)

set baselist = (038 \ 038)

# In case you want to analyze only Huey and Louie

# Default: Run analysis on all time points and subjects

# set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)

# If original DICOMs don't exist, these can be in other image format

# but then bvecfile and bvalfile must be specified (see below)

set dcmroot = /raw_data

set dcmlist = (3LT038_s2_170326/MR.1.3.12.2.1107.5.2.43.67026.2017032618105239345859665 \ 3LT038_s3_170702/MR.1.3.12.2.1107.5.2.43.67026.2017070217300596695273345)

##### KEEP THE FOLLOWING UNCHANGED #####

# set nb0 = 10

# Perform registration-based B0-inhomogeneity compensation?

# Default: 0 (no)

# set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)

# Only used if dob0 = 1

# Default: None

# set b0mlist = ( huey/year1/fmag/XXX-1.dcm \

# huey/year2/fmag/XXX-1.dcm \

# dewey/year1/fmag/XXX-1.dcm \

# dewey/year2/fmag/XXX-1.dcm \

# louie/year1/fmag/XXX-1.dcm \

# louie/year2/fmag/XXX-1.dcm )

# Input B0 field map phase DICOMs (file names relative to dcmroot)

# Only used if dob0 = 1

# Default: None

# set b0plist = ( huey/year1/fphas/XXX-1.dcm \

# huey/year2/fphas/XXX-1.dcm \

# dewey/year1/fphas/XXX-1.dcm \

# dewey/year2/fphas/XXX-1.dcm \

# louie/year1/fphas/XXX-1.dcm \

# louie/year2/fphas/XXX-1.dcm )

# Echo spacing for field mapping sequence (from sequence printout)

# Only used if dob0 = 1

# Default: None

# set echospacing = 0.7

# Perform registration-based eddy-current compensation?

# Default: 1 (yes)

set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation?

# Only used if doeddy = 1

# Default: 1 (yes)

set dorotbvecs = 1

# Fractional intensity threshold for BET mask extraction from low-b images

# This mask is used only if usemaskanat = 0

# Default: 0.3

set thrbet = 0.5

# Perform diffusion-to-T1 registration by flirt?

# Default: 0 (no)

set doregflt = 0

# 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

# CVS template subject ID

# Only used if doregcvs = 1

# Default: cvs_avg35

# set cvstemp = donald

# Parent directory of the CVS template subject

# Only used if doregcvs = 1

# Default: $FREESURFER_HOME/subjects

# set cvstempdir = /path/to/cvs/atlases/of/ducks

# 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 )

# set pathlist = (lh.unc_AS \

# fmajor_PP \

# rh.atr_PP \

# lh.ccg_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)

# set ncpts = (5 7 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

2018-02-27 18:36 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

This how the program knows that you’re doing a longitudinal analysis. You need to include the list of base templates in the configuration file.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, February 27, 2018 at 6:33 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

No, in my -stat configuration file I just included the subject list (set subjlist).

I am sorry, I didn't understand your second question. Signals?

Thanks again, gabriela

2018-02-27 18:05 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

Hi Gabriela – When you ran trac-all -stat, did your configuration file include the baselist, which signals to trac-all that you’re running the longitudinal stream?

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 3:35 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

Yes, got it. But in these text files, the first line is already "#!ascii label, vox2ras=scanner".

It seems the problem is before the -stat step because I got many NaN in the group analysis. My impression is that the inter-subjects tracts are not well aligned. I also verified the registration:

1) dfifit_FA with MNI, that looks good;

2) merged_avg33_mni_bbr.mgz x dtifit_FA.nii.gz, that also looks good;

3) and then when I checked the merged_avg33_mni_bbr.mgz with MNI, it looks incorrect.

(I couldn't send the pictures due to the size of the email).

2018-02-23 15:26 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

Sorry – I meant freeview, not trackvis!

From: Anastasia <ayendiki@mgh.harvard.edu>
Date: Friday, February 23, 2018 at 2:11 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

So you may have been caught in that transition. The paths that you load into trackvis with the –w option are text files. Change the first line in those files to:

#!ascii label, vox2ras=scanner

When you do that and load the paths into freeview again, do they show up inside the brain?

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 1:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

thanks for your email.

I did the whole analysis in the developmental version, even the -stat.

Thanks, Gabriela

2018-02-23 13:21 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

Hi Gabriela – Any chance that you generated the paths with an older version of TRACULA, and viewed them in a newer version of freeview? There was a change in freeview at some point, in terms of the header that it expects those path files to have. This change happened between the 5.3 and 6.0 freesurfer releases, so if you ran TRACULA from the 5.3 release and used freeview from 6.0 or from a patched version that you downloaded in between 5.3 and 6.0, they may be incompatible. This would explain the outside the brain part. Now beyond that it seems that there's more strangeness going on, but let’s figure that part out first.

Thanks,

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 11:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA registration

Hi,

I processed some subjects in TRACULA for a longitudinal evaluation.

I registered all of them in the MNI template (set doregmni = 1

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz).

I checked the registration of my dtifit_FA.bbr.nii.gz with the MNI of all subjects.

However, when I performed the group analysis, I got more NaN than expected and I checked the images and the results are outside the MNI template (I am sending a picture).

I went back and checked the registration of the paths. Despite the dtifit_FA.bbr.nii.gz is correctly registered in the MNI, the paths aren't.

I am struggling here to find solutions. I really appreciate any insight to help me to solve this issue.

Thanks in advance,

Gabriela Longo

_______________________________________________
Freesurfer mailing list
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.

_______________________________________________
Freesurfer mailing list
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.

_______________________________________________
Freesurfer mailing list
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.

_______________________________________________
Freesurfer mailing list
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.