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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.commailto:gabrielalongo.radiologia@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, February 23, 2018 at 1:34 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.commailto:gabrielalongo.radiologia@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, February 23, 2018 at 11:25 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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

[Imagem inline 2]

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

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

[image: Imagem inline 2]

---

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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.

---

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.

Ok, thanks. Just sent the files.

2018-02-23 16:07 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

Hi – The tractography is performed in the individual diffusion space of each subject, so the merged tract volumes are in that space. That’s why they align with the original FA map, which is also computed in diffusion space. I’m guessing that the FA map that you’re referring to in 1) is one that has been transformed to MNI space. That one will not align with the individual tracts.

Maybe the best way to troubleshoot this is for you to upload a zip file with all the output directories from a single subject, as well as the stats directory that contains the mean paths. https://gate.nmr.mgh.harvard.edu/filedrop2/

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

[image: Imagem inline 2]

---

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.

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

[image: Imagem inline 2]

---

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.

---

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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.

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

[image: Imagem inline 2]

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Hi Anastasia,

the reason I didn't include the baselist at the -stat is because of I always have an ERROR message. I was trying again this morning, with different scripts including the baselist, but I didn't have success. Every time I include the baselist, I have the same error:

trac-all -stat -c dmrirc6

Too many )'s.

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon

INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev

ERROR: no pathway reconstructions found

Thanks again for the help, Gabriela

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

# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)

#

set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above)

#

set baselist = ( 3LT002 \ 3LT002 \ 3LT002 \ 3LT003 \ 3LT003 \ 3LT003 \ 3LT006 \ 3LT006 \ 3LT006 \ 3LT010 \ 3LT010 \ 3LT010 \ 3LT013 \ 3LT013 \ 3LT013 \ 3LT016 \ 3LT016 \ 3LT016 \ 3LT019 \ 3LT019 \ 3LT019 \ 3LT020 \ 3LT020 \ 3LT020 \ 3LT023 \ 3LT023 \ 3LT023 \ 3LT024 \ 3LT024 \ 3LT024 \ 3LT032 \ 3LT032 \ 3LT032 \ 3LT033 \ 3LT033 \ 3LT033 \ 3LT034 \ 3LT034 \ 3LT034 \ 3LT037 \ 3LT037 \ 3LT037 \ 3LT040 \ 3LT040 \ 3LT040 \ 3LT043 \ 3LT043 \ 3LT043 \ 3LT044 \ 3LT044 \ 3LT044 \ 3LT046 \ 3LT046 \ 3LT046 \ 3LT049 \ 3LT049 \ 3LT049 \ 3LT051 \ 3LT051 \ 3LT051 )

# 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 the gradient table and b-value table must be specified (see below)

#

set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.1107.5.2.43.67026.2015121713193168069764425 \

3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \

3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \

3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \

3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \

3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \

3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \

3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \

3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \

3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \

3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \

3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \

3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \

3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \

3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \

3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \

3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \

3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \

3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \

3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \

3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD.0032.0001.2016.12.13.17.51.00.574265.512114511.IMA \

3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \

3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \

3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \

3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \

3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2.1107.5.2.43.67026.2017030416172638234753390 \

3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \

3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \

3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \

3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.201712011834367925843035)

# Diffusion gradient tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# The tables must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bveclist = (/path/to/huey/year1/bvecs.txt \

/path/to/huey/year2/bvecs.txt \

/path/to/dewey/year1/bvecs.txt \

/path/to/dewey/year2/bvecs.txt \

/path/to/louie/year1/bvecs.txt \

/path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)

# Must be specified if it cannot be read from the DICOM headers

# The table must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvallist = (/path/to/huey/year1/bvals.txt \

/path/to/huey/year2/bvals.txt \

/path/to/dewey/year1/bvals.txt \

/path/to/dewey/year2/bvals.txt \

/path/to/louie/year1/bvals.txt \

/path/to/louie/year2/bvals.txt)

# Diffusion b-value table

# Must be specified if it cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-27 19:16 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

You need to include the baselist for all steps, including -stat.

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 7:13 PM

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

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

[image: Imagem inline 2]

---

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---

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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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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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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.

Thanks, I finally got to run the -stat with the baselist. However, the MNI space problem in the freeview persists....

2018-02-28 13:57 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

You only need a “\” when you want to continue the same command on the next line. You don’t need them between subject names that are on the same line.

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: Wednesday, February 28, 2018 at 11:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

the reason I didn't include the baselist at the -stat is because of I always have an ERROR message. I was trying again this morning, with different scripts including the baselist, but I didn't have success. Every time I include the baselist, I have the same error:

trac-all -stat -c dmrirc6

Too many )'s.

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon

INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev

ERROR: no pathway reconstructions found

Thanks again for the help, Gabriela

---

---

# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)

#

set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above)

#

set baselist = ( 3LT002 \ 3LT002 \ 3LT002 \ 3LT003 \ 3LT003 \ 3LT003 \ 3LT006 \ 3LT006 \ 3LT006 \ 3LT010 \ 3LT010 \ 3LT010 \ 3LT013 \ 3LT013 \ 3LT013 \ 3LT016 \ 3LT016 \ 3LT016 \ 3LT019 \ 3LT019 \ 3LT019 \ 3LT020 \ 3LT020 \ 3LT020 \ 3LT023 \ 3LT023 \ 3LT023 \ 3LT024 \ 3LT024 \ 3LT024 \ 3LT032 \ 3LT032 \ 3LT032 \ 3LT033 \ 3LT033 \ 3LT033 \ 3LT034 \ 3LT034 \ 3LT034 \ 3LT037 \ 3LT037 \ 3LT037 \ 3LT040 \ 3LT040 \ 3LT040 \ 3LT043 \ 3LT043 \ 3LT043 \ 3LT044 \ 3LT044 \ 3LT044 \ 3LT046 \ 3LT046 \ 3LT046 \ 3LT049 \ 3LT049 \ 3LT049 \ 3LT051 \ 3LT051 \ 3LT051 )

# 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 the gradient table and b-value table must be specified (see below)

#

set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.1107.5.2.43.67026.2015121713193168069764425 \

3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \

3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \

3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \

3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \

3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \

3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \

3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \

3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \

3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \

3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \

3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \

3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \

3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \

3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \

3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \

3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \

3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \

3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \

3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \

3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD. 0032.0001.2016.12.13.17.51.00.574265.512114511.IMA \

3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \

3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \

3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \

3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \

3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2. 1107.5.2.43.67026.2017030416172638234753390 \

3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \

3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \

3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \

3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.201712011834367925843035)

# Diffusion gradient tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# The tables must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bveclist = (/path/to/huey/year1/bvecs.txt \

            /path/to/huey/year2/bvecs.txt \

            /path/to/dewey/year1/bvecs.txt \

            /path/to/dewey/year2/bvecs.txt \

            /path/to/louie/year1/bvecs.txt \

            /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)

# Must be specified if it cannot be read from the DICOM headers

# The table must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvallist = (/path/to/huey/year1/bvals.txt \

            /path/to/huey/year2/bvals.txt \

            /path/to/dewey/year1/bvals.txt \

            /path/to/dewey/year2/bvals.txt \

            /path/to/louie/year1/bvals.txt \

            /path/to/louie/year2/bvals.txt)

# Diffusion b-value table

# Must be specified if it cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-27 19:16 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

...

You need to include the baselist for all steps, including -stat.

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 7:13 PM

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

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

[image: Imagem inline 2]

---

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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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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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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.

There is no stat.long directory, just stats.

This is the final script that worked (for some reason, it doesn't run without the "" in the subjlist - the error message pops up):

# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output/

# Subject IDs (one per time point per subject) # set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT002 3LT002 3LT002 3LT003 3LT003 3LT003 3LT006 3LT006 3LT006 3LT010 3LT010 3LT010 3LT013 3LT013 3LT013 3LT016 3LT016 3LT016 3LT019 3LT019 3LT019 3LT020 3LT020 3LT020 3LT023 3LT023 3LT023 3LT024 3LT024 3LT024 3LT032 3LT032 3LT032 3LT033 3LT033 3LT033 3LT034 3LT034 3LT034 3LT037 3LT037 3LT037 3LT040 3LT040 3LT040 3LT043 3LT043 3LT043 3LT044 3LT044 3LT044 3LT046 3LT046 3LT046 3LT049 3LT049 3LT049 3LT051 3LT051 3LT051 )

# 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 the gradient table and b-value table must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.1107.5.2.43.67026.2015121713193168069764425 \ 3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \ 3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \ 3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \ 3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \ 3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \ 3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \ 3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \ 3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \ 3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \ 3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \ 3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \ 3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \ 3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \ 3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \ 3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \ 3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \ 3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \ 3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \ 3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \ 3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD.0032.0001.2016.12.13.17.51.00.574265.512114511.IMA \ 3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \ 3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \ 3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \ 3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \ 3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2.1107.5.2.43.67026.2017030416172638234753390 \ 3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \ 3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \ 3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \ 3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.201712011834367925843035)

# Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = (/path/to/huey/year1/bvecs.txt \ /path/to/huey/year2/bvecs.txt \ /path/to/dewey/year1/bvecs.txt \ /path/to/dewey/year2/bvecs.txt \ /path/to/louie/year1/bvecs.txt \ /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans) # Must be specified if it cannot be read from the DICOM headers # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = (/path/to/huey/year1/bvals.txt \ /path/to/huey/year2/bvals.txt \ /path/to/dewey/year1/bvals.txt \ /path/to/dewey/year2/bvals.txt \ /path/to/louie/year1/bvals.txt \ /path/to/louie/year2/bvals.txt)

# Diffusion b-value table # Must be specified if it cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-28 14:41 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

Are you looking in the stats.long/ directory?

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: Wednesday, February 28, 2018 at 2:18 PM

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

Thanks, I finally got to run the -stat with the baselist. However, the MNI space problem in the freeview persists....

2018-02-28 13:57 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

...

You only need a “\” when you want to continue the same command on the next line. You don’t need them between subject names that are on the same line.

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: Wednesday, February 28, 2018 at 11:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

the reason I didn't include the baselist at the -stat is because of I always have an ERROR message. I was trying again this morning, with different scripts including the baselist, but I didn't have success. Every time I include the baselist, I have the same error:

trac-all -stat -c dmrirc6

Too many )'s.

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon

INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev

ERROR: no pathway reconstructions found

Thanks again for the help, Gabriela

---

---

# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)

#

set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above)

#

set baselist = ( 3LT002 \ 3LT002 \ 3LT002 \ 3LT003 \ 3LT003 \ 3LT003 \ 3LT006 \ 3LT006 \ 3LT006 \ 3LT010 \ 3LT010 \ 3LT010 \ 3LT013 \ 3LT013 \ 3LT013 \ 3LT016 \ 3LT016 \ 3LT016 \ 3LT019 \ 3LT019 \ 3LT019 \ 3LT020 \ 3LT020 \ 3LT020 \ 3LT023 \ 3LT023 \ 3LT023 \ 3LT024 \ 3LT024 \ 3LT024 \ 3LT032 \ 3LT032 \ 3LT032 \ 3LT033 \ 3LT033 \ 3LT033 \ 3LT034 \ 3LT034 \ 3LT034 \ 3LT037 \ 3LT037 \ 3LT037 \ 3LT040 \ 3LT040 \ 3LT040 \ 3LT043 \ 3LT043 \ 3LT043 \ 3LT044 \ 3LT044 \ 3LT044 \ 3LT046 \ 3LT046 \ 3LT046 \ 3LT049 \ 3LT049 \ 3LT049 \ 3LT051 \ 3LT051 \ 3LT051 )

# 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 the gradient table and b-value table must be specified (see below)

#

set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.11 07.5.2.43.67026.2015121713193168069764425 \

3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \

3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \

3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \

3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \

3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \

3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \

3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \

3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \

3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \

3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \

3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \

3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \

3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \

3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \

3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \

3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \

3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \

3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \

3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \

3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD.0032 .0001.2016.12.13.17.51.00.574265.512114511.IMA \

3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \

3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \

3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \

3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \

3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2.1 107.5.2.43.67026.2017030416172638234753390 \

3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \

3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \

3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \

3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.2017120118343 67925843035)

# Diffusion gradient tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# The tables must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bveclist = (/path/to/huey/year1/bvecs.txt \

            /path/to/huey/year2/bvecs.txt \

            /path/to/dewey/year1/bvecs.txt \

            /path/to/dewey/year2/bvecs.txt \

            /path/to/louie/year1/bvecs.txt \

            /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)

# Must be specified if it cannot be read from the DICOM headers

# The table must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvallist = (/path/to/huey/year1/bvals.txt \

            /path/to/huey/year2/bvals.txt \

            /path/to/dewey/year1/bvals.txt \

            /path/to/dewey/year2/bvals.txt \

            /path/to/louie/year1/bvals.txt \

            /path/to/louie/year2/bvals.txt)

# Diffusion b-value table

# Must be specified if it cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-27 19:16 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

...

You need to include the baselist for all steps, including -stat.

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 7:13 PM

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

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.1.3.12.2.1107.5.2.43.67026.2017070217300 596695273345)

##### 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 > > [image: Imagem inline 2] > > > _______________________________________________ > 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. > >

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Really sorry about this, but I still couldn't create the stats.long:

same script with baselist:

1) using: set baselist = ( 3LT002 \ 3LT002 \ 3LT002 \ 3LT003 \ 3LT003 \ 3LT003 \ 3LT006 \ 3LT006 \ 3LT006 \ 3LT010 \ 3LT010 \ 3LT010 \ 3LT013 \ 3LT013 \ 3LT013 \ 3LT016 \ 3LT016 \ 3LT016 \ 3LT019 \ 3LT019 \ 3LT019 \ 3LT020 \ 3LT020 \ 3LT020 \ 3LT023 \ 3LT023 \ 3LT023 \ 3LT024 \ 3LT024 \ 3LT024 \ 3LT032 \ 3LT032 \ 3LT032 \ 3LT033 \ 3LT033 \ 3LT033 \ 3LT034 \ 3LT034 \ 3LT034 \ 3LT037 \ 3LT037 \ 3LT037 \ 3LT040 \ 3LT040 \ 3LT040 \ 3LT043 \ 3LT043 \ 3LT043 \ 3LT044 \ 3LT044 \ 3LT044 \ 3LT046 \ 3LT046 \ 3LT046 \ 3LT049 \ 3LT049 \ 3LT049 \ 3LT051 \ 3LT051 \ 3LT051 )

*It generates a stats.long directory empty.*

2) using:

set baselist = ( 3LT002 3LT002 3LT002 3LT003 3LT003 3LT003 3LT006 3LT006 3LT006 3LT010 3LT010 3LT010 3LT013 3LT013 3LT013 3LT016 3LT016 3LT016 3LT019 3LT019 3LT019 3LT020 3LT020 3LT020 3LT023 3LT023 3LT023 3LT024 3LT024 3LT024 3LT032 3LT032 3LT032 3LT033 3LT033 3LT033 3LT034 3LT034 3LT034 3LT037 3LT037 3LT037 3LT040 3LT040 3LT040 3LT043 3LT043 3LT043 3LT044 3LT044 3LT044 3LT046 3LT046 3LT046 3LT049 3LT049 3LT049 3LT051 3LT051 3LT051 )

the error message pops up and the script doesn't run.

2018-02-28 15:59 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

You have to either not use “\” and put all the names in one line, or, if you’re going to put each name on a different line, use “\” at the end of the lines. It can’t read your baselist this way, that’s why there’s no stats.long.

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: Wednesday, February 28, 2018 at 3:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA registration

There is no stat.long directory, just stats.

This is the final script that worked (for some reason, it doesn't run without the "" in the subjlist - the error message pops up):

# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output/

# Subject IDs (one per time point per subject) # set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT002 3LT002 3LT002 3LT003 3LT003 3LT003 3LT006 3LT006 3LT006 3LT010 3LT010 3LT010 3LT013 3LT013 3LT013 3LT016 3LT016 3LT016 3LT019 3LT019 3LT019 3LT020 3LT020 3LT020 3LT023 3LT023 3LT023 3LT024 3LT024 3LT024 3LT032 3LT032 3LT032 3LT033 3LT033 3LT033 3LT034 3LT034 3LT034 3LT037 3LT037 3LT037 3LT040 3LT040 3LT040 3LT043 3LT043 3LT043 3LT044 3LT044 3LT044 3LT046 3LT046 3LT046 3LT049 3LT049 3LT049 3LT051 3LT051 3LT051 )

# 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 the gradient table and b-value table must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.1107.5.2.43.67026.2015121713193168069764425 \ 3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \ 3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \ 3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \ 3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \ 3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \ 3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \ 3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \ 3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \ 3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \ 3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \ 3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \ 3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \ 3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \ 3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \ 3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \ 3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \ 3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \ 3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \ 3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \ 3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD. 0032.0001.2016.12.13.17.51.00.574265.512114511.IMA \ 3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \ 3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \ 3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \ 3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \ 3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2. 1107.5.2.43.67026.2017030416172638234753390 \ 3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \ 3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \ 3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \ 3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.201712011834367925843035)

# Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = (/path/to/huey/year1/bvecs.txt \ /path/to/huey/year2/bvecs.txt \ /path/to/dewey/year1/bvecs.txt \ /path/to/dewey/year2/bvecs.txt \ /path/to/louie/year1/bvecs.txt \ /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans) # Must be specified if it cannot be read from the DICOM headers # The table must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = (/path/to/huey/year1/bvals.txt \ /path/to/huey/year2/bvals.txt \ /path/to/dewey/year1/bvals.txt \ /path/to/dewey/year2/bvals.txt \ /path/to/louie/year1/bvals.txt \ /path/to/louie/year2/bvals.txt)

# Diffusion b-value table # Must be specified if it cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-28 14:41 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

...

Are you looking in the stats.long/ directory?

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: Wednesday, February 28, 2018 at 2:18 PM

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

Thanks, I finally got to run the -stat with the baselist. However, the MNI space problem in the freeview persists....

2018-02-28 13:57 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu:

...

You only need a “\” when you want to continue the same command on the next line. You don’t need them between subject names that are on the same line.

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: Wednesday, February 28, 2018 at 11:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

the reason I didn't include the baselist at the -stat is because of I always have an ERROR message. I was trying again this morning, with different scripts including the baselist, but I didn't have success. Every time I include the baselist, I have the same error:

trac-all -stat -c dmrirc6

Too many )'s.

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon

INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev

ERROR: no pathway reconstructions found

Thanks again for the help, Gabriela

---

---

# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here

#

setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved

# Default: Same as SUBJECTS_DIR

#

set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject)

#

set subjlist = ( 3LT002_s1_151217.long.3LT002 \ 3LT002_s2_151231.long.3LT002 \ 3LT002_s3_160419.long.3LT002 \ 3LT003_s1_151225.long.3LT003 \ 3LT003_s2_160109.long.3LT003 \ 3LT003_s3_160410.long.3LT003 \ 3LT006_s1_160116.long.3LT006 \ 3LT006_s2_160130.long.3LT006 \ 3LT006_s3_160527.long.3LT006 \ 3LT010_s1_160323.long.3LT010 \ 3LT010_s2_160424.long.3LT010 \ 3LT010_s3_160706.long.3LT010 \ 3LT013_s1_160524.long.3LT013 \ 3LT013_s2_160605.long.3LT013 \ 3LT013_s3_160903.long.3LT013 \ 3LT016_s1_160605.long.3LT016 \ 3LT016_s2_160619.long.3LT016 \ 3LT016_s3_160903.long.3LT016 \ 3LT019_s1_160616.long.3LT019 \ 3LT019_s2_160630.long.3LT019 \ 3LT019_s3_160926.long.3LT019 \ 3LT020_s1_160716.long.3LT020 \ 3LT020_s2_160730.long.3LT020 \ 3LT020_s3_161009.long.3LT020 \ 3LT023_s1_160817.long.3LT023 \ 3LT023_s2_160904.long.3LT023 \ 3LT023_s3_161115.long.3LT023 \ 3LT024_s1_160824.long.3LT024 \ 3LT024_s2_160918.long.3LT024 \ 3LT024_s3_170409.long.3LT024 \ 3LT032_s1_161210.long.3LT032 \ 3LT032_s2_161223.long.3LT032 \ 3LT032_s3_170319.long.3LT032 \ 3LT033_s1_161213.long.3LT033 \ 3LT033_s2_161222.long.3LT033 \ 3LT033_s3_170311.long.3LT033 \ 3LT034_s1_170107.long.3LT034 \ 3LT034_s2_170115.long.3LT034 \ 3LT034_s3_170409.long.3LT034 \ 3LT037_s1_170304.long.3LT037 \ 3LT037_s2_170311.long.3LT037 \ 3LT037_s3_170606.long.3LT037 \ 3LT040_s1_170422.long.3LT040 \ 3LT040_s2_170504.long.3LT040 \ 3LT040_s3_170728.long.3LT040 \ 3LT043_s1_170520.long.3LT043 \ 3LT043_s2_170715.long.3LT043 \ 3LT043_s3_170829.long.3LT043 \ 3LT044_s1_170526.long.3LT044 \ 3LT044_s2_170607.long.3LT044 \ 3LT044_s3_170822.long.3LT044 \ 3LT046_s1_170609.long.3LT046 \ 3LT046_s2_170620.long.3LT046 \ 3LT046_s3_170929.long.3LT046 \ 3LT049_s1_170705.long.3LT049 \ 3LT049_s2_170723.long.3LT049 \ 3LT049_s3_171012.long.3LT049 \ 3LT051_s1_170816.long.3LT051 \ 3LT051_s2_170830.long.3LT051 \ 3LT051_s3_171201.long.3LT051 )

# Longitudinal base template subject IDs (one for each time point above)

#

set baselist = ( 3LT002 \ 3LT002 \ 3LT002 \ 3LT003 \ 3LT003 \ 3LT003 \ 3LT006 \ 3LT006 \ 3LT006 \ 3LT010 \ 3LT010 \ 3LT010 \ 3LT013 \ 3LT013 \ 3LT013 \ 3LT016 \ 3LT016 \ 3LT016 \ 3LT019 \ 3LT019 \ 3LT019 \ 3LT020 \ 3LT020 \ 3LT020 \ 3LT023 \ 3LT023 \ 3LT023 \ 3LT024 \ 3LT024 \ 3LT024 \ 3LT032 \ 3LT032 \ 3LT032 \ 3LT033 \ 3LT033 \ 3LT033 \ 3LT034 \ 3LT034 \ 3LT034 \ 3LT037 \ 3LT037 \ 3LT037 \ 3LT040 \ 3LT040 \ 3LT040 \ 3LT043 \ 3LT043 \ 3LT043 \ 3LT044 \ 3LT044 \ 3LT044 \ 3LT046 \ 3LT046 \ 3LT046 \ 3LT049 \ 3LT049 \ 3LT049 \ 3LT051 \ 3LT051 \ 3LT051 )

# 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 the gradient table and b-value table must be specified (see below)

#

set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data

set dcmlist = ( LT002_s1_151217/MR.1.3.12.2.11 07.5.2.43.67026.2015121713193168069764425 \

3LT002_s2_151231/MR.1.3.12.2.1107.5.2.43.67026.2015123111065360071202663 \

3LT002_s3_160419/MR.1.3.12.2.1107.5.2.43.67026.2016041918170979479231584 \ 3LT003_s1_151225/MR.1.3.12.2.1107.5.2.43.67026.2015122515384641207462486 \

3LT003_s2_160109/MR.1.3.12.2.1107.5.2.43.67026.201601091604145183451399 \

3LT003_s3_160410/MR.1.3.12.2.1107.5.2.43.67026.2016041016353563431992287 \ 3LT010_s1_160323/MR.1.3.12.2.1107.5.2.43.67026.2016032317352671496105301 \

3LT010_s2_160424/MR.1.3.12.2.1107.5.2.43.67026.2016042416265149395486511 \

3LT010_s3_160706/MR.1.3.12.2.1107.5.2.43.67026.2016070619223814540052652 \ 3LT013_s1_160524/MR.1.3.12.2.1107.5.2.43.67026.2016052418555023973692111 \

3LT013_s2_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060517014531268804822 \

3LT013_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.2016090313413840902231149 \ 3LT016_s1_160605/MR.1.3.12.2.1107.5.2.43.67026.2016060515362278064666044 \

3LT016_s2_160619/MR.1.3.12.2.1107.5.2.43.67026.2016061917305247726130238 \

3LT016_s3_160903/MR.1.3.12.2.1107.5.2.43.67026.30000016090316002555900004015 \ 3LT019_s1_160616/MR.1.3.12.2.1107.5.2.43.67026.2016061618520597113969031 \

3LT019_s2_160630/MR.1.3.12.2.1107.5.2.43.67026.2016063015480110096022089 \

3LT019_s3_160926/MR.1.3.12.2.1107.5.2.43.67026.201609262043291976670285 \ 3LT020_s1_160716/MR.1.3.12.2.1107.5.2.43.67026.2016071616440062644096 \

3LT020_s2_160730/MR.1.3.12.2.1107.5.2.43.67026.2016073011201234691831980 \

3LT020_s3_161009/MR.1.3.12.2.1107.5.2.43.67026.2016100913272059880867043 \ 3LT023_s1_160817/MR.1.3.12.2.1107.5.2.43.67026.2016081711053611293538565 \

3LT023_s2_160904/MR.1.3.12.2.1107.5.2.43.67026.2016090410420327398821461 \

3LT023_s3_161115/MR.1.3.12.2.1107.5.2.43.67026.2016111522004175923345684 \ 3LT024_s1_160824/MR.1.3.12.2.1107.5.2.43.67026.2016082419242493546003846 \

3LT024_s2_160918/MR.1.3.12.2.1107.5.2.43.67026.2016091820020855929243396 \

3LT024_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040913341226655113621 \ 3LT032_s1_161210/MR.1.3.12.2.1107.5.2.43.67026.201612101228231339603153 \

3LT032_s2_161223/MR.1.3.12.2.1107.5.2.43.67026.2016122318000387030682717 \

3LT032_s3_170319/MR.1.3.12.2.1107.5.2.43.67026.2017031911202465140782311 \ 3LT033_s1_161213/3LT033_S1_161213.MR.INVESTIGATORS_EMAD.0032 .0001.2016.12.13.17.51.00.574265.512114511.IMA \

3LT033_s2_161222/MR.1.3.12.2.1107.5.2.43.67026.2016122215310361252246399 \

3LT033_s3_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031109523425116628157 \ 3LT034_s1_170107/MR.1.3.12.2.1107.5.2.43.67026.201701071232495112831391 \

3LT034_s2_170115/MR.1.3.12.2.1107.5.2.43.67026.2017011511420054721827909 \

3LT034_s3_170409/MR.1.3.12.2.1107.5.2.43.67026.2017040911232114239329831 <(423)%20932-9831> \ 3LT006_s1_160116/IM-0003-0008.dcm \ 3LT006_s2_160130/IM-0031-0001.dcm \

3LT006_s3_160527/IM-0098-0001.dcm \ 3LT037_s1_170304/MR.1.3.12.2.1 107.5.2.43.67026.2017030416172638234753390 \

3LT037_s2_170311/MR.1.3.12.2.1107.5.2.43.67026.2017031112153124569418632 \

3LT037_s3_170606/MR.1.3.12.2.1107.5.2.43.67026.2017060614202730087254421 \ 3LT040_s1_170422/MR.1.3.12.2.1107.5.2.43.67026.2017042219555513983971539 \

3LT040_s2_170504/MR.1.3.12.2.1107.5.2.43.67026.201705042316493645479250 \

3LT040_s3_170728/MR.1.3.12.2.1107.5.2.43.67026.2017072820561984616039079 \ 3LT043_s1_170520/MR.1.3.12.2.1107.5.2.43.67026.2017052010245552753124131 \ 3LT043_s2_170715/MR.1.3.12.2.1107.5.2.43.67026.2017071512275943314046998 \ 3LT043_s3_170829/MR.1.3.12.2.1107.5.2.43.67026.2017082914284643399903578 \ 3LT044_s1_170526/MR.1.3.12.2.1107.5.2.43.67026.2017052609445145325359209 \ 3LT044_s2_170607/MR.1.3.12.2.1107.5.2.43.67026.30000017072900205929400004857 \ 3LT044_s3_170822/MR.1.3.12.2.1107.5.2.43.67026.2017082216405998282389824 \ 3LT046_s1_170609/MR.1.3.12.2.1107.5.2.43.67026.2017060916422453865256023 \ 3LT046_s2_170620/MR.1.3.12.2.1107.5.2.43.67026.201706201421572485725883 \ 3LT046_s3_170929/MR.1.3.12.2.1107.5.2.43.67026.2017092916223220231137852 \ 3LT049_s1_170705/MR.1.3.12.2.1107.5.2.43.67026.2017070511412866743409142 \ 3LT049_s2_170723/MR.1.3.12.2.1107.5.2.43.67026.2017072313051737632893439 \ 3LT049_s3_171012/MR.1.3.12.2.1107.5.2.43.67026.2017101208354350820531536 \ 3LT051_s1_170816/MR.1.3.12.2.1107.5.2.43.67026.2017081617314838285379481 \ 3LT051_s2_170830/MR.1.3.12.2.1107.5.2.43.67026.2017083017410816564658249 \ 3LT051_s3_171201/MR.1.3.12.2.1107.5.2.43.67026.2017120118343 67925843035)

# Diffusion gradient tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# The tables must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bveclist = (/path/to/huey/year1/bvecs.txt \

            /path/to/huey/year2/bvecs.txt \

            /path/to/dewey/year1/bvecs.txt \

            /path/to/dewey/year2/bvecs.txt \

            /path/to/louie/year1/bvecs.txt \

            /path/to/louie/year2/bvecs.txt)

# Diffusion gradient table (if using the same one for all scans)

# Must be specified if it cannot be read from the DICOM headers

# The table must have either three columns, where each row is a gradient vector

# or three rows, where each column is a gradient vector

# There must be as many gradient vectors as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan)

# Must be specified if they cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvallist = (/path/to/huey/year1/bvals.txt \

            /path/to/huey/year2/bvals.txt \

            /path/to/dewey/year1/bvals.txt \

            /path/to/dewey/year2/bvals.txt \

            /path/to/louie/year1/bvals.txt \

            /path/to/louie/year2/bvals.txt)

# Diffusion b-value table

# Must be specified if it cannot be read from the DICOM headers

# There must be as many b-values as volumes in the diffusion data set

# Default: Read from DICOM header

# set bvalfile = /path/to/bvals.txt

# 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 = /path/to/mni_template.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 )

# 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

2018-02-27 19:16 GMT-05:00 Yendiki, Anastasia AYENDIKI@mgh.harvard.edu :

...

You need to include the baselist for all steps, including -stat.

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 7:13 PM

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

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.1.3.12.2.1107.5.2.43.67026.2017070217300 596695273345)

##### 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.ed >> u> >> 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 >> >> [image: Imagem inline 2] >> >> >> _______________________________________________ >> 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. > >

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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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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.