Re: [Freesurfer] TRACULA GLM output question

[Douglas N. Greve]

The easiest thing is to set up contrasts to pull out the parameters you 
want. The next easiest (or maybe the easiest) is to look in the beta 
file. It will have a frame for each column in the design matrix. The 
value is the regression coefficient.


On 3/5/2024 11:33 AM, Hoskinson, Kristen wrote:


External Email - Use Caution

We’re working on a project where we ran 3 groups, 1 covariate, and ran 
a glm looking at white matter at cross-sections from TRACULA output, 
covarying for functional activation. We’re now wanting to plot out the 
interaction/slopes per group, but are having trouble locating the data 
that would allow that step.  Could anyone direct us?


Thank you!

--

*Kristen R. Hoskinson, Ph.D. *(she/her)

Associate Professor of Pediatrics

The Ohio State University College of Medicine

Principal Investigator, /Social Cognition, Adjustment, and 
Neurodevelopment (SCAN) Lab/


Center for Biobehavioral Health

The Abigail Wexner Research Institute at Nationwide Children's Hospital

700 Children's Drive
Columbus, Ohio  43205

(614) 722-3021

kristen.hoskin...@nationwidechildrens.org 




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[Freesurfer] TRACULA GLM output question

[Hoskinson, Kristen]

External Email - Use Caution

We’re working on a project where we ran 3 groups, 1 covariate, and ran a glm 
looking at white matter at cross-sections from TRACULA output, covarying for 
functional activation. We’re now wanting to plot out the interaction/slopes per 
group, but are having trouble locating the data that would allow that step.  
Could anyone direct us?

Thank you!

--
Kristen R. Hoskinson, Ph.D. (she/her)
Associate Professor of Pediatrics
The Ohio State University College of Medicine
Principal Investigator, Social Cognition, Adjustment, and Neurodevelopment 
(SCAN) Lab
Center for Biobehavioral Health
The Abigail Wexner Research Institute at Nationwide Children's Hospital
700 Children's Drive
Columbus, Ohio  43205
(614) 722-3021
kristen.hoskin...@nationwidechildrens.org

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[Freesurfer] [TRACULA] how to setup with opposite phase-encoding

[Fahad Hannan]

External Email - Use Caution

Hi,

I've been trying to use TRACULA on my data, trying to setup a configuration 
file but I am having some difficulty on how to incorporate my data.

I have a DWI scan with 65 volumes (1 b0 image, 64 with b = 1000)
I also have separate volumes for b0 pairs having opposite phase-encoding 
directions.

I am not sure how to incorporate these into the configuration file. I can do it 
with using just the one b0 image, but I'd like to use the opposite 
phase-encoding as well.

How would I go about this in the configuration file?

Thanks,
Fahad Hannan
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[Freesurfer] tracula using FS 7.2

[Alexopoulos, Dimitrios]

External Email - Use Caution

We'd like to use FS7.2 to generate hi-re surfaces on 0.8mm data on 6yo subject. 
However, we'd like to be able to generate the white matter tracts that are 
produced with older versions (specifically 6.0), not the new 42 tracts with 7.2.

Can a FS 6.0 dmrirc config file be used with 7.2 to get the WM tracts generated 
 from the older tracula versions?

Jim



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[Freesurfer] TRACULA error: lowb_brain_mask.bbr.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi FreeSurfers,

I am attempting to run tracula on longitudinal DTI data however during trac-all 
-prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz 
from mri_concat.


#-

/Applications/freesurfer/7.3.2/bin/trac-preproc

#-

#@# Intra-subject registration (base template) Mon Nov 13 14:13:56 PST 2023

mri_concat --i 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/aparc+aseg_mask.nii.gz
 --min --o 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz

ninputs = 1

Checking inputs

nframestot = 1

Allocing output

Done allocing

nframes = 1

Computing min across all frames

Writing to 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz

mri_concat --i 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz
 --min --o 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

ninputs = 1

Checking inputs

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

ERROR: reading 
/Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz

Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed 
Oct  4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Nov 13 14:13:58 PST 2023


I am using FreeSurfer 7.3.2 on an iMac Pro running Ventura 13.6.1.


Any suggestions for how to clear this error would be greatly appreciated!


Thank you,


Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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[Freesurfer] TRACULA Stat error: no pathway reconstructions found

[Lauren Stephens]

External Email - Use Caution

Hi FreeSurfers,

I have successfully run trac-all -prep, -bedp, and -path on all of my files.  
However on two of my files when i ran trac-all -stat -c 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R007A/R007A.txt  and trac-all -stat 
-c on /Users/corpuscallosum/Desktop/TRACULA/RRD/R006B/R006B.txt I got the 
errors: no pathway reconstructions found.

For both files I went to dpath and they both have the correct information and 
files present.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  The log files 
were too large to attach to this email.

Any suggestions for getting the stats files extracted?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi Woo-Suk,

The change you suggested did work when i made a second attempt.  The files were 
getting mixed in with the trac-preproc copy I created in case of errors.

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Woo-Suk Tae 

Sent: Monday, October 30, 2023 8:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you 
corrected?

best regards

Woo-Suk, Tae

On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi Woo-Suk,

I was able to make the change however, I am still receiving the same error.


mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

reading from 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

Darwin 
PSYC-C02DP05D0833.stanford.edu<http://secure-web.cisco.com/1hfiYFGQhzjFVnZavl-fTMAJOa_JE9bzjVA8nrzYF3yRbWe4VzGqfDesdrYhWYxOR5nsphpAwt1gyWvjHUHQdWEiA9qbrEWmQFdrmnEbo5BDDYjQ6O-KnWv9c1QD7bhdcX5EzX6HzbBIFX0ir6HvpcK-2VMbNvy-cC26PgUPAXxjO_gI43uMjUhPyKeIEY1j_k9KKcxCGxdVYQrCLxLSs0xrHxxEIjtuNcmEEMkiviG30UZwoYYCAL2B9dYpccBFZ_PcMy-xXHxsefxUDMgA-ehOWri2bOrXsubbsWH6K3u6VLMCziEZcNfVMRF2yYF4_/http%3A%2F%2FPSYC-C02DP05D0833.stanford.edu>
 22.6.0 Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; 
root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023

Do you have any further suggestions to fix this issue?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Woo-Suk Tae mailto:woos...@gmail.com>>
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can 
get  an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic 
nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medic

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Woo-Suk Tae]

External Email - Use Caution

Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file,
you corrected?

best regards

Woo-Suk, Tae

On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens 
wrote:

> External Email - Use Caution
>
> Hi Woo-Suk,
>
> I was able to make the change however, I am still receiving the same
> error.
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
>
> reading from
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...
>
> error: niiRead(): error opening file
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
>
> Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version
> 22.6.0: Fri Sep 15 13:39:52 PDT 2023;
> root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023
>
> Do you have any further suggestions to fix this issue?
>
> Thank you,
>
> Lauren Stephens
>
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae <
> woos...@gmail.com>
> *Sent:* Saturday, October 28, 2023 10:34 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation
> aparc+aseg+thalnuc.nii.gz
>
>
> External Email - Use Caution
>
> Hi, Lauren Stephens.
> If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
> can get  an aparc+aseg+thalnuc.nii.gz file without error, and make
> subthalamic nuclei related tracks.
>
> #chage codes from
> set cmd = mri_binarize
> set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
> set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)
>
> #to
> set cmd = mri_convert
> set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
> set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)
>
> Woo-Suk, Tae Ph.D.
> Seoul, Korea
>
> On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
> wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfers,
>
> I am trying to troubleshoot an error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The
> subregion segmentation prior to trac-all -prep was successful and 
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated.  In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
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> &

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi Woo-Suk,

I was able to make the change however, I am still receiving the same error.


mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

mri_convert -at 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
 -rt nearest 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

reading from 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...

error: niiRead(): error opening file 
/Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Fri 
Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023

Do you have any further suggestions to fix this issue?

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Woo-Suk Tae 

Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can 
get  an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic 
nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716

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--


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr<mailto:ws...@korea.ac.kr>, 
woo

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Woo-Suk Tae]

External Email - Use Caution

Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get  an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.

#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.
Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens 
wrote:

> External Email - Use Caution
>
> Hi FreeSurfers,
>
> I am trying to troubleshoot an error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The
> subregion segmentation prior to trac-all -prep was successful and 
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated.  In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
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>


-- 


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
  wo os...@gmail.com

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Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

[Lauren Stephens]

External Email - Use Caution

Hi FreeSurfers,

I wanted to follow up on my post.  I am still receiving this error when running 
the preprocessing step of TRACULA.  We have run our files without the thalamic 
nuclei included, however, that is not ideal because we are interested in tracts 
that end nearby.

I believe this is a bug in the code because otherwise the following TRACULA 
steps run all the way through with no error.

If you have any suggests we would really appreciate it!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lauren Stephens 

Sent: Friday, October 6, 2023 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA Error: Subregion Segmentation 
aparc+aseg+thalnuc.nii.gz


External Email - Use Caution

Hi FreeSurfers,

I am trying to troubleshoot an error during TRACULA preprocessing and the issue 
seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion 
segmentation prior to trac-all -prep was successful and 
mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were 
generated.  In the archives I saw two others have experienced a similar issue 
without a resolution in the thread.

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached 
the log file, log error, and my configuration file.

Any help would be greatly appreciated!

Thank you,

Lauren Stephens


Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

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[Freesurfer] Tracula -bedp and -prep exited with errors

[Ramtilak Gattu]

External Email - Use Caution

Hello,

The following command

trac-all -c dmrirc.example -bedp

always exits with the following error.

{

WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 
/home/developer/Desktop/DATA_VB/Data/TRACULA/trc/Sub_01/dmri
/usr/local/freesurfer/7.4.1/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/7.4.1/freesurfer/bin/bedpostx_mgh: Syntax error: "(" 
unexpected

}

The processing doesn't even get started. It exits immediately

I tried freesurfer 7.2 and 7.4.1 versions on virtual box thinking there might 
be some problem with the bedpostx_mgh source code. But it does the same with 
both the versions.

Trac-all with -prep argument runs for a while and exited with

{

Pre-sorted training .trk file detected
INFO: Rejected 114 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
INFO: Have 19886 total streamlines (min/mean/max length: 60/88/115)
Processing pathway 29 of 42...
INFO: Have 19886 non-truncated streamlines (min/mean/max length: 60/88/115)
Computing path histograms
INFO: Total streamline volume is 25477 voxels
Finding outlier streamlines
Updating streamline distance ranking
INFO: Split streamlines into 25 segments
Computing prior on underlying anatomy (all streamlines)
Killed
Linux developer-VirtualBox 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Jul 26 18:08:00 EDT 2023

}

-Prep getting killed because of insufficient memory??


Can someone please help.

Thanks

Regards
Tilak
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Re: [Freesurfer] Tracula statistics outputs for version 7.2

[Alan Francis]

External Email - Use Caution

Hi Chiara -

Please ignore the previous email. I set my doB0 = 0, but it gives me this
error message:

copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_4
ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for model-based eddy-current distortion correction,
ERROR: must specify PE direction

Where does one get details of the phase encoding direction?

Thanks,

Alan


On Tue, Jul 18, 2023 at 1:24 PM Maffei, Chiara,PHD 
wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> It looks like you have specified the ncpts variable but not the pathlist.
> If you do not specify pathlist, TRACULA will include all 42 tracts by
> default, so your pathlist and ncpts variables will have different lengths.
>
> If you want to focus your analysis on a subset of tracts, specify those
> using pathlist (e.g., set pathlist = (rh.uf lh.uf)). If not, do not specify
> ncpts either (comment out or remove line 59 from your config file) and
> TRACULA will reconstruct all 42 tracts.
>
> I also noticed you specified dob0 = 2 but did not set pedir. If you want
> to use topup to correct for b0 inhomogeneity distortions you need to
> provide the PE direction of your volumes.
>
> Best,
>
> Chiara
>
>
> > On Jul 18, 2023, at 1:01 PM, Alan Francis 
> wrote:
> >
> > External Email - Use Caution
> >
> >
> > Hi King-Wai:
> >
> > I have been running Tracula on 7T images and it keeps giving me an
> error. The error is as follows:
> >
> > copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
> > Unmatched '"'.
> >
> > I have attached my config file. Can you please let me know what I am
> doing wrong?
> >
> > Thanks,
> >
> > Alan
> > --
> > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> >
> > Alan N. Francis PhD
> > Assistant Professor of Neuroscience
> > Institute of Neuroscience
> > University of Texas, School of Medicine
> > Rio Grande Valley
> > Texas.
> >
>
> > ___
> > Freesurfer mailing list
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*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*


dmrirc-109123_7T_4
Description: Binary data
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Re: [Freesurfer] Tracula statistics outputs for version 7.2

[Alan Francis]

External Email - Use Caution

Hi King-Wai/ Chiara

Thank you for your excellent suggestions.

Chiara: I have made the changes you suggested. Can you please check if the
config file looks workable?

King-Wai - I made the change you suggested. But the problem still persists.
I have attached the config file.

best,

Alan

On Tue, Jul 18, 2023 at 12:26 PM King-Wai Chu  wrote:

> Hi Alan,
>
> I think in your "set dcmlist", you are missing
> /home/alanfrancis/IMAGING/DTI/
> before 109123
> It should be
> set dcmlist =
> /home/alanfrancis/IMAGING/DTI/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz
>
> Best,
>
> King-Wai
>
> On Tue, Jul 18, 2023 at 12:59 PM Alan Francis 
> wrote:
>
>> Hi King-Wai:
>>
>> I have been running Tracula on 7T images and it keeps giving me an error.
>> The error is as follows:
>>
>> copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
>> Unmatched '"'.
>>
>> I have attached my config file. Can you please let me know what I am
>> doing wrong?
>>
>> Thanks,
>>
>> Alan
>> --
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>
>>
>>
>> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
>> Neuroscience*
>> *University of Texas, School of Medicine*
>>
>> *Rio Grande Valley*
>>
>> *Texas.*
>>
>>
>>
>
>
> --
> King-Wai Chu, Ph.D.
> Program Analyst
> Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
> James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
> 130 W. Kingsbridge Road
> Bronx, NY 10468
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*


dmrirc-109123_7T_3
Description: Binary data
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Re: [Freesurfer] Tracula statistics outputs for version 7.2

[Maffei, Chiara,PHD]

External Email - Use Caution

Hi Alan, 

It looks like you have specified the ncpts variable but not the pathlist. If 
you do not specify pathlist, TRACULA will include all 42 tracts by default, so 
your pathlist and ncpts variables will have different lengths.

If you want to focus your analysis on a subset of tracts, specify those using 
pathlist (e.g., set pathlist = (rh.uf lh.uf)). If not, do not specify ncpts 
either (comment out or remove line 59 from your config file) and TRACULA will 
reconstruct all 42 tracts. 

I also noticed you specified dob0 = 2 but did not set pedir. If you want to use 
topup to correct for b0 inhomogeneity distortions you need to provide the PE 
direction of your volumes. 

Best,

Chiara 


> On Jul 18, 2023, at 1:01 PM, Alan Francis  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi King-Wai:
> 
> I have been running Tracula on 7T images and it keeps giving me an error. The 
> error is as follows:
> 
> copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
> Unmatched '"'.
> 
> I have attached my config file. Can you please let me know what I am doing 
> wrong?
> 
> Thanks,
> 
> Alan
> -- 
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> Alan N. Francis PhD
> Assistant Professor of Neuroscience
> Institute of Neuroscience
> University of Texas, School of Medicine
> Rio Grande Valley
> Texas.
>   
>  
> ___
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Re: [Freesurfer] Tracula statistics outputs for version 7.2

[Alan Francis]

External Email - Use Caution

Hi King-Wai:

I have been running Tracula on 7T images and it keeps giving me an error.
The error is as follows:

copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
Unmatched '"'.

I have attached my config file. Can you please let me know what I am doing
wrong?

Thanks,

Alan
-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*


dmrirc-109123_7T_2
Description: Binary data
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Re: [Freesurfer] Tracula dpath Missing Files

[Maffei, Chiara,PHD]

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Hi Lauren,

>From the log it actually looks like you have never run "trac-all -c dmrirc 
>-path", but  "trac-all -c dmrirc -prep" twice.

Chiara


On May 24, 2023, at 11:51 AM, Lauren Stephens 
mailto:laure...@stanford.edu>> wrote:

External Email - Use Caution

Dear Freesurfer Experts,

We have been working to run a test data set through tracula and have seemingly 
had success, however when we ran trac-all -path it completed without error but 
the files created did not go into a dpath folder.  The files that were created 
went into the dmri and dlabel folders.  We are specifically looking for the 
dpath/merged_avg__.mgz file.

We are using Freesurfer 7.3.2 on an iMac Pro running Ventura 13.3.1 in a bash 
shell.  I have attached the dmrirc file.  I have also attached the trac-all.log.

Thank you for any help you can provide.

Lauren Stephens

Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laure...@stanford.edu
P: (650)-725-1716

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[Freesurfer] TRACULA intensity normalization

[Silvia De Francesco]

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Dear developers, 

Does TRACULA perform an intensity normalization of the DWI image, as recon-all 
do for the T1? 

Thanks, 
Silvia 


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[Freesurfer] FreeSurfer / Tracula segmentation between seed points?

[Christian Owen]

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Hi,

Does Freesurfer / Tracula provide any way to automatically segment a tract
between two arbitrarily selected points?

Christian
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[Freesurfer] Tracula, trac-all, bug in interreg

[Tan Li Kuo]

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Hi, I've been trying to configure Tracula to use different inter-subject
registration methods.
It fails for type #3 (robust cost) and #4 (nonlinear CVS).

From the trac-all script (line #1634), it looks like Tracula points to
different trctrain templates depending on the registration method used
(mni, rob, cvs, syn, fnt).
The problem is, the FreeSurfer distribution appears to only include
template files for mni and syn.
E.g., $FREESURFER_HOME/trctrain/hcp/mgh_1001

Basic info:
1) FreeSurfer version:
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
2) Platform: Ubuntu 22.04.1 LTS
3) uname -a: Linux medphys-rtx 5.15.0-53-generic #59-Ubuntu SMP Mon Oct 17
18:53:30 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

Thanks!


-- 
Tan Li Kuo
Medical Physics, Dept. Biomedical Imaging
Faculty of Medicine
Universiti Malaya

-- 
"
 PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya 
("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang
 
termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini 
dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat 
penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin 
Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada 
penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah 
menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini 
dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan 
e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di 
dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya 
adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak 
yang disebut.



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[Freesurfer] Tracula 6.0 - : Command not found. set: Variable name must begin with a letter. does not exist.DIR

[Thorn, Kathryn]

External Email - Use Caution

Hi Freesurfer Experts,

I’m attempting to run Tracula and receiving the same error for both Tracula 6.0.

Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which 
runs without issue) and then Tracula (which returns the same error as 6.0), so 
I don’t think version is my issue.

I have gotten Tracula 6.0 to run in the past on the machine I’m using now and I 
have not made any major modifications or updates since then.

Here is the set of commands I am passing to Tracula:

export FREESURFER_HOME=/Applications/freesurfer/6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export TUTORIAL_DATA=/Users/kayti/Desktop/Projects/MIND/Freesurfer6
export SUBJECTS_DIR=$TUTORIAL_DATA/02_Data/01_recon_all
cd $SUBJECTS_DIR
trac-all -prep -c $TUTORIAL_DATA/01_Protocols/dmrirc.mind95

And here is the full text of my config file:

setenv SUBJECTS_DIR $SUBJECTS_DIR
set subjlist = (A201)
set dcmlist = 
(/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.nii)
set bveclist = 
(/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bvec)
set bvallist = 
(/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bval)
set dob0 = 0
set doeddy = 0
set intrareg = 2
set interreg = 2

And here is the full text of the error message:


domainname: Command not found.

: Command not found.

set: Variable name must begin with a letter.

 does not exist.DIR 
/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all

I have ensured that the directory above DOES exist.

I have seen other posts in these forums with this issue and I have tried all of 
the fixes I’ve found: removing trailing/extraneous spaces, correcting my paths, 
etc.

Does anyone have any ideas why this is happening?

Thank you!

Ryn Thorn
(she/her)
Lab Manager
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425



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[Freesurfer] TRACULA cluster statistics visualization

[miracle ozzoude]

External Email - Use Caution

I have a similar question to this unanswer one (see link)
https://secure-web.cisco.com/1TPpYYjX_nTrm6lqczxoG15eSKbWRPZCXEekOMWT-xtyurpqfBqaFyz4aiSqrY42eu_2JI_dWX-HNfM9jWT5eTLES0zDZCVeGrslztLwHYrbkr_R08eoTG2wWnG2Be3lJlA5KOn3C00RFTWSpD7jyXDn6V0cmzukr2a1BZ66xTC3yOB_AAERXQC7DBDBNJDlDlTkg6iRJu8DlOzJUmIUSISa13MhDz7w6b4oF-97h09B4FeeO-GescFCpFpBxd8OvjZgQVzb9_ok9K4yzL79Rx0r6nqi_I-8maz_cpd4zCpITmOtKAPtXatUA-N9L0Di7HUO_3hEUmJaGqxQN__cqEg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74147.html
*Also*
1) If I run along-tract stats with mri_glmfit/mri_glmfit-sim and I found a
significant result, how do I know the entire length of the tract and how
much was affected? Also, is it measured in mm?

2) When performing clusterwise correction for multiple comparison for
along-tract analyses, should the bonferroni flag (--2spaces) be included?
This is because it wasn't mentioned/included in the tracula statistics
tutorial nor the publication "Using diffusion MRI data acquired with
ultra-high gradient strength to improve tractography in routine-quality data
".

Many thanks,
Paul
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[Freesurfer] Freesurfer TRACULA Error

[Stylianos Charalampous]

External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to apply TRACULA for the reconstruction of white matter pathways 
but I am getting an error when running the trac-all command which I haven’t 
managed to resolve. The TRACULA is applied on an MRI sample from the ADNI 
dataset that has been preprocessed using recon-all.

I've searched the list but I was not able to found a similar error. Does anyone 
have any thoughts on how to trouble-shoot this one?
I have also attached the trac-all.log in case it's of any use.

1) FreeSurfer version: 7.3.2
2) Platform: Ubuntu 22.04
3) trac-all.log: see attached

Kind regards,
Stylianos Charalampous



trac-all.log
Description: trac-all.log
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Re: [Freesurfer] TRACULA trac-all error

[Huang, Yujing]

Hi Nita,

What is your FREESURFER_HOME points to?  It should be set to your Freesurfer 
7.3.2 install directory.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nita Akoh
Sent: Wednesday, January 18, 2023 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA trac-all error


External Email - Use Caution
Hey, I'm trying to run "trac-all -prep -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial" but keep getting this error 
: /shared/centos7/freesurfer/7.3.2/bin/free/sources.csh: No such file or 
directory.

My colleague ran this step on the same data and it worked for her but not for 
me. We load the same freesurfer version and use the exact same commands.

Thanks,
Nita Akoh
Candidate for B.S in Behavioral Neuroscience & International Affairs
College of Science
Northeastern University
+17165011641| ako...@northeastern.edu<mailto:ako...@northeastern.edu>
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[Freesurfer] TRACULA trac-all error

[Nita Akoh]

External Email - Use Caution

Hey, I'm trying to run "trac-all -prep -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial" but keep getting this error 
: /shared/centos7/freesurfer/7.3.2/bin/free/sources.csh: No such file or 
directory.

My colleague ran this step on the same data and it worked for her but not for 
me. We load the same freesurfer version and use the exact same commands.

Thanks,
Nita Akoh
Candidate for B.S in Behavioral Neuroscience & International Affairs
College of Science
Northeastern University
+17165011641| ako...@northeastern.edu
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[Freesurfer] TRACULA cluster statistics visualization

[Makenna B McGill]

External Email - Use Caution

Hi Freesurfer Developers,

I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat,
and I was wondering how to best visualize and interpret the results of the
cluster-wise correction in freeview.

I referenced this page (
https://secure-web.cisco.com/1Wn0Jo3ZhV2QIp8R6uvzRorN2zYdL69NgfN7PXt5cTq22hhH3aS9QimeQbmh38pVCMpxzQwEXmO6rwHLlmcziA-EF5XkZzaQahAFzMM-xXafAUgB7EBLdEFxK5Cf-SDIMN4gepn6yup_RurCijHEfIu5Xa6mZ_Pk5Xkc9nvxfOyv8F69rQhxcAJdlfvullsSK7YZwZ8IFo6N74uk4nrsBWampKmvI3dZyAuF6Qem5_4sc6IYkl_56riDKVZ4s_tTEI9g7zcNC_sWUK0F7OMTP4LxNLekjnocxOBXIQ7MuwzC1pUWo1gzw-fHUFqfJzBDgGGLGdU84j0lOuyx5QorP0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics%23Visualizingresultsfromstatisticalanalysesalongapathway),
which describes how to do this for uncorrected statistics, and used
dmri_trk2trk to embed the *perm.th13.abs.sig.cluster.mgh files produced by
mri_glmfit-sim into the template .trk files (--in
$FREESURFER_HOME/trctrain/hcp/syn/"$tract".display.trk).

However, I'm noticing inconsistencies in the location along the tract of
significant clusters between the projection of the uncorrected statistics
in freeview, projection of the corrected statistics in freeview, and the
cluster location as indicated by the cluster summary file
(*perm.th13.abs.sig.cluster.summary.txt).

I've attached the cluster summary file for FA in the rh.cst tract as an
example. My understanding is that for pathways with superior-inferior
orientation, points along the tract are ordered from superior to inferior.
Given that this significant cluster is at a VoxX of 68 (of 80 total points
along the tract), I would have thought that this cluster would be located
at a more inferior position along the right cst -- instead, the cluster
appears to be located superiorly. Similar to this FS user (
https://secure-web.cisco.com/1W2wWzty4LvZ-noLr4zvkjNMq5qwway38c9kYyxk8c8a4AoIQuxySOQwiqND_VWT6SsWWSgAQYiw6izF1Xr-Y7kVM5mis2O1RSe3BOA7u4JGkGg5iN_doXYKGSxcPvcsYb1M86VDFdrhwu4DCtmLZqJiW4P3vdLPEyZWsWsV5BFNStVqLGmIk4eqV1dZYGqod6OG_OoNhEkZ8lkI6V3exnx8PPbBBMfhe8fVG9JEbGI83yfWrxhO_FYtC51gIfYpyrT5ZCMedL6_eHtWNySTwuYTOst03Fujn6xYUrBvJgzNPHduh0ckdhHWzvx7LguLxieRhJPs-y4g8oqhPhLi76A/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73534.html),
I'm wondering: (1) Am I missing something regarding this embedding process?
(2) Is it appropriate to embed the *perm.th13.abs.sig.cluster.mgh file to
visualize the results of the cluster-wise correction?

Please let me know if there is any other information you'd like me to
provide. Any thoughts on where I might be going wrong would be greatly
appreciated. Thank you!

Best,
Makenna

*Makenna McGill *(she/her)
Doctoral Student in Clinical Psychology
The University of Texas at Austin


perm.th13.abs.sig.cluster.summary
Description: Binary data
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[Freesurfer] TRACULA tutorial and processing questions

[Tran, Diana]

Dear FreeSurfer TRACULA experts,

I am new to FreeSurfer and using TRACULA to process DTI data. From the 
mail-archive, I understand TRACULA mainly needs the aparc+aseg output from 
recon_all in order to run. Using the recon_all output information, I was able 
to complete the 3 steps in TRACULA, but only after switching from the 7.1.1 
version to the 6.0.5.1 version of FreeSurfer. I have the following questions 
about TRACULA:


  1.  Some of the tutorial files that are needed to run the TRACULA tutorial 
are not there upon downloading or do not match the tutorial instructions. Is 
there an updated version of the tutorial instructions that match the current 
files?
  2.  Do you have insight as to why TRACULA -prep exits with ERRORS when it's 
run with version 7.1.1 of FreeSurfer, but exits without errors when it's run 
with version 6.0.5.1? Reviewing the scripts, it seems the most notable 
difference are the values for i_ras, j_ras, and k_ras. Version 6.0.5.1 gives 
varying numbers, while version 7.1.1 gives values of -1, 0, or 1.
  3.  I came across the webpage introducing version 7.2 with substantial 
updates for TRACULA after having run my dataset with version 6.0 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes). It states, "Unless 
the new features are employed, recon-all will give the same exact result as 
7.1.1 and 7.1.0." Is this also true for TRACULA? Would you advise rerunning my 
dataset with version 7.2 of TRACULA (or even 7.3, but the recent release notes 
for this version didn't mention TRACULA changes)?
  4.  Is there another location to find the dwi_motion_byvol.txt output file? 
Currently the instructions say it should be located in the /subject#/dmri 
folder but only the dwi_motion.txt can be found there 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs).
  5.  For some subjects with visible motion distortions in manual quality 
check, I ran TRACULA as a second QC measure. However, they are still given a 
score of 0 and 1 for percent bad slices and average dropout score, 
respectively, according to the dwi_motion.txt. In fact, for all the subjects I 
ran, they all received those scores with the exception of one subject, who 
actually had minimal motion artifacts in manual QC. I'm not sure how to 
interpret this and was wondering if you could please advise.
  6.  While combing through the mail-archive to better understand how to use 
TRACULA, I noticed dt_recon being mentioned with TRACULA processing. Is this a 
step that needs to be completed before running TRACULA? Or is it part of an 
older version of processing that is already built into the updated versions 
6.0+ of TRACULA?

Thank you in advance for your time!

Warm regards,
Diana

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[Freesurfer] [Tracula] ERRORS when using trac-all -prep

[h21ms-utsumi]

External Email - Use Caution

Dear Freesurfer experts

I'm attempting to running TRACULA in a two subjects(one visit per 
subject and multiple deffusion scans per visit), as described on the 
TRACULA tutorial 
(https://secure-web.cisco.com/1YZplCc8ElxyKpvsfXb9OH_SNhToXmmPHixjCRlcZ51VHS12nUQQG4rMQybDPmP5RRwTYpZXLYBDCgi-aVwgAkIbD7f1nuv3qCRerbwqiEFE3PYEbp8GmUG0QZj8fv0kGh0sKwEI4r8ULPKz8OVdmWBr0me7wibJF1a8l5S74YstX_dkTB88f-aX5wFUKO798aWohHBR8zND-FMrt7oygYVYxsL29Q_PPvrSO9pY3WzpuLzpxcRYLe5zFQCaLJXJBW7T8VmIUQnJULc6AZpBWEUkPcavsBb5sLnWOQo8mARajKxbGYJ0zVdvJ3F9BgYZk/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula,
 
https://secure-web.cisco.com/1nYtHW48eZdU7uUKv6TSjlFm9HP9CHGRmfSeoCOA7uunK3kIdhbSPNPcLfk5dxLcxWFiX2iHtjYsKFFHkoFhohA_CBpmhn00TFI7dj_A6_Ysx-lUshF_hf_8PUjxAdpehn-lqUTRnrPxgpYcsx8A0aJH2TTRWCAIqy17bdWBFVgQAQXbJRvtSUG4WJIHGUl8JnW7AvLKo8ViJ0qpfJKeQBkqJjtDD6vV1cJ-eyupl192QAfm_n0WbMnvunlfpzAz7Gt1ah6Mj6aSc5x3uQJeB0H0geYTLMZzvPA2AGFf8b1ADynWtOKW4a5-jHY9CyqkY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc,
 and 
https://secure-web.cisco.com/1i1x3WraESWH3k6zfmnPSieIq0qc66z7vq-nTTa6dKs81QaXyWb6SELvy3WVyD4G2zXOxWyMoa9XtbxMRvjRsZ8tCmHNGXEDfM3VvK19JRnw0BNx6bRO_1uIqy-6a2bcwHFYJ8Wpsym4MKm4wLCe8sqjV1P1uLv0rPNiOI771Wzr84BYMrpjzpwRR71UoYzZtPxhIN-6WqahEpeiW4OVNDbAMgz1WtV3OkZCxRKIR2CiF8R5TgCo6YpME4qVk5AgiEQFOpb86ElM97aPZcBORWVC4QR_7uCE_2Wrn1yTXf-9xfT2DGJhaCR9NpAzjOaVZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FRunningTracula),
 
but for my subjects I get the following error when I run the trac-all -
prep:

cp dwi.nii.gz /media/sf_share\freesurfer\7.3.2/subjects/diffusion_
tutorial/trc/subject1/dmri/data.nii.gz 
cp: cannot stat 'dwi.nii.gz': No such file or directory.

I checked the "dmri" directory and found that "data.nii.gz" was missing 
and "dwi.nii.gz " was there.

I've searched the archive list and I found the following two things;
 the dwi.nii.gz file is the DWI after all corrections have been made 
and the data.nii.gz file is a symbolic link to the other, so they should 
be the exact same file.
(https://secure-web.cisco.com/1qq_o3GFIoLx7Luv5Fgj2ZN5KBHCJCZzPPrZqzLzT3BdzI8z8iY0s3aw9ZiV1ZqrrmxTI8XTA7nXUIB1qpFj5LqqBdPnBFaZ7iS_mKC527GAIGxaf0Xr1d2hXyykfiJOg9la8SZsvG8hbRNzs9LKMucBEe_Qsq-Te92e_afgT0lgv8YjlwRCN8x4bLchbzgTax5xSIp36ImbKD-ULL5sKdOAT5Pt0iuy9S3llRWzxBj7k662wVU597F1GBdua-M2DqRsS_Ma2-VjUuqnpz_xJdR-CTlUc7ijJhoRDUMxdkCoZUzK06Oqx9Idmes9tVreb/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg39432.html)

 the data.nii.gz file is necessary for the process of "trac-all -bedp", 
not "trac-all -prep." 
(https://secure-web.cisco.com/1pjKE3HFIeU-FqIoHgU1xkoI3rom-BBboaeTQQ7MDiNVT78circo6cATHKBmSd6J0ggcrbRvJqQf9IqYLORohmBgZdmcnpjU0riT_Om05ORgE8YJiCXCAmGSQgA6bQw4ha8P5_aKiMWMMgVUnzTTyI4H1y9WPnVdAAGVvbf1a7xYUQHr4BKvE2zHSekVxYMsuHjf7wzvKK8F5QBedOY7m2_gAJA1y5HMgkJegAV_UG7qtaryWKAw2h2YWsWvJaig4iDNnu3bIRvxRxdg57lv8ZdiG6JgvjMwo1IsofvAdHvq9F47TrXAwtRnT8bgoBDMu/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg24254.html).


However, no similar errors have been reported. Does anyone have any 
thoughts on how to trouble-shoot this one? Also, Ive attached the dmrirc.
tutorial, trac-all.log, pre-diffusion_tutorial_tree.text, and post-
diffusion_tutorial_tree.text in case it's of any use. 

Best regards, 

Tomohiro Utsumi.


 
Tomohiro Utsumi, PhD Student.
Department of Psychiatry, The Jikei University School of Medicine, Tokyo,
 Japan.




dmrirc.tutorial
Description: Binary data
brain@l4n:/media/sf_share/freesurfer/7.3.2/subjects/diffusion_tutorial$ tree
.
|-- diffusion_tutorial_tree.txt
|-- fs
|   |-- subject1
|   |   |-- label
|   |   |   |-- BA_exvivo.ctab
|   |   |   |-- BA_exvivo.thresh.ctab
|   |   |   |-- aparc.annot.DKTatlas.ctab
|   |   |   |-- aparc.annot.a2009s.ctab
|   |   |   |-- aparc.annot.ctab
|   |   |   |-- lh.BA1_exvivo.label
|   |   |   |-- lh.BA1_exvivo.thresh.label
|   |   |   |-- lh.BA2_exvivo.label
|   |   |   |-- lh.BA2_exvivo.thresh.label
|   |   |   |-- lh.BA3a_exvivo.label
|   |   |   |-- lh.BA3a_exvivo.thresh.label
|   |   |   |-- lh.BA3b_exvivo.label
|   |   |   |-- lh.BA3b_exvivo.thresh.label
|   |   |   |-- lh.BA44_exvivo.label
|   |   |   |-- lh.BA44_exvivo.thresh.label
|   |   |   |-- lh.BA45_exvivo.label
|   |   |   |-- lh.BA45_exvivo.thresh.label
|   |   |   |-- lh.BA4a_exvivo.label
|   |   |   |-- lh.BA4a_exvivo.thresh.label
|   |   |   |-- lh.BA4p_exvivo.label
|   |   |   |-- lh.BA4p_exvivo.thresh.label
|   |   |   |-- lh.BA6_exvivo.label
|   |   |   |-- lh.BA6_exvivo.thresh.label
|   |   |   |-- lh.BA_exvivo.annot
|   |   |   |-- lh.BA_exvivo.thresh.annot
|   |   |   |-- lh.FG1.mpm.vpnl.label
|   |   |   |-- lh.FG2.mpm.vpnl.label
|   |   |   |-- lh.FG3.mpm.vpnl.label
|   |   |   |-- lh.FG4.mpm.vpnl.label
|   |   |   |-- 

[Freesurfer] TRACULA: domainname: Command not found.

[Ward Deferm]

External Email - Use Caution

DearFreesurfer developers,


when trying to run trac-all -prep I am running into this error


gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c 
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt

domainname: Command not found.

Too many ('s.

ERROR: Syntax error in configuration file 
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt


I checked the file but there seem to be no errors in the ('s.


This error has previously been encountered 
https://secure-web.cisco.com/1sKX4EXSdl-lzzKBfb369ful1KJMpWkExgYjXUfdMyAgEiLxmN-7MUWuEnZfe6fFIgowB68U2mNgao0KjS4PAfFLRsTmh7OkFg6D4IV4CMi-68OueIKNIDatn-hDv1YZ15W7tXz_fi2msIxxR_qP6YQk4asNuiMw9V9LHaembEzvAAr-oMUyw8yw_mrwjKGcR189BLip2OKFKDJS1qiS9UVHptmlDleX7ja_VsDq6QHHrrE2n0R8vFbYXAM1IkF6tbv6cfSKV91f3sbBxrvJgl16Yba47czO4agSUB9yuP0UTkvcJfaHXzQ6nM7-r0Xvq/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70662.html%23
 but there is no solution proposed for the facts that the domainname command is 
missing from my mac in the /usr/bin folder. What can i do to solve this error. 
In the attachments you can find the tracula config file if this would be 
helpful. Thank you for the help.



Kind regards,



Ward Deferm






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

setenv SUBJECTS_DIR /Users/r0755008/Desktop/mri_data/STRUCT

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Users/r0755008/Desktop/mri_data/TRACULA

# Subject IDs
# Here each subject is listed twice because it has two diffusion scans
#
set subjlist = (NT001 \
NT001 \ 
NT002 \
NT002 \ 
NT003 \
NT003 \ 
NT004 \
NT004 \ 
NT005 \
NT005 \ 
NT006 \
NT006 \ 
NT007 \
NT007 \ 
NT009 \
NT009 \ 
NT010 \
NT010 \ 
NT011 \
NT011 \ 
NT012 \
NT012 \ 
NT013 \
NT013 \ 
NT014 \
NT014 \ 
NT015 \
NT015 \ 
NT016 \
NT016 \ 
NT017 \
NT017 \ 
NT018 \
NT018 \ 
NT020 \
NT020 \ 
NT021 \
NT021 \ 
NT024 \
NT024 \ 
NT025 \
NT025 \ 
NT026 \
NT026 \ 
NT027 \
NT027 \ 
NT028 \
NT028 \ 
NT029 \
NT029 \ 
NT030 \
NT030 \ 
NT032 \
NT032 \ 
NT033 \
NT033 \ 
NT034 \
NT034 \ 
NT035 \
NT035 \ 
NT036 \
NT036 \ 
NT037 \
NT037 \ 
NT038 \
NT038 \ 
NT039 \
NT039 \ 
NT040 \
NT040 \ 
PT002 \
PT002 \
PT003 \
PT003 \
PT004 \
PT004 \
PT005 \
PT005 \
PT007 \
PT007 \
PT008 \
PT008 \ 
PT010 \
PT010 \ 
PT011 \
PT011 \
PT013 \
PT013 \
PT014 \
PT014 \
PT015 \
PT015 \
PT016 \
PT017 \
PT018 \
PT018 \
PT019 \
PT019 \
PT020 \
PT020 \
PT021 \
PT021 \
PT022 \
PT022 \
PT023 \
PT023 \
PT024 \
PT024 \
PT025 \
PT025 \
PT026 \
PT026 \
PT027 \
PT027 \
PT028 \
PT028 \
PT029 \
PT029 \
PT030 \
PT030 \
PT030 \
PT031 \
PT031 \
PT032 \
PT032 \
PT033 \
PT033 \
PT034 \
PT034 \
PT035 \
PT035 \
PT036 \
PT036 \
PT037 \
PT037 \
PT038 \
PT038 \
PT039 \
   

[Freesurfer] Tracula path outputs quality checking

[Shanika Jayakody]

External Email - Use Caution

Dear FreeSurfer TRACULA team

I have processed subjects using TRACULA on FS6.0 and 7.2.
With both pipelines all the steps are completed without errors but for most 
subjects when I checked the pathstats.overall.txt file volume of the tract is 
almost equal to the length average. (unlike the example in Freesufer Wiki)
I have attached pathstats for two people with (ID30720) and without (ID 30018) 
that problem (also attached one of my configuration files). Does this mean the 
tracts are not fully constructed? I was referring tracula freesurfer page and 
the following paper 
https://secure-web.cisco.com/1dIfxly6kRVrrbDgNkmQxrmTgb-DRd5cF1t7FkABP7tQosKUizgyMUWBx6hITrcmfSzRIl4pxl9LDRAwHZ5Ow0-ADMs_HaG-rwy14B2Y03rCPJQund4JmkSYDTsm4ozwRaMczRnzDMvr0D0ahgbfOV8MtCX-wSOmu2zF09pEO996UcVTtDOg4ReK_YFL_cskM_vn9DBaz1AjEOhiDcr-LV_3eojajF2sdNWTIr1Ny7s1ifLYosseu0eVTui7pr0dNO2-tj57d6jBRF_Y_pZrqlW-q4m7LMLMmKTvGTwnvwTy6evufcONsn1rARKuneDYwLE8dY6DF4CrOmwNpjD4Fxg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0165027021000340
I have done re-initializing of the tracts too without any luck of improving
Even in freeview the tracts for 30720 looks like thin lines.

I have been having this problem for a while and any suggestion to correct it 
will be much appreciated!
Regrards
Shanika
# Title Pathway Statistics
#
# generating_program /public/apps/freesurfer/7.2.0//bin/dmri_pathstats
# cvs_version 7.2.0
# cmdline /public/apps/freesurfer/7.2.0//bin/dmri_pathstats --intrc 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr 
--dtbase /gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/dtifit --path 
lh.ilf --subj 30018 --invox path.ref.txt --out 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr/pathstats.overall.txt
 --outvox 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/lh.ilf_avg16_syn_bbr/pathstats.byvoxel.txt
 
# sysname Linux
# hostname cpu-731.cluster.local
# machine x86_64
# user sjayakody
# anatomy_type pathway
#
# subjectname 30018
# pathwayname lh.ilf
#
Count 1500
Volume 1877
Len_Min 62
Len_Max 104
Len_Avg 80.7613
Len_Center 89
AD_Avg 0.000585198
AD_Avg_Weight 0.000572661
AD_Avg_Center 0.000399619
RD_Avg 0.000249489
RD_Avg_Weight 0.00024237
RD_Avg_Center 0.000166555
MD_Avg 0.000361392
MD_Avg_Weight 0.000352467
MD_Avg_Center 0.000244243
FA_Avg 0.599611
FA_Avg_Weight 0.601226
FA_Avg_Center 0.618726
# Title Pathway Statistics
#
# generating_program /public/apps/freesurfer/7.2.0//bin/dmri_pathstats
# cvs_version 7.2.0
# cmdline /public/apps/freesurfer/7.2.0//bin/dmri_pathstats --intrc 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr 
--dtbase /gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dmri/dtifit --path 
lh.ilf --subj 30720 --invox path.ref.txt --out 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr/pathstats.overall.txt
 --outvox 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30720/dpath/lh.ilf_avg16_syn_bbr/pathstats.byvoxel.txt
 
# sysname Linux
# hostname cpu-782.cluster.local
# machine x86_64
# user sjayakody
# anatomy_type pathway
#
# subjectname 30720
# pathwayname lh.ilf
#
Count 1500
Volume 58
Len_Min 58
Len_Max 58
Len_Avg 58
Len_Center 89
AD_Avg 0.000937952
AD_Avg_Weight 0.000937952
AD_Avg_Center 0.000931482
RD_Avg 0.000740375
RD_Avg_Weight 0.000740375
RD_Avg_Center 0.000719722
MD_Avg 0.000806234
MD_Avg_Weight 0.000806234
MD_Avg_Center 0.000790309
FA_Avg 0.16653
FA_Avg_Weight 0.16653
FA_Avg_Center 0.183197
setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30018
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii
set bvecfile = 30018/bvecs.txt
set bvalfile = 30018/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the 

[Freesurfer] Tracula statistics outputs for version 7.2

[King-Wai Chu]

External Email - Use Caution

Hi,

Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt,
I have 2 more questions.
Since my previous 3 questions still have not been answered, I'm including
them here
so that they are all in one place.  The 2 new questions are 4) and 5), my
previous 3
questions are appended after.

4) I have noticed that the averages of AD, RD, MD and FA in
pathstats.byvoxel.txt
are exactly the same as the *_Avg_Center in pathstats.overall.txt.
According to the tutorial, *_Avg_Center in pathstats.overall.txt is
the "average over highest-probability path only" and the
AD, RD, MD and FA in pathstats.byvoxel.txt is the value at the
"position on the maximum a posteriori path".
Does it mean that "highest-probability path only" and "position on the
maximum a posteriori path" are the same or one of them should be changed to
the other one?

5) Are the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg in
pathstats.byvoxel.txt
suppose to match *_Avg(average over the entire support of the path
distribution)
in pathstats.overall.txt?
When I removed the duplicate points in pathstats.byvoxel.txt, the averages
of
AD_Avg, RD_Avg, MD_Avg and FA_Avg come very close to the value of *_Avg in
pathstats.overall.txt

I don't think I can calculate the averages by including the duplicate
points in 4)
but removing them in 5).  Either including them in both or not at all.

Questions from my previous email.

1) There are duplicate points in pathstats.byvoxel.txt, is it normal?
I didn't try it on all 42 tractcs.  For the few I've looked at, they all
have duplicate points.
I used the default setting in the config file to run trac-all.

2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D
files.
When embed the sig.mgh and z.mgh statistical maps from the analysis into
the template .trk
(*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't
have enough information to give *.display.trk the voxel values for the
*.overlay.trk.  There is no one-to-one voxel corresponding between sig.mgh
and *.display.trk.  What am I missing?  Or what's the embedding process do?

3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using
dmri_trk2trk or
mri_convert the voxel values of the .trk file don't get converted into the
.nii.gz or ascii file,
only the x,y,z coordinates are converted.  Is there a way to get the voxels
values of the .trk file
when converting to .nii.gz or ascii format?

Thanks,

King-Wai

-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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[Freesurfer] Tracula statistics outputs

[King-Wai Chu]

External Email - Use Caution

Hi,

I have 3 questions on tracula statistics outputs.

1) There are duplicate points in pathstats.byvoxel.txt, is it normal?
I didn't try it on all 42 tractcs.  For the few I've looked at, they all
have duplicate points.
I used the default setting in the config file to run trac-all.

2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D
files.
When embed the sig.mgh and z.mgh statistical maps from the analysis into
the template .trk
(*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't
have enough information to give *.display.trk the voxel values for the
*.overlay.trk.  There is no one-to-one voxel corresponding between sig.mgh
and *.display.trk.  What am I missing?  Or what's the embedding process do?

3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using
dmri_trk2trk or
mri_convert the voxel values of the .trk file don't get converted into the
.nii.gz or ascii file,
only the x,y,z coordinates are converted.  Is there a way to get the voxels
values of the .trk file
when converting to .nii.gz or ascii format?

Thanks,

King-Wai

-- 
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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[Freesurfer] TRACULA pathways to MNI space

[Woo-Suk Tae]

External Email - Use Caution

Dear Freesurfer experts

I finished TRACULA's trac-all steps. Then I'd like to transform all DTI
pathways to MNI space.
Are there any commands in freesurfer or any external neuroimaging softwares.

My scripts did not provided no transformation to MNI space.

#bet /Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
/Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz
#flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in
/Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz -omat
/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat
fnirt --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
--aff=/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat
--cout=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm
--in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
--warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--out=/Users/anal/RH_nml/FS/01/mri/orig/warped_001.nii.gz
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm
--in=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/path.pd.nii.gz
--warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--premat=func2struct.mat
--out=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/warped_fmajor.nii.gz

Sincerely

Woo-Suk, Tae
Seoul, Korea

-- 


Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
  wo os...@gmail.com

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[Freesurfer] TRACULA - Ball-and-stick model fit running time

[Liliana Wu]

External Email - Use Caution

Hi,

I have successfully run the preprocessing steps for my DWI data, and I was 
wondering how long does bedpostx  usually take to process DWI? I am running on 
a high-powered computer (cluster) and a multi-shell data 3 b-values of (b= 
1000s/mm2, 34 directions; b= 1600s/mm2, 45 directions; and b= 2600s/mm2, 66 
directions).

Thank you,
Liliana

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Re: [Freesurfer] TRACULA - preprocessing error

[Yendiki, Anastasia]

Hi Liliana - It looks like you are using a very old FreeSurfer build (from 
2016) and an old TRACULA configuration file. You should update to the latest 
version of FreeSurfer and follow the instructions on the wiki for how to set up 
TRACULA. We have many more tracts now and the naming has changed. To 
reconstruct the subset of tracts you want with the new version, you just need 
this in the config file:

set pathlist = (lh.cst rh.cst lh.uf rh.uf lh.cbd rh.cbd lh.cbv rh.cbv)

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Liliana Wu 

Sent: Friday, August 19, 2022 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] TRACULA - preprocessing error


External Email - Use Caution

Here is the error log information:

INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/dmrirc.local 
-log /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.log -cmd 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc
#-
#@# Image corrections Fri Aug 19 13:27:09 EDT 2022
mri_convert --bvec-voxel /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvecs_path.txt 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvals_path.txt 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.tmp 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals.tmp 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
orientLAS /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8
mri_convert -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 -ojd 
-0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc -0.949776 
14.1753 25.1557 -rt nearest 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 
-ojd -0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc 
-0.949776 14.1753 25.1557 -rt nearest 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999551, 0.00440173, 0.0296355) -> (-0.999551, 
0.00440173, 0.0296355)
normalizing out_j_direction: (-0.0024424, 0.973885, -0.227028) -> (-0.0024424, 
0.973885, -0.227028)
normalizing out_k_direction: (0.0298609, 0.226998, 0.973437) -> (0.0298609, 
0.226998, 0.973437)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
Reslicing using nearest
writing to 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz...
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals, 
copying
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs, 
converting to LAS
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvecs 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvals 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals
eddy_correct 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz 0
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0001
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0002
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0003
processing /home/lwu/Desktop/O

Re: [Freesurfer] TRACULA - preprocessing error

[Liliana Wu]

External Email - Use Caution

Here is the error log information:

INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/dmrirc.local 
-log /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.log -cmd 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc
#-
#@# Image corrections Fri Aug 19 13:27:09 EDT 2022
mri_convert --bvec-voxel /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvecs_path.txt 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvals_path.txt 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.tmp 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals.tmp 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals
orientLAS /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8
mri_convert -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 -ojd 
-0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc -0.949776 
14.1753 25.1557 -rt nearest 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 
-ojd -0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc 
-0.949776 14.1753 25.1557 -rt nearest 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999551, 0.00440173, 0.0296355) -> (-0.999551, 
0.00440173, 0.0296355)
normalizing out_j_direction: (-0.0024424, 0.973885, -0.227028) -> (-0.0024424, 
0.973885, -0.227028)
normalizing out_k_direction: (0.0298609, 0.226998, 0.973437) -> (0.0298609, 
0.226998, 0.973437)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999551, 0.00440173, 0.0296355)
j_ras = (-0.0024424, 0.973885, -0.227028)
k_ras = (0.0298609, 0.226998, 0.973437)
Reslicing using nearest
writing to 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz...
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals, 
copying
INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs, 
converting to LAS
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvecs 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs
mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvals 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals
eddy_correct 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz 
/home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz 0
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0001
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0002
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0003
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0004
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0005
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0006
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0007
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0008
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0009
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0010
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0011
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0012
processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0013
processing 

[Freesurfer] TRACULA - preprocessing error

[Liliana Wu]

External Email - Use Caution

Hi,

I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am 
getting the following error
ERROR:  fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni

I don’t see the mni folder created in my files… I am trying to only reconstruct 
the following pathways.


set pathlist = ( lh.cst_JL rh.cst_JL \

  lh.unc_JL rh.unc_JL \

  lh.ccg_PP rh.ccg_PP \

  lh.cab_PP rh.cab_PP)



set ncpts = (6 6 5 5 5 5 4 4)

I appreciate any help,

Thank you
Liliana
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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 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA - custom tracts and path labelling

[Yendiki, Anastasia]

Hi Liliana - Please see here for info on TRACULA and the tracts included so far:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
https://dmri.mgh.harvard.edu/tract-atlas/

We do not include the IFOF because it is controversial. Many anatomists believe 
that it is an artifact of tractography methods merging parts of the EmC and the 
ILF into a single pathway.

TRACULA is not a multi-ROI or seed-target type method. See the references at 
the bottom of the wiki page above for how it works.

Best,
Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Liliana Wu 

Sent: Wednesday, August 17, 2022 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA - custom tracts and path labelling


External Email - Use Caution

Hi,



I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF)  
but I am seeing that this tract is not included in TRACULA. Does TRACULA enable 
manually selecting seed and target ROIs ?

Also, I am trying to access the list of the abbreviated names for 42 pathways 
but I don’t seem to find it. I have tried looking at 
$FREESURFER_HOME/trctrain/hcp/pathlist.txt. as suggested per tutorial.



I am new to TRACULA and I appreciate any help,



Thank you,

Liliana
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Re: [Freesurfer] Tracula - Preproc

[Yendiki, Anastasia]

Earlier versions of TRACULA didn't have the option to use ANTs for 
registration. Now you have that option, but you also have the option not to use 
it, if you're finding it hard to install.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Wednesday, August 17, 2022 4:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula - Preproc


External Email - Use Caution

Thank you King Wai and Philip. I am reworking the config file to see if that 
works. The earlier Tracula versions were much easier to run.

best,

Alan

On Mon, Aug 15, 2022 at 3:15 PM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

Check the ANTs version. If you are using the binaries version  2.1.0
"antsRegistration --version" should return
All_Command_lines_OK
ANTs Version: 2.1.0-g78931
Compiled: Jan 23 2015 03:27:59

If not, you are not using the version 2.1.0

Do you know where is the binaries?
You need to change ANTSPATH to point to the binaries.

Or open a new terminal and try again.

Best,

King-Wai



On Mon, Aug 15, 2022 at 3:46 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hi King Wai -

Thanks for your help. I downloaded version 2.1.0 as you suggested and installed 
it. But the error message keeps coming back. It is looking for this file:

/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh

But this file is not present in the binary folder.

Thanks,

Alan

On Mon, Aug 15, 2022 at 12:54 PM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below
antsRegistration --version

If it is below 2.1.0
download the 2.1.0 binaries here, it works for me.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://github.com/ANTsX/ANTs/releases/tag/v2.1.0<https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0>

If you want to use your script, edit the yellow lines to remove "#"
# If you want to build a particular release, do so here
# cd ANTs
# git checkout v2.3.1
# cd -

# If you want to build a particular release, do so here
cd ANTs
git checkout v2.3.1
cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script could 
be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs?
It should be 2.1.0
Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error message 
right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m 
/home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f 
/usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o 
/home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found.
Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the antsRegistrationSyNQuick.sh 
script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:
Thank you so much King Wai,

On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

For bash shell
ANTSPATH=/home/afrancis/Imaging/ANTs

For tcsh
setenv ANTSPATH /home/afrancis/Imaging/ANTs

On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hi Anastasia :

I installed ANTS and tried this

set ANTSPATH = /home/afrancis/Imaging/ANTs

[Freesurfer] TRACULA - custom tracts and path labelling

[Liliana Wu]

External Email - Use Caution

Hi,

I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF)  
but I am seeing that this tract is not included in TRACULA. Does TRACULA enable 
manually selecting seed and target ROIs ?
Also, I am trying to access the list of the abbreviated names for 42 pathways 
but I don’t seem to find it. I have tried looking at 
$FREESURFER_HOME/trctrain/hcp/pathlist.txt. as suggested per tutorial.

I am new to TRACULA and I appreciate any help,

Thank you,
Liliana
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] TRACULA: trac-all -bedp error only with -jobs flag

[Christopher Machle]

External Email - Use Caution

Hi Freesurfer team!

I am having an issue with the -jobs flag for trac-all -bedp in 
freesurfer/7.3.0. I ran trac-all -prep with the -jobs flag with no issue, and 
submitted the commands as jobs on my cluster without error. However, when I try 
to create the commands for -bedp with the -jobs flag, I get the following error 
message:

ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/projects/dsnlab/shared/tag/nonbids_data/dMRI/tracula/sub-001w01/dmri/nodif_brain_mask.nii.gz
pre./projects/dsnlab/shared/tag/TAG_scripts/dMRI/tracula/trac-all_bedp: No such 
file or directory.

The directory in the last line does not exist, so perhaps it's not surprising 
that I am getting an error with that. However, if I submit the trac-all -bedp 
command on my cluster directly (without the -jobs flag), it runs without error. 
I am also able to get the desired output with the -jobs flag for trac-all -path 
and trac-all -stat (both after running -bedp), so I am not sure what is causing 
the error using the -jobs flag with trac-all -bedp.

Does anyone have any insight as to how I can address this? Ultimately, I'll be 
running trac-all on a longitudinal data set with many subjects, so I plan to 
run everything in parallel.

I've attached my config file (just one test subject) below. Thanks in advance 
for the help!

Best,
Chris
# practice config file for TRACULA
# txt file with tcsh commands

# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR 
/projects/dsnlab/shared/tag/bids_data/derivatives/LongFreeSurfer/freesurf_7.2.0/

# Output directory where trac-all results will be saved
#
set dtroot = /projects/dsnlab/shared/tag/nonbids_data/dMRI/tracula

# Subject IDs (one per time point per subject)
# (ie what the subject was named when ran recon-all)
#
set subjlist = sub-001w01


# 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 = /projects/dsnlab/shared/tag/nonbids_data/dMRI/topup_eddy
set dcmlist = 001/wave1/001_wave1_eddy_corrected_data_repol.nii.gz


# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only 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 = 001/wave1/bvecs_65_rotated.txt


# Diffusion b-value tables (file names can be relative to dcmroot)
# Must be specified only 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 = 001/wave1/bvals_65.txt

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 0



# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 9

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Target brain for inter-subject registration
# Default for affine T1-to-T1: 
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1: 
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA: 
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz


# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
# still running... will use in later versions of config
set usethalnuc = 0

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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 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to 

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

gt;>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis <
>>>>>> alandarkene...@gmail.com> wrote:
>>>>>>
>>>>>>> External Email - Use Caution
>>>>>>>
>>>>>>> Hi Anastasia :
>>>>>>>
>>>>>>> I installed ANTS and tried this
>>>>>>>
>>>>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>>>>
>>>>>>> but it did not work. Is there a different set path?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Alan
>>>>>>>
>>>>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>>>
>>>>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>>>>> installed and set ANTSPATH to its location.
>>>>>>>> --
>>>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>>>>> alandarkene...@gmail.com>
>>>>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>>>>> *To:* Freesurfer support list 
>>>>>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>>>>>
>>>>>>>>
>>>>>>>> External Email - Use Caution
>>>>>>>>
>>>>>>>> Hi Anastasia and King_Wei :
>>>>>>>>
>>>>>>>> Thank you for your suggestions. I have fixed the bet issue by
>>>>>>>> reinstalling FSL. But I have one more error:
>>>>>>>>
>>>>>>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>>>>>>
>>>>>>>> I tried setting
>>>>>>>>
>>>>>>>> set ANTSPATH = 0 but that did not work.
>>>>>>>>
>>>>>>>> I looked up the web to see if there were any default values I could
>>>>>>>> use for ANTs but did not come up with any.
>>>>>>>>
>>>>>>>> Thanks again for your help,
>>>>>>>>
>>>>>>>> Alan
>>>>>>>>
>>>>>>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu <
>>>>>>>> kingwai@gmail.com> wrote:
>>>>>>>>
>>>>>>>> External Email - Use Caution
>>>>>>>>
>>>>>>>> Hi Alan,
>>>>>>>>
>>>>>>>> If you really have FSL installed inside Freesurfer, it is not the
>>>>>>>> way to do it.
>>>>>>>> If you type
>>>>>>>> echo $FSLDIR
>>>>>>>> does it return anything?
>>>>>>>> If FSL is installed the way you said it is, echo $FSLDIR should
>>>>>>>> give something like
>>>>>>>> /usr/local/freesurfer/7.2.0-1/FSL
>>>>>>>> in your system
>>>>>>>>
>>>>>>>> Also, if you type
>>>>>>>> which bet
>>>>>>>> It should return something like
>>>>>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>>>>> or type
>>>>>>>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>>>>> Does it say "No such file or directory" or return
>>>>>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>>>>>
>>>>>>>> If you don't get all these, your FSL is not installed correctly.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> King-Wai
>>>>>>>>
>>>>>>>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis <
>>>>>>>> alandarkene...@gmail.com> wrote:
>>>>>>>>
>>>>>>>> External Email - Use Caution
>>>>>>>>
>>>>>>>> Hi Anastasia and King wei -
>>>>>>>>
>>>>>>>> I checked the

Re: [Freesurfer] Tracula - Preproc

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

First find out the version of ANTs you have by running the command below
antsRegistration --version

If it is below 2.1.0
download the 2.1.0 binaries here, it works for me.
https://secure-web.cisco.com/1NMd_rcPaYSvhGkOTDq6LZhGGFrvJPOKYz-pvH2Y8mi4GpUZhsdzgMiDYBrwA13AACNGNmIhkqZqQoEIs5fSIgISExrttLBYgDTATDAQ5lxNqC2J_SgADNsbw4OyIDVabLhAWxR0PqOIHYjqGICgWOpQSNH1KD1ng_fPfLqRfhcavePNTbCgLbM4n3fXSDbP6PkHxNn-F5ty6DhoULggX1RmZNaLXy5ad4UjX_cUhC3H6numGQgfYK7nFTnaFrdDP9WDUJluOnkqsLIJNcn3L2REEr0O3ZIwDrPHmuuMMo7mlcUTrG86Jmy5muPEYeTBs/https%3A%2F%2Fgithub.com%2FANTsX%2FANTs%2Freleases%2Ftag%2Fv2.1.0

If you want to use your script, edit the yellow lines to remove "#"
# If you want to build a particular release, do so here
# cd ANTs
# git checkout v2.3.1
# cd -

# If you want to build a particular release, do so here
cd ANTs
git checkout v2.3.1
cd -

you can also try v2.3.5 or v2.4.0.

I don't know if it will work or not because I don't write this script.

Best,

King-Wai

On Mon, Aug 15, 2022 at 1:15 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi King Wai -
>
> I used a script (enclosed) to install ANTs. Is there anyway this script
> could be modified to install the latest version?
>
> Thank you so much,
>
> Alan
>
> On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> Do you have the latest version of ANTs?
>> It should be 2.1.0
>> Older version don't have all the binaries and scripts required by
>> trac-all.
>>
>> Best,
>>
>> King-Wai
>>
>> On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hello King Wai -
>>>
>>> I used the C shell pathway just as you specified. But I got this error
>>> message right at the end of the processing:
>>>
>>> #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
>>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
>>> /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
>>> /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
>>> /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
>>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not
>>> found.
>>> Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
>>> 2022 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022
>>>
>>> In the installed ANTs folder I could not find the
>>> *antsRegistrationSyNQuick.sh* script. Should I create this script?
>>>
>>> Thanks ever so much!
>>>
>>> Alan
>>>
>>> On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
>>> wrote:
>>>
>>>> Thank you so much King Wai,
>>>>
>>>> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> For bash shell
>>>>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>>>>
>>>>> For tcsh
>>>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>>>
>>>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>>>>> wrote:
>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Hi Anastasia :
>>>>>>
>>>>>> I installed ANTS and tried this
>>>>>>
>>>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>>>
>>>>>> but it did not work. Is there a different set path?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Alan
>>>>>>
>>>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>>
>>>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>>>> installed and set ANTSPATH to its location.
>>>>>>> --
>>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>>>> alandarkene...@gmail.com>
>>>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>>>> *To:* Freesurfer support lis

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hi King Wai -

I used a script (enclosed) to install ANTs. Is there anyway this script
could be modified to install the latest version?

Thank you so much,

Alan

On Mon, Aug 15, 2022 at 11:40 AM King-Wai Chu  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> Do you have the latest version of ANTs?
> It should be 2.1.0
> Older version don't have all the binaries and scripts required by trac-all.
>
> Best,
>
> King-Wai
>
> On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Hello King Wai -
>>
>> I used the C shell pathway just as you specified. But I got this error
>> message right at the end of the processing:
>>
>> #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
>> /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
>> /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
>> /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
>> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not
>> found.
>> Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
>> 2022 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022
>>
>> In the installed ANTs folder I could not find the
>> *antsRegistrationSyNQuick.sh* script. Should I create this script?
>>
>> Thanks ever so much!
>>
>> Alan
>>
>> On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
>> wrote:
>>
>>> Thank you so much King Wai,
>>>
>>> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> For bash shell
>>>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>>>
>>>> For tcsh
>>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>>
>>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Anastasia :
>>>>>
>>>>> I installed ANTS and tried this
>>>>>
>>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>>
>>>>> but it did not work. Is there a different set path?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Alan
>>>>>
>>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>
>>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>>> installed and set ANTSPATH to its location.
>>>>>> --
>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>>> alandarkene...@gmail.com>
>>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>>> *To:* Freesurfer support list 
>>>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>>>
>>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Hi Anastasia and King_Wei :
>>>>>>
>>>>>> Thank you for your suggestions. I have fixed the bet issue by
>>>>>> reinstalling FSL. But I have one more error:
>>>>>>
>>>>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>>>>
>>>>>> I tried setting
>>>>>>
>>>>>> set ANTSPATH = 0 but that did not work.
>>>>>>
>>>>>> I looked up the web to see if there were any default values I could
>>>>>> use for ANTs but did not come up with any.
>>>>>>
>>>>>> Thanks again for your help,
>>>>>>
>>>>>> Alan
>>>>>>
>>>>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>>>>>> wrote:
>>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Hi Alan,
>>>>>>
>>>>>> If you really have FSL installed inside Freesurfer, it is not the way
>>>>>> to do it.
>>>>

Re: [Freesurfer] Tracula - Preproc

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

Do you have the latest version of ANTs?
It should be 2.1.0
Older version don't have all the binaries and scripts required by trac-all.

Best,

King-Wai

On Mon, Aug 15, 2022 at 11:49 AM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hello King Wai -
>
> I used the C shell pathway just as you specified. But I got this error
> message right at the end of the processing:
>
> #@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
> /home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
> /usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
> /home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
> /home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found.
> Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
> 2022 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022
>
> In the installed ANTs folder I could not find the
> *antsRegistrationSyNQuick.sh* script. Should I create this script?
>
> Thanks ever so much!
>
> Alan
>
> On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
> wrote:
>
>> Thank you so much King Wai,
>>
>> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> For bash shell
>>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>>
>>> For tcsh
>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>
>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Anastasia :
>>>>
>>>> I installed ANTS and tried this
>>>>
>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>
>>>> but it did not work. Is there a different set path?
>>>>
>>>> Thanks,
>>>>
>>>> Alan
>>>>
>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> If you want to use ANTs for registration, you have to have ANTs
>>>>> installed and set ANTSPATH to its location.
>>>>> --
>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>> alandarkene...@gmail.com>
>>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>>> *To:* Freesurfer support list 
>>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>>
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Anastasia and King_Wei :
>>>>>
>>>>> Thank you for your suggestions. I have fixed the bet issue by
>>>>> reinstalling FSL. But I have one more error:
>>>>>
>>>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>>>
>>>>> I tried setting
>>>>>
>>>>> set ANTSPATH = 0 but that did not work.
>>>>>
>>>>> I looked up the web to see if there were any default values I could
>>>>> use for ANTs but did not come up with any.
>>>>>
>>>>> Thanks again for your help,
>>>>>
>>>>> Alan
>>>>>
>>>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>>>>> wrote:
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Alan,
>>>>>
>>>>> If you really have FSL installed inside Freesurfer, it is not the way
>>>>> to do it.
>>>>> If you type
>>>>> echo $FSLDIR
>>>>> does it return anything?
>>>>> If FSL is installed the way you said it is, echo $FSLDIR should give
>>>>> something like
>>>>> /usr/local/freesurfer/7.2.0-1/FSL
>>>>> in your system
>>>>>
>>>>> Also, if you type
>>>>> which bet
>>>>> It should return something like
>>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>> or type
>>>>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>> Does it say "No such file or directory" or return
>>>>> /usr/local/freesur

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hello King Wai -

I used the C shell pathway just as you specified. But I got this error
message right at the end of the processing:

#@# Inter-subject registration Mon Aug 15 10:32:25 CDT 2022
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh -d 3 -m
/home/afrancis/Imaging/111312-2/dmri/dtifit_FA.nii.gz -f
/usr/local/freesurfer/7.2.0-1/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o
/home/afrancis/Imaging/111312-2/dmri/xfms/diff2syn
/home/afrancis/Imaging/ANTs/antsRegistrationSyNQuick.sh: Command not found.
Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT
2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug 15 10:32:25 CDT 2022

In the installed ANTs folder I could not find the
*antsRegistrationSyNQuick.sh* script. Should I create this script?

Thanks ever so much!

Alan

On Mon, Aug 15, 2022 at 10:13 AM Alan Francis 
wrote:

> Thank you so much King Wai,
>
> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> For bash shell
>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>
>> For tcsh
>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>
>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia :
>>>
>>> I installed ANTS and tried this
>>>
>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>
>>> but it did not work. Is there a different set path?
>>>
>>> Thanks,
>>>
>>> Alan
>>>
>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> If you want to use ANTs for registration, you have to have ANTs
>>>> installed and set ANTSPATH to its location.
>>>> ----------
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>> alandarkene...@gmail.com>
>>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>>> *To:* Freesurfer support list 
>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>
>>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Anastasia and King_Wei :
>>>>
>>>> Thank you for your suggestions. I have fixed the bet issue by
>>>> reinstalling FSL. But I have one more error:
>>>>
>>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>>
>>>> I tried setting
>>>>
>>>> set ANTSPATH = 0 but that did not work.
>>>>
>>>> I looked up the web to see if there were any default values I could use
>>>> for ANTs but did not come up with any.
>>>>
>>>> Thanks again for your help,
>>>>
>>>> Alan
>>>>
>>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>>>> wrote:
>>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Alan,
>>>>
>>>> If you really have FSL installed inside Freesurfer, it is not the way
>>>> to do it.
>>>> If you type
>>>> echo $FSLDIR
>>>> does it return anything?
>>>> If FSL is installed the way you said it is, echo $FSLDIR should give
>>>> something like
>>>> /usr/local/freesurfer/7.2.0-1/FSL
>>>> in your system
>>>>
>>>> Also, if you type
>>>> which bet
>>>> It should return something like
>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>> or type
>>>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>> Does it say "No such file or directory" or return
>>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>>
>>>> If you don't get all these, your FSL is not installed correctly.
>>>>
>>>> Best,
>>>>
>>>> King-Wai
>>>>
>>>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>>>> wrote:
>>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Anastasia and King wei -
>>>>
>>>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that
>>>> FSL is part of that installation. Do you recommend a second installation of
>>>> FSL separately?
>>>>
>>>> Thanks so much for your help and comme

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Thank you so much King Wai,

On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu  wrote:

> External Email - Use Caution
>
> For bash shell
> ANTSPATH=/home/afrancis/Imaging/ANTs
>
> For tcsh
> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>
> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Anastasia :
>>
>> I installed ANTS and tried this
>>
>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>
>> but it did not work. Is there a different set path?
>>
>> Thanks,
>>
>> Alan
>>
>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> If you want to use ANTs for registration, you have to have ANTs
>>> installed and set ANTSPATH to its location.
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>>> *Sent:* Friday, August 12, 2022 4:35 PM
>>> *To:* Freesurfer support list 
>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>
>>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia and King_Wei :
>>>
>>> Thank you for your suggestions. I have fixed the bet issue by
>>> reinstalling FSL. But I have one more error:
>>>
>>> ERROR: must set ANTSPATH environment variable to use ANTs
>>>
>>> I tried setting
>>>
>>> set ANTSPATH = 0 but that did not work.
>>>
>>> I looked up the web to see if there were any default values I could use
>>> for ANTs but did not come up with any.
>>>
>>> Thanks again for your help,
>>>
>>> Alan
>>>
>>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi Alan,
>>>
>>> If you really have FSL installed inside Freesurfer, it is not the way to
>>> do it.
>>> If you type
>>> echo $FSLDIR
>>> does it return anything?
>>> If FSL is installed the way you said it is, echo $FSLDIR should give
>>> something like
>>> /usr/local/freesurfer/7.2.0-1/FSL
>>> in your system
>>>
>>> Also, if you type
>>> which bet
>>> It should return something like
>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>> or type
>>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>> Does it say "No such file or directory" or return
>>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>>
>>> If you don't get all these, your FSL is not installed correctly.
>>>
>>> Best,
>>>
>>> King-Wai
>>>
>>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia and King wei -
>>>
>>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>>> is part of that installation. Do you recommend a second installation of FSL
>>> separately?
>>>
>>> Thanks so much for your help and comments!
>>>
>>> Alan
>>>
>>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi Alan,
>>>
>>>
>>>
>>> As Anastasia said, bet is part of FSL.
>>>
>>> If you don’t have it installed already, you need to install FSL.
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>>
>>> King-Wai
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki,
>>> Anastasia
>>> *Sent:* Thursday, August 11, 2022 3:42 PM
>>> *To:* Freesurfer support list 
>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>
>>>
>>>
>>> Yes that's from FSL. It's needs to be in $FSLDIR.
>>> --
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>>> *Sent:* Thursday, August 11, 2022 

Re: [Freesurfer] Tracula - Preproc

[King-Wai Chu]

External Email - Use Caution

For bash shell
ANTSPATH=/home/afrancis/Imaging/ANTs

For tcsh
setenv ANTSPATH /home/afrancis/Imaging/ANTs

On Fri, Aug 12, 2022 at 5:54 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi Anastasia :
>
> I installed ANTS and tried this
>
> set ANTSPATH = /home/afrancis/Imaging/ANTs
>
> but it did not work. Is there a different set path?
>
> Thanks,
>
> Alan
>
> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> If you want to use ANTs for registration, you have to have ANTs installed
>> and set ANTSPATH to its location.
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Friday, August 12, 2022 4:35 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia and King_Wei :
>>
>> Thank you for your suggestions. I have fixed the bet issue by
>> reinstalling FSL. But I have one more error:
>>
>> ERROR: must set ANTSPATH environment variable to use ANTs
>>
>> I tried setting
>>
>> set ANTSPATH = 0 but that did not work.
>>
>> I looked up the web to see if there were any default values I could use
>> for ANTs but did not come up with any.
>>
>> Thanks again for your help,
>>
>> Alan
>>
>> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> If you really have FSL installed inside Freesurfer, it is not the way to
>> do it.
>> If you type
>> echo $FSLDIR
>> does it return anything?
>> If FSL is installed the way you said it is, echo $FSLDIR should give
>> something like
>> /usr/local/freesurfer/7.2.0-1/FSL
>> in your system
>>
>> Also, if you type
>> which bet
>> It should return something like
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> or type
>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> Does it say "No such file or directory" or return
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>
>> If you don't get all these, your FSL is not installed correctly.
>>
>> Best,
>>
>> King-Wai
>>
>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>> wrote:
>>
>> External Email - Use Caution
>>
>> Hi Anastasia and King wei -
>>
>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>> is part of that installation. Do you recommend a second installation of FSL
>> separately?
>>
>> Thanks so much for your help and comments!
>>
>> Alan
>>
>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>>
>>
>> As Anastasia said, bet is part of FSL.
>>
>> If you don’t have it installed already, you need to install FSL.
>>
>>
>>
>> Best,
>>
>>
>>
>> King-Wai
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
>> *Sent:* Thursday, August 11, 2022 3:42 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>>
>> Yes that's from FSL. It's needs to be in $FSLDIR.
>> --
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Thursday, August 11, 2022 3:30 PM
>> *To:* Freesurfer 
>> *Subject:* [Freesurfer] Tracula - Preproc
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Anastasia, King Wei:
>>
>>
>>
>> I did as you suggested with the config file and the preprocessing ran for
>> a bit but then an error occurred. I have attached the run script. It says
>> BET not found. Is this the Brain Extraction tool?
>>
>>
>>
>> Could you please shed some light on this?
>>
>>
>>
>> thanks so much,
>>
>>
>>
>> Alan
>>
>>
>> --
>>
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>
&

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hi Anastasia :

I installed ANTS and tried this

set ANTSPATH = /home/afrancis/Imaging/ANTs

but it did not work. Is there a different set path?

Thanks,

Alan

On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia 
wrote:

> If you want to use ANTs for registration, you have to have ANTs installed
> and set ANTSPATH to its location.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Friday, August 12, 2022 4:35 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Tracula - Preproc
>
>
> External Email - Use Caution
>
> Hi Anastasia and King_Wei :
>
> Thank you for your suggestions. I have fixed the bet issue by reinstalling
> FSL. But I have one more error:
>
> ERROR: must set ANTSPATH environment variable to use ANTs
>
> I tried setting
>
> set ANTSPATH = 0 but that did not work.
>
> I looked up the web to see if there were any default values I could use
> for ANTs but did not come up with any.
>
> Thanks again for your help,
>
> Alan
>
> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
> wrote:
>
> External Email - Use Caution
>
> Hi Alan,
>
> If you really have FSL installed inside Freesurfer, it is not the way to
> do it.
> If you type
> echo $FSLDIR
> does it return anything?
> If FSL is installed the way you said it is, echo $FSLDIR should give
> something like
> /usr/local/freesurfer/7.2.0-1/FSL
> in your system
>
> Also, if you type
> which bet
> It should return something like
> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
> or type
> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
> Does it say "No such file or directory" or return
> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>
> If you don't get all these, your FSL is not installed correctly.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
> wrote:
>
> External Email - Use Caution
>
> Hi Anastasia and King wei -
>
> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
> is part of that installation. Do you recommend a second installation of FSL
> separately?
>
> Thanks so much for your help and comments!
>
> Alan
>
> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>
> External Email - Use Caution
>
> Hi Alan,
>
>
>
> As Anastasia said, bet is part of FSL.
>
> If you don’t have it installed already, you need to install FSL.
>
>
>
> Best,
>
>
>
> King-Wai
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
> *Sent:* Thursday, August 11, 2022 3:42 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Tracula - Preproc
>
>
>
> Yes that's from FSL. It's needs to be in $FSLDIR.
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 11, 2022 3:30 PM
> *To:* Freesurfer 
> *Subject:* [Freesurfer] Tracula - Preproc
>
>
>
> *External Email - Use Caution*
>
> Hi Anastasia, King Wei:
>
>
>
> I did as you suggested with the config file and the preprocessing ran for
> a bit but then an error occurred. I have attached the run script. It says
> BET not found. Is this the Brain Extraction tool?
>
>
>
> Could you please shed some light on this?
>
>
>
> thanks so much,
>
>
>
> Alan
>
>
> --
>
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
>
> *Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
> Neuroscience*
>
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley*
>
> *Texas.*
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1kmGk3eaVED_r9v2sch0zUwDQf_N1l7oRm0rXzQZrFiO9Qe2oToTdA6VNhB1sMV8WewODy8rtaT5aZgsHm4mn79Feu4jQV2PEL7D_56ZO680gA5g1VWd6Q9DMFVdkVg6T__bkr7lYT51johrjzh-7OUnNhpGGCz5bMwhHR_3vH5w3Fvx0CxzDc1OM0P3kdnRufUqDhnSIG6xtyhFRGaUF9HdVBPvSRMIxVbXXMBrw5ziw5cpjI-bhpnEJgIe9Z_aaMSh_jL-48zGleSExo_7q7vu1DoqsWuNwdf5DcjoSPEaTM0FLI3w1i_AzNKTcC8oL3-1bsyo2KnSAVYHOeuWLdg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> <https://s

Re: [Freesurfer] Tracula - Preproc

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

You need to install Advanced Normalization Tools(ANTS)
https://secure-web.cisco.com/1xl8ADqLGMhYjn7TbMOsRonEy_R5C4feN8mMJ-Q7bddD3E_kk_PzT6LUVVJPXi70pbS8fDlYVtT5FZrovy4oO8F6esYTNDGGmBMZIcnfJjKjqysycppupQwOtlATRsVGkxuOe_hdaI5TbjfjkBv6w3Sy0DIhpR6yfl6YYGbceEbrDPEyiri7niCivYdPtWY7roMFW1urF87IjvtXzJTpdRjnKuM_GCbZ1A7MarsQB-elnw6ZSy-uE4Jo5QALYd1tAMpAVAb1JVbjj2DImfV5v3vsL5T0Ftffq2F7_UmQy8JDepEGdgvtyOH5Zt0aM_Yo9ZBBOdUfHr-ZPBJfino6Xgg/https%3A%2F%2Fsourceforge.net%2Fprojects%2Fadvants%2F

You can compile from source or get the binaries.

Best,

King-Wai

On Fri, Aug 12, 2022 at 4:37 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi Anastasia and King_Wei :
>
> Thank you for your suggestions. I have fixed the bet issue by reinstalling
> FSL. But I have one more error:
>
> ERROR: must set ANTSPATH environment variable to use ANTs
>
> I tried setting
>
> set ANTSPATH = 0 but that did not work.
>
> I looked up the web to see if there were any default values I could use
> for ANTs but did not come up with any.
>
> Thanks again for your help,
>
> Alan
>
> On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> If you really have FSL installed inside Freesurfer, it is not the way to
>> do it.
>> If you type
>> echo $FSLDIR
>> does it return anything?
>> If FSL is installed the way you said it is, echo $FSLDIR should give
>> something like
>> /usr/local/freesurfer/7.2.0-1/FSL
>> in your system
>>
>> Also, if you type
>> which bet
>> It should return something like
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> or type
>> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>> Does it say "No such file or directory" or return
>> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>>
>> If you don't get all these, your FSL is not installed correctly.
>>
>> Best,
>>
>> King-Wai
>>
>> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia and King wei -
>>>
>>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>>> is part of that installation. Do you recommend a second installation of FSL
>>> separately?
>>>
>>> Thanks so much for your help and comments!
>>>
>>> Alan
>>>
>>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Alan,
>>>>
>>>>
>>>>
>>>> As Anastasia said, bet is part of FSL.
>>>>
>>>> If you don’t have it installed already, you need to install FSL.
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>>
>>>> King-Wai
>>>>
>>>>
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki,
>>>> Anastasia
>>>> *Sent:* Thursday, August 11, 2022 3:42 PM
>>>> *To:* Freesurfer support list 
>>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>>
>>>>
>>>>
>>>> Yes that's from FSL. It's needs to be in $FSLDIR.
>>>> --
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>> alandarkene...@gmail.com>
>>>> *Sent:* Thursday, August 11, 2022 3:30 PM
>>>> *To:* Freesurfer 
>>>> *Subject:* [Freesurfer] Tracula - Preproc
>>>>
>>>>
>>>>
>>>> *External Email - Use Caution*
>>>>
>>>> Hi Anastasia, King Wei:
>>>>
>>>>
>>>>
>>>> I did as you suggested with the config file and the preprocessing ran
>>>> for a bit but then an error occurred. I have attached the run script. It
>>>> says BET not found. Is this the Brain Extraction tool?
>>>>
>>>>
>>>>
>>>> Could you please shed some light on this?
>>>>
>>>>
>>>>
>>>> thanks so much,
>>>>
>>>>
>>>>
>>>> Alan
>>>>
>>>>
>>>> --
>>>>
>>>> *|~|~|~|~|~|~|~|~|~|

Re: [Freesurfer] Tracula - Preproc

[Yendiki, Anastasia]

If you want to use ANTs for registration, you have to have ANTs installed and 
set ANTSPATH to its location.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Friday, August 12, 2022 4:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula - Preproc


External Email - Use Caution

Hi Anastasia and King_Wei :

Thank you for your suggestions. I have fixed the bet issue by reinstalling FSL. 
But I have one more error:

ERROR: must set ANTSPATH environment variable to use ANTs

I tried setting

set ANTSPATH = 0 but that did not work.

I looked up the web to see if there were any default values I could use for 
ANTs but did not come up with any.

Thanks again for your help,

Alan

On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

If you really have FSL installed inside Freesurfer, it is not the way to do it.
If you type
echo $FSLDIR
does it return anything?
If FSL is installed the way you said it is, echo $FSLDIR should give something 
like
/usr/local/freesurfer/7.2.0-1/FSL
in your system

Also, if you type
which bet
It should return something like
/usr/local/freesurfer/7.2.0-1/FSL/bin/bet
or type
ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
Does it say "No such file or directory" or return
/usr/local/freesurfer/7.2.0-1/FSL/bin/bet

If you don't get all these, your FSL is not installed correctly.

Best,

King-Wai

On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hi Anastasia and King wei -

I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is 
part of that installation. Do you recommend a second installation of FSL 
separately?

Thanks so much for your help and comments!

Alan

On Thu, Aug 11, 2022 at 2:50 PM 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,



As Anastasia said, bet is part of FSL.

If you don’t have it installed already, you need to install FSL.



Best,



King-Wai



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Yendiki, Anastasia
Sent: Thursday, August 11, 2022 3:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula - Preproc



Yes that's from FSL. It's needs to be in $FSLDIR.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alan Francis 
mailto:alandarkene...@gmail.com>>
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula - Preproc



External Email - Use Caution

Hi Anastasia, King Wei:



I did as you suggested with the config file and the preprocessing ran for a bit 
but then an error occurred. I have attached the run script. It says BET not 
found. Is this the Brain Extraction tool?



Could you please shed some light on this?



thanks so much,



Alan

--

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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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 Mass General Brigham 
Compliance HelpLine at MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzC

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hi Anastasia and King_Wei :

Thank you for your suggestions. I have fixed the bet issue by reinstalling
FSL. But I have one more error:

ERROR: must set ANTSPATH environment variable to use ANTs

I tried setting

set ANTSPATH = 0 but that did not work.

I looked up the web to see if there were any default values I could use for
ANTs but did not come up with any.

Thanks again for your help,

Alan

On Fri, Aug 12, 2022 at 12:03 PM King-Wai Chu  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> If you really have FSL installed inside Freesurfer, it is not the way to
> do it.
> If you type
> echo $FSLDIR
> does it return anything?
> If FSL is installed the way you said it is, echo $FSLDIR should give
> something like
> /usr/local/freesurfer/7.2.0-1/FSL
> in your system
>
> Also, if you type
> which bet
> It should return something like
> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
> or type
> ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
> Does it say "No such file or directory" or return
> /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
>
> If you don't get all these, your FSL is not installed correctly.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Anastasia and King wei -
>>
>> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
>> is part of that installation. Do you recommend a second installation of FSL
>> separately?
>>
>> Thanks so much for your help and comments!
>>
>> Alan
>>
>> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi Alan,
>>>
>>>
>>>
>>> As Anastasia said, bet is part of FSL.
>>>
>>> If you don’t have it installed already, you need to install FSL.
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>>
>>> King-Wai
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki,
>>> Anastasia
>>> *Sent:* Thursday, August 11, 2022 3:42 PM
>>> *To:* Freesurfer support list 
>>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>>
>>>
>>>
>>> Yes that's from FSL. It's needs to be in $FSLDIR.
>>> --
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>>> *Sent:* Thursday, August 11, 2022 3:30 PM
>>> *To:* Freesurfer 
>>> *Subject:* [Freesurfer] Tracula - Preproc
>>>
>>>
>>>
>>> *External Email - Use Caution*
>>>
>>> Hi Anastasia, King Wei:
>>>
>>>
>>>
>>> I did as you suggested with the config file and the preprocessing ran
>>> for a bit but then an error occurred. I have attached the run script. It
>>> says BET not found. Is this the Brain Extraction tool?
>>>
>>>
>>>
>>> Could you please shed some light on this?
>>>
>>>
>>>
>>> thanks so much,
>>>
>>>
>>>
>>> Alan
>>>
>>>
>>> --
>>>
>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>>
>>>
>>>
>>>
>>> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
>>> Neuroscience*
>>>
>>> *University of Texas, School of Medicine*
>>>
>>> *Rio Grande Valley*
>>>
>>> *Texas.*
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1RNwSit2rkfAZobK86FQ-0u2W7rCOisOJGNJUdXTjn4JJ_YYTEc5JfrFEULZiLkFuBHufgfdpKHdpMqnUv8zvjqfHCJR2rIHnmHtA-D8ugMIJRy9iJz0o-vcL3JGmXuBvnVtYjC3GelPiAUEhCPrpSeC065rIfDq5flQonzJ7AMYasSka968hktBTOEpmUxwNSGzp0b7LZXcoSOnynpezXd6sg9UGQnpQ1q92SLi4mG-ougxszyUvzXx14aTviYybE3wAQ1O1YTLZUHDGd_GyKeLeCmjnqJnozZbRW_l5BNHcTTm_dorYVy4VzLnEKjRTBdBua2iPb3b1NL1wsextrw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1jeB_jxkGKWxaafWD_KPYT2IRAgjmZbPF2G

Re: [Freesurfer] Tracula - Preproc

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

If you really have FSL installed inside Freesurfer, it is not the way to do
it.
If you type
echo $FSLDIR
does it return anything?
If FSL is installed the way you said it is, echo $FSLDIR should give
something like
/usr/local/freesurfer/7.2.0-1/FSL
in your system

Also, if you type
which bet
It should return something like
/usr/local/freesurfer/7.2.0-1/FSL/bin/bet
or type
ls /usr/local/freesurfer/7.2.0-1/FSL/bin/bet
Does it say "No such file or directory" or return
/usr/local/freesurfer/7.2.0-1/FSL/bin/bet

If you don't get all these, your FSL is not installed correctly.

Best,

King-Wai

On Fri, Aug 12, 2022 at 12:34 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hi Anastasia and King wei -
>
> I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL
> is part of that installation. Do you recommend a second installation of FSL
> separately?
>
> Thanks so much for your help and comments!
>
> Alan
>
> On Thu, Aug 11, 2022 at 2:50 PM  wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>>
>>
>> As Anastasia said, bet is part of FSL.
>>
>> If you don’t have it installed already, you need to install FSL.
>>
>>
>>
>> Best,
>>
>>
>>
>> King-Wai
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
>> *Sent:* Thursday, August 11, 2022 3:42 PM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>>
>> Yes that's from FSL. It's needs to be in $FSLDIR.
>> --
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Thursday, August 11, 2022 3:30 PM
>> *To:* Freesurfer 
>> *Subject:* [Freesurfer] Tracula - Preproc
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Anastasia, King Wei:
>>
>>
>>
>> I did as you suggested with the config file and the preprocessing ran for
>> a bit but then an error occurred. I have attached the run script. It says
>> BET not found. Is this the Brain Extraction tool?
>>
>>
>>
>> Could you please shed some light on this?
>>
>>
>>
>> thanks so much,
>>
>>
>>
>> Alan
>>
>>
>> --
>>
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>
>>
>>
>>
>> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
>> Neuroscience*
>>
>> *University of Texas, School of Medicine*
>>
>> *Rio Grande Valley*
>>
>> *Texas.*
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1ya6JvGMaiTaLdV_RFI9p755zjyL9Xf7XygbVoLWjVcp1aMfCW54Ve6BXwyVTgw-sXgRlCbmWpM_HbJqT31X3b13LFy66hGznBK01PvWGqUimueqP9QVQYDFwMKYAt-U07t8W-9hFs5dcHM0tuz8fwSxvrgoEdY77mF3-sRfq_zNd6fLw9A_2iJlecVDkDmPNVs8t6YO5uEV2HK1MIO2GjjVBCgqOOAOroVb6ZNL5Y2hJus5WrH8CVwLBN5mijz1uxDoKZENg4ESJj8LMFh9_AYnIRkIenN3xWRP1hhC9yuBAAL732Uw4iEB7CAATwQSGjvqdGG1W_Opkjw8eqCL96A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1jeB_jxkGKWxaafWD_KPYT2IRAgjmZbPF2GIUKKyvtF0_D3f3h4-FmZEPPt9Qlxio_CsG9mZaxY9l6gxc1MaZ1iWaodvNxwaCqKduHKs28N2e5-Ycc3MCG6UECKEzDxEG0UXLO8ukNiQwGgEvtS2-e8Svdio6FYyK1C7gtXoQcMpXR-IPcYaUbo0H8VOFKQIwfrheBtub-PMCrbzUzE-iUjRIbJiEH4f2uV4-blBzqVw-z1gFbivJ4DmwHoNYrb9CIBq2QHpqSQ_-TkUtUpKWGRi9GSaECcvVcox4xu6wwXOnLGGkGtRj1-BIJ7pSoe_wZR823aE7968dYs6eiAFnoA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>> 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 Mass General
>> Brigham Compliance HelpLine at *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1q5No534S3eCaYMPbpL73aDavRve-q80-4p88Pn9BopRGlLQI1tU_C1Z7nerNEfGNQG7jtovxmvHvXxNMPROSRiAKNw2aZ-q3aq1WmtcmpOoXvRwiwdnnjRKwChdCmOnfIT8wofo0PX29IeXcb94DlmzuNYshWxDX5mgBposqt4Tys2fjDnSQ4D3zTn54qHmF3wWW4XON5ejopaNPdibMgayrdMIHwFKy3VnpiyiJVpjBIMpH9Nml3JU

Re: [Freesurfer] Tracula - Preproc

[Yendiki, Anastasia]

The error message that you got says that the bet command isn't in your Unix 
path. You need to fix that, so that you don't get that error. If bet and all 
the other FSL executables are already installed somewhere on your computer, you 
need to add that directory to your Unix path. I'm not sure what "It shows that 
FSL is part of that installation" means (what does "it" refer to?), but if 
"which bet" doesn't show you a directory where bet can be found, you won't be 
able to get any further.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Friday, August 12, 2022 12:33 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula - Preproc


External Email - Use Caution

Hi Anastasia and King wei -

I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is 
part of that installation. Do you recommend a second installation of FSL 
separately?

Thanks so much for your help and comments!

Alan

On Thu, Aug 11, 2022 at 2:50 PM 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,



As Anastasia said, bet is part of FSL.

If you don’t have it installed already, you need to install FSL.



Best,



King-Wai



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Yendiki, Anastasia
Sent: Thursday, August 11, 2022 3:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula - Preproc



Yes that's from FSL. It's needs to be in $FSLDIR.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alan Francis 
mailto:alandarkene...@gmail.com>>
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula - Preproc



External Email - Use Caution

Hi Anastasia, King Wei:



I did as you suggested with the config file and the preprocessing ran for a bit 
but then an error occurred. I have attached the run script. It says BET not 
found. Is this the Brain Extraction tool?



Could you please shed some light on this?



thanks so much,



Alan

--

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.



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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.

__

Re: [Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hi Anastasia and King wei -

I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is
part of that installation. Do you recommend a second installation of FSL
separately?

Thanks so much for your help and comments!

Alan

On Thu, Aug 11, 2022 at 2:50 PM  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
>
>
> As Anastasia said, bet is part of FSL.
>
> If you don’t have it installed already, you need to install FSL.
>
>
>
> Best,
>
>
>
> King-Wai
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
> *Sent:* Thursday, August 11, 2022 3:42 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Tracula - Preproc
>
>
>
> Yes that's from FSL. It's needs to be in $FSLDIR.
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 11, 2022 3:30 PM
> *To:* Freesurfer 
> *Subject:* [Freesurfer] Tracula - Preproc
>
>
>
> *External Email - Use Caution*
>
> Hi Anastasia, King Wei:
>
>
>
> I did as you suggested with the config file and the preprocessing ran for
> a bit but then an error occurred. I have attached the run script. It says
> BET not found. Is this the Brain Extraction tool?
>
>
>
> Could you please shed some light on this?
>
>
>
> thanks so much,
>
>
>
> Alan
>
>
> --
>
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
>
> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
> Neuroscience*
>
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley*
>
> *Texas.*
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1jeB_jxkGKWxaafWD_KPYT2IRAgjmZbPF2GIUKKyvtF0_D3f3h4-FmZEPPt9Qlxio_CsG9mZaxY9l6gxc1MaZ1iWaodvNxwaCqKduHKs28N2e5-Ycc3MCG6UECKEzDxEG0UXLO8ukNiQwGgEvtS2-e8Svdio6FYyK1C7gtXoQcMpXR-IPcYaUbo0H8VOFKQIwfrheBtub-PMCrbzUzE-iUjRIbJiEH4f2uV4-blBzqVw-z1gFbivJ4DmwHoNYrb9CIBq2QHpqSQ_-TkUtUpKWGRi9GSaECcvVcox4xu6wwXOnLGGkGtRj1-BIJ7pSoe_wZR823aE7968dYs6eiAFnoA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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>  <
> https://secure-web.cisco.com/1u4v3sPgHzaXdLUOyn7NSBcwLUbsaUfJPkKo-3t0w4fXcImxk_xuMfLQll6xZ2YFSHmPfHUaZw0VMjWf9kazYVfq7aHHpucMy9wcOUGpeiaxj-NrRsKNlR6iBlpo5q2VkcyekjXdIVQ2-egNx91gbi7Tq2DWlvDP3JiriUpmB6Wg6jGq5MdlXrbY8AB85_tLKO0bQR3Jj3o1xfI8MQwayoplrJRbUN9RdbJCPExC-3FGkw1eWk5H7Uc8fAc1m7uedJzDKzrX3NBd0bXty0SAXzCMAD3ZeH7i0TMQH5Zhg4QbeZG7s_QdP_E5obZXlgHiw-nadkn11dbv3lBRemXneow/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
___
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Re: [Freesurfer] Tracula - Preproc

[kingwai.chu]

External Email - Use Caution

Hi Alan,

 �

As Anastasia said, bet is part of FSL.

If you don’t have it installed already, you need to install FSL.

 �

Best,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Thursday, August 11, 2022 3:42 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula - Preproc

 �

Yes that's from FSL. It's needs to be in $FSLDIR.

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Alan Francis 
mailto:alandarkene...@gmail.com> >
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: [Freesurfer] Tracula - Preproc 

 �

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia, King Wei:

 �

I did as you suggested with the config file and the preprocessing ran for a bit 
but then an error occurred. I have attached the run script. It says BET not 
found. Is this the Brain Extraction tool?

 �

Could you please shed some light on this?

 �

thanks so much,

 �

Alan


-- 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.



 

___
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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula - Preproc

[Yendiki, Anastasia]

Yes that's from FSL. It's needs to be in $FSLDIR.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer 
Subject: [Freesurfer] Tracula - Preproc


External Email - Use Caution

Hi Anastasia, King Wei:

I did as you suggested with the config file and the preprocessing ran for a bit 
but then an error occurred. I have attached the run script. It says BET not 
found. Is this the Brain Extraction tool?

Could you please shed some light on this?

thanks so much,

Alan

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.

___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Tracula - Preproc

[Alan Francis]

External Email - Use Caution

Hi Anastasia, King Wei:

I did as you suggested with the config file and the preprocessing ran for a
bit but then an error occurred. I have attached the run script. It says BET
not found. Is this the Brain Extraction tool?

Could you please shed some light on this?

thanks so much,

Alan

-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*


111312_Script
Description: Binary data
___
Freesurfer mailing list
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Thank you Anastasia and King-Wai.

On Fri, Aug 5, 2022 at 4:12 PM Yendiki, Anastasia 
wrote:

> You only need to specify path names if you don't want to reconstruct all
> 42 paths. But from the list, it looks like you want all 42 paths, so you
> don't need to specify anything. Skip all of those lines and you'll get the
> default behavior.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of King-Wai Chu <
> kingwai@gmail.com>
> *Sent:* Friday, August 5, 2022 5:03 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Tracula Config file.
>
>
> External Email - Use Caution
>
> Hi Alan,
>
> In your pathlist, the 1st path is acomm.  You have "ac" in your file.
> Change ac to acomm and you should be good to go.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 5, 2022 at 4:23 PM Alan Francis 
> wrote:
>
> External Email - Use Caution
>
> Hi King-Wai -
>
> First of all, thank you so much for taking the time to investigate my RC
> file. I made the changes that you suggested, but the error keeps coming up.
>
> I have attached the file.
>
> Thanks again,
>
> Alan
>
> On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu  wrote:
>
> External Email - Use Caution
>
> Hi Alan,
>
> They still don't match.
> See attached excel file.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
> wrote:
>
> External Email - Use Caution
>
> Hello King-Wai -
>
> I made the change to the ncpts. But still an error message persists.
>
> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af
> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
> rh.af
> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
> lh.ar
> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
> rh.ar
> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc
> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1
> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID
> list
> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0
> 0 0 10 49 0 0 0 0 0 0 0 0) do not match
>
>
>
> I have attached the RC file. Could you please shed some light on this?
>
> Thank you
>
> Alan
>
> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
> wrote:
>
> External Email - Use Caution
>
> Hi Alan,
>
> Your pathlist and "Number of path control points"(ncpts) don't match.
> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>
> Best,
>
> King-Wai
>
>
>
>
> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
> wrote:
>
> External Email - Use Caution
>
> Good morning Anastasia -
>
> I made the changes you suggested and removed "extraneous" commands. But
> the error message still persists. Could you please shed some light on this?
> Attached - latest RC file.
>
> The error message is : unmatched ' " '
>
> Thank you
>
> Alan
>
> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Alan - dcmroot is the root directory under which the dicom files are
> save

Re: [Freesurfer] Tracula Config file.

[Yendiki, Anastasia]

You only need to specify path names if you don't want to reconstruct all 42 
paths. But from the list, it looks like you want all 42 paths, so you don't 
need to specify anything. Skip all of those lines and you'll get the default 
behavior.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of King-Wai Chu 

Sent: Friday, August 5, 2022 5:03 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula Config file.


External Email - Use Caution

Hi Alan,

In your pathlist, the 1st path is acomm.  You have "ac" in your file.
Change ac to acomm and you should be good to go.

Best,

King-Wai

On Fri, Aug 5, 2022 at 4:23 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hi King-Wai -

First of all, thank you so much for taking the time to investigate my RC file. 
I made the changes that you suggested, but the error keeps coming up.

I have attached the file.

Thanks again,

Alan

On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

They still don't match.
See attached excel file.

Best,

King-Wai

On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Hello King-Wai -

I made the change to the ncpts. But still an error message persists.

ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm 
cc.bodyt cc.genu cc.rostrum cc.splenium mcp 
lh.af<http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
 
rh.af<http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
 
lh.ar<http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
 
rh.ar<http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
 lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat 
rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 
lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list
ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 
10 49 0 0 0 0 0 0 0 0) do not match



I have attached the RC file. Could you please shed some light on this?

Thank you

Alan

On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

Your pathlist and "Number of path control points"(ncpts) don't match.
You have more than 3 paths in the pathlist and only 3 numbers in ncpts.

Best,

King-Wai




On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Good morning Anastasia -

I made the changes you suggested and removed "extraneous" commands. But the 
error message still persists. Could you please shed some light on this? 
Attached - latest RC file.

The error message is : unmatched ' " '

Thank you

Alan

On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. 
It's actually optional. In your case, either of the following will have the 
same, correct effect:

set dcmroot = /home/afrancis/Imaging
set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

OR

set dcmlist = 
(/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

In addition, there are a lot of things that you left in there from the example 
RC file. You should delete them entirely, unless you specifically want to set 
one of those things to something other than the default. These are examples 
that may not give you the default behavior. Also the fi

Re: [Freesurfer] Tracula Config file.

[King-Wai Chu]

tory under which the dicom files
>>>>>> are saved. It's actually optional. In your case, either of the following
>>>>>> will have the same, correct effect:
>>>>>>
>>>>>> set dcmroot = /home/afrancis/Imaging
>>>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>>
>>>>>> OR
>>>>>>
>>>>>> set dcmlist =
>>>>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>>
>>>>>> In addition, there are *a lot *of things that you left in there from
>>>>>> the example RC file. You should delete them entirely, unless you
>>>>>> specifically want to set one of those things to something other than the
>>>>>> default. These are examples that may not give you the default behavior.
>>>>>> Also the field mapping files - delete those lines because you're just 
>>>>>> using
>>>>>> the example names and they're not going to work. You want your RC file to
>>>>>> have the minimum necessary for your analysis.
>>>>>>
>>>>>> Best,
>>>>>> Anastasia.
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>>>>> alandarkene...@gmail.com>
>>>>>> *Sent:* Thursday, August 4, 2022 12:23 PM
>>>>>> *To:* Freesurfer 
>>>>>> *Subject:* [Freesurfer] Tracula Config file.
>>>>>>
>>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Hi Anastasia -
>>>>>>
>>>>>> Hope you are well. I am running tracula on FS 7.2. I created the RC
>>>>>> file based on your recommendations. However it is giving me an error
>>>>>> message when I run it. The error is : Unmatched ' " "
>>>>>>
>>>>>> I have attached the RC file. Could you please see where I have made
>>>>>> an error.
>>>>>>
>>>>>> Thanks so much,
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Alan
>>>>>>
>>>>>> --
>>>>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>>>>>
>>>>>>
>>>>>>
>>>>>> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute
>>>>>> of Neuroscience*
>>>>>> *University of Texas, School of Medicine*
>>>>>>
>>>>>> *Rio Grande Valley *
>>>>>>
>>>>>> *Texas. *
>>>>>>
>>>>>>
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> *MailScanner has detected a possible fraud attempt from
>>>>>> "secure-web.cisco.com" claiming to be*
>>>>>> https://secure-web.cisco.com/1XlCWn3g7bLYkF8PVtxFGc9r5F-BB3nFMLFsiBFhEvLPv48HxOzfHI7H4oBTrnwC3JEsGro052TRQmVVPsl6SEJ66mtJF0vrRmC8uj5DspNHA7HcwwGrc5iM99Wutcbt2KzLTPxw8PN7qW8FbKNmJhtUdt2Fb3q6ov3ifYaqVmpzbGmCe9uRlujCgWXe1Rpt339DGqiXqCsfWFXdZAVYC-RAUIHNvA_TmDiHvuGhV32Ok6CSRaE20GQ74yS8XT6JtPPL5oEYE9yirA_l5Za3c_z5HtNSL6Jo580YF031znbkdV-ez1WRGJ9AgsNkhxvg1LB2fUMHqF5BbKWaFmO-OQg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>>>> <https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>>>>> 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 Mass
>>>>>> General Brigham Compliance HelpLine at *MailScanner has detected a
>>>>>> possible fraud attempt from "secure-w

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Hi King-Wai -

First of all, thank you so much for taking the time to investigate my RC
file. I made the changes that you suggested, but the error keeps coming up.

I have attached the file.

Thanks again,

Alan

On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> They still don't match.
> See attached excel file.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Hello King-Wai -
>>
>> I made the change to the ncpts. But still an error message persists.
>>
>> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
>> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af
>> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
>> rh.af
>> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
>> lh.ar
>> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
>> rh.ar
>> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
>> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc
>> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1
>> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID
>> list
>> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0
>> 0 0 10 49 0 0 0 0 0 0 0 0) do not match
>>
>>
>>
>> I have attached the RC file. Could you please shed some light on this?
>>
>> Thank you
>>
>> Alan
>>
>> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hi Alan,
>>>
>>> Your pathlist and "Number of path control points"(ncpts) don't match.
>>> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>>>
>>> Best,
>>>
>>> King-Wai
>>>
>>>
>>>
>>>
>>> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Good morning Anastasia -
>>>>
>>>> I made the changes you suggested and removed "extraneous" commands. But
>>>> the error message still persists. Could you please shed some light on this?
>>>> Attached - latest RC file.
>>>>
>>>> The error message is : unmatched ' " '
>>>>
>>>> Thank you
>>>>
>>>> Alan
>>>>
>>>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> Hi Alan - dcmroot is the root directory under which the dicom files
>>>>> are saved. It's actually optional. In your case, either of the following
>>>>> will have the same, correct effect:
>>>>>
>>>>> set dcmroot = /home/afrancis/Imaging
>>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>
>>>>> OR
>>>>>
>>>>> set dcmlist =
>>>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>
>>>>> In addition, there are *a lot *of things that you left in there from
>>>>> the

Re: [Freesurfer] Tracula Config file.

[Yendiki, Anastasia]

You don't need all that stuff. You should remove everything below the bvalfile 
line and use the default parameters.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Friday, August 5, 2022 2:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula Config file.


External Email - Use Caution

Hello King-Wai -

I made the change to the ncpts. But still an error message persists.

ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm 
cc.bodyt cc.genu cc.rostrum cc.splenium mcp 
lh.af<http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
 
rh.af<http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
 
lh.ar<http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
 
rh.ar<http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
 lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat 
rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 
lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list
ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 
10 49 0 0 0 0 0 0 0 0) do not match



I have attached the RC file. Could you please shed some light on this?

Thank you

Alan

On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
mailto:kingwai@gmail.com>> wrote:

External Email - Use Caution

Hi Alan,

Your pathlist and "Number of path control points"(ncpts) don't match.
You have more than 3 paths in the pathlist and only 3 numbers in ncpts.

Best,

King-Wai




On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

External Email - Use Caution

Good morning Anastasia -

I made the changes you suggested and removed "extraneous" commands. But the 
error message still persists. Could you please shed some light on this? 
Attached - latest RC file.

The error message is : unmatched ' " '

Thank you

Alan

On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved. 
It's actually optional. In your case, either of the following will have the 
same, correct effect:

set dcmroot = /home/afrancis/Imaging
set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

OR

set dcmlist = 
(/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

In addition, there are a lot of things that you left in there from the example 
RC file. You should delete them entirely, unless you specifically want to set 
one of those things to something other than the default. These are examples 
that may not give you the default behavior. Also the field mapping files - 
delete those lines because you're just using the example names and they're not 
going to work. You want your RC file to have the minimum necessary for your 
analysis.

Best,
Anastasia.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alan Francis 
mailto:alandarkene...@gmail.com>>
Sent: Thursday, August 4, 2022 12:23 PM
To: Freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula Config file.


External Email - Use Caution

Hi Anastasia -

Hope you are well. I am running tracula on FS 7.2. I created the RC file based 
on your recommendations. However it is giving me an error message when I run 
it. The error is : Unmatched ' " "

I have attached the RC file. Could you please see where I have made an error.

Thanks so much,

Bes

Re: [Freesurfer] Tracula Config file.

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

They still don't match.
See attached excel file.

Best,

King-Wai

On Fri, Aug 5, 2022 at 2:35 PM Alan Francis 
wrote:

> External Email - Use Caution
>
> Hello King-Wai -
>
> I made the change to the ncpts. But still an error message persists.
>
> ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
> cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af
> <http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
> rh.af
> <http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
> lh.ar
> <http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
> rh.ar
> <http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
> lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc
> lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1
> rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID
> list
> ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0
> 0 0 10 49 0 0 0 0 0 0 0 0) do not match
>
>
>
> I have attached the RC file. Could you please shed some light on this?
>
> Thank you
>
> Alan
>
> On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu 
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Alan,
>>
>> Your pathlist and "Number of path control points"(ncpts) don't match.
>> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>>
>> Best,
>>
>> King-Wai
>>
>>
>>
>>
>> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Good morning Anastasia -
>>>
>>> I made the changes you suggested and removed "extraneous" commands. But
>>> the error message still persists. Could you please shed some light on this?
>>> Attached - latest RC file.
>>>
>>> The error message is : unmatched ' " '
>>>
>>> Thank you
>>>
>>> Alan
>>>
>>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> Hi Alan - dcmroot is the root directory under which the dicom files are
>>>> saved. It's actually optional. In your case, either of the following will
>>>> have the same, correct effect:
>>>>
>>>> set dcmroot = /home/afrancis/Imaging
>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>
>>>> OR
>>>>
>>>> set dcmlist =
>>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>
>>>> In addition, there are *a lot *of things that you left in there from
>>>> the example RC file. You should delete them entirely, unless you
>>>> specifically want to set one of those things to something other than the
>>>> default. These are examples that may not give you the default behavior.
>>>> Also the field mapping files - delete those lines because you're just using
>>>> the example names and they're not going to work. You want your RC file to
>>>> have the minimum necessary for your analysis.
>>>>
>>>> Best,
>>>> Anastasia.
>>>>
>>>>
>>>> --
>>>&g

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Hello King-Wai -

I made the change to the ncpts. But still an error message persists.

ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af rh.af lh.ar rh.ar lh.atr
rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat
rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1
lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list
ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0
0 10 49 0 0 0 0 0 0 0 0) do not match



I have attached the RC file. Could you please shed some light on this?

Thank you

Alan

On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> Your pathlist and "Number of path control points"(ncpts) don't match.
> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>
> Best,
>
> King-Wai
>
>
>
>
> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Good morning Anastasia -
>>
>> I made the changes you suggested and removed "extraneous" commands. But
>> the error message still persists. Could you please shed some light on this?
>> Attached - latest RC file.
>>
>> The error message is : unmatched ' " '
>>
>> Thank you
>>
>> Alan
>>
>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Hi Alan - dcmroot is the root directory under which the dicom files are
>>> saved. It's actually optional. In your case, either of the following will
>>> have the same, correct effect:
>>>
>>> set dcmroot = /home/afrancis/Imaging
>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>
>>> OR
>>>
>>> set dcmlist =
>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>
>>> In addition, there are *a lot *of things that you left in there from
>>> the example RC file. You should delete them entirely, unless you
>>> specifically want to set one of those things to something other than the
>>> default. These are examples that may not give you the default behavior.
>>> Also the field mapping files - delete those lines because you're just using
>>> the example names and they're not going to work. You want your RC file to
>>> have the minimum necessary for your analysis.
>>>
>>> Best,
>>> Anastasia.
>>>
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>>> *Sent:* Thursday, August 4, 2022 12:23 PM
>>> *To:* Freesurfer 
>>> *Subject:* [Freesurfer] Tracula Config file.
>>>
>>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia -
>>>
>>> Hope you are well. I am running tracula on FS 7.2. I created the RC file
>>> based on your recommendations. However it is giving me an error message
>>> when I run it. The error is : Unmatched ' " "
>>>
>>> I have attached the RC file. Could you please see where I have made an
>>> error.
>>>
>>> Thanks so much,
>>>
>>> Best regards,
>>>
>>> Alan
>>>
>>> --
>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>>
>>>
>>>
>>> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
>>> Neuroscience*
>>> *University of Texas, School of Medicine*
>>>
>>> *Rio Grande Valley *
>>>
>>> *Texas. *
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1Lfe2uITav2vXc0zNVAljyksn9GdVJ5yNEldxqSOiDRCgtedGCVVdJIOm5kd6a76BoTS6TbbWjdEydBwn--cnf-KWxVRGYecYUpcHixusyO0YuqpNp-wcndwty6XEAMRaOJWT-FW1PdVnA8LfKa1_SiYOYJkU28aRprSMgRW7e2xvhNpBDqn990cMjAb0fVlTgDGT-s4GXDfRAkDN8WLOgIPnIX8obIm_peiACS_1zg4gugrBA5TXxl4t7DaTSYXLl3nW2D0mMPVWzrs8hrVyFlcfrPJG4yfdQ4MUbCVhEWNHaLsSXBpky3mP52RE7Jk-Fk0FuXWCvuOE903URgv96Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Fli

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Thank you King-Wai.

On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu  wrote:

> External Email - Use Caution
>
> Hi Alan,
>
> Your pathlist and "Number of path control points"(ncpts) don't match.
> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>
> Best,
>
> King-Wai
>
>
>
>
> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
> wrote:
>
>> External Email - Use Caution
>>
>> Good morning Anastasia -
>>
>> I made the changes you suggested and removed "extraneous" commands. But
>> the error message still persists. Could you please shed some light on this?
>> Attached - latest RC file.
>>
>> The error message is : unmatched ' " '
>>
>> Thank you
>>
>> Alan
>>
>> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Hi Alan - dcmroot is the root directory under which the dicom files are
>>> saved. It's actually optional. In your case, either of the following will
>>> have the same, correct effect:
>>>
>>> set dcmroot = /home/afrancis/Imaging
>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>
>>> OR
>>>
>>> set dcmlist =
>>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>
>>> In addition, there are *a lot *of things that you left in there from
>>> the example RC file. You should delete them entirely, unless you
>>> specifically want to set one of those things to something other than the
>>> default. These are examples that may not give you the default behavior.
>>> Also the field mapping files - delete those lines because you're just using
>>> the example names and they're not going to work. You want your RC file to
>>> have the minimum necessary for your analysis.
>>>
>>> Best,
>>> Anastasia.
>>>
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>>> *Sent:* Thursday, August 4, 2022 12:23 PM
>>> *To:* Freesurfer 
>>> *Subject:* [Freesurfer] Tracula Config file.
>>>
>>>
>>> External Email - Use Caution
>>>
>>> Hi Anastasia -
>>>
>>> Hope you are well. I am running tracula on FS 7.2. I created the RC file
>>> based on your recommendations. However it is giving me an error message
>>> when I run it. The error is : Unmatched ' " "
>>>
>>> I have attached the RC file. Could you please see where I have made an
>>> error.
>>>
>>> Thanks so much,
>>>
>>> Best regards,
>>>
>>> Alan
>>>
>>> --
>>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>>
>>>
>>>
>>> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
>>> Neuroscience*
>>> *University of Texas, School of Medicine*
>>>
>>> *Rio Grande Valley *
>>>
>>> *Texas. *
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/19VhWc0-IQ2-vY6VvZ_Xa-9akD2Cd1BClFs7YJo3ZLQw2n7yuyv6wCX0aW6KI0voS0HboxGKbcngaYts7VTAERq0_4yRHdrSScRvJxyb1NCDr7DN6pYr-cYr_xTNtjTOd_tlqagLllCvd1B_5Lth6082dYXTZ1AmoIPiQl3F4SoxnlZJ4fjax8XubcDcxhyYOffEHLd2TQvupqH2YjmMJdAhN4V7v2C7_fV6dgjJIGwlR9TXnYuvdCjWSeBywDtJCTt8f52S-3rKmbkxalVV5YdCra4YrsLNTvBb08riF2ZiIDUPyrjkVtJIqriOOBWU-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>> <https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>> 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 Mass Ge

Re: [Freesurfer] Tracula Config file.

[King-Wai Chu]

External Email - Use Caution

Hi Alan,

Your pathlist and "Number of path control points"(ncpts) don't match.
You have more than 3 paths in the pathlist and only 3 numbers in ncpts.

Best,

King-Wai




On Fri, Aug 5, 2022 at 10:53 AM Alan Francis 
wrote:

> External Email - Use Caution
>
> Good morning Anastasia -
>
> I made the changes you suggested and removed "extraneous" commands. But
> the error message still persists. Could you please shed some light on this?
> Attached - latest RC file.
>
> The error message is : unmatched ' " '
>
> Thank you
>
> Alan
>
> On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Hi Alan - dcmroot is the root directory under which the dicom files are
>> saved. It's actually optional. In your case, either of the following will
>> have the same, correct effect:
>>
>> set dcmroot = /home/afrancis/Imaging
>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>
>> OR
>>
>> set dcmlist =
>> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>
>> In addition, there are *a lot *of things that you left in there from the
>> example RC file. You should delete them entirely, unless you specifically
>> want to set one of those things to something other than the default. These
>> are examples that may not give you the default behavior. Also the field
>> mapping files - delete those lines because you're just using the example
>> names and they're not going to work. You want your RC file to have the
>> minimum necessary for your analysis.
>>
>> Best,
>> Anastasia.
>>
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Thursday, August 4, 2022 12:23 PM
>> *To:* Freesurfer 
>> *Subject:* [Freesurfer] Tracula Config file.
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia -
>>
>> Hope you are well. I am running tracula on FS 7.2. I created the RC file
>> based on your recommendations. However it is giving me an error message
>> when I run it. The error is : Unmatched ' " "
>>
>> I have attached the RC file. Could you please see where I have made an
>> error.
>>
>> Thanks so much,
>>
>> Best regards,
>>
>> Alan
>>
>> --
>> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>>
>>
>>
>> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
>> Neuroscience*
>> *University of Texas, School of Medicine*
>>
>> *Rio Grande Valley *
>>
>> *Texas. *
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/147r4yKWXDa0ksyQ_uy68dtWkcYD3-JmqjORDjb8wn1yq_rsrwgA_BsryMv4A4tG4MDuknwm94cEnJDZbHhKopKetiFD1jOAz8LydOql5U6nIxNQOmhIOpsL546Pz2jHWWcBaCjM9zwxc1v7wLO1YnJ0jwqPjYSuLPLnmU7ik9jKak1dH9olnDiywVCLo2Ki1ikF7Otbd1osYYzRZkuguuxYM8Vjt12MrHYJd34xLd4ZX2a8D7xCcJyH85YOqRe3Mh9k13cvwOa6elIfClYhwJmEeWNZXi2YLSgZHtIrSwwf8lIrX5PE_5CaDIZmPGIwm/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1ZQKTkD6Bp8HD_8RxmSuRqJz-pPK-zmOUYeLWCu07WHc_McPfQIF9GIgch6R1MarCZCXLRHAp6i_-dzV6JaRoWj7CmBhSSasQFjX_wX-WdCU0JBnpWNrdBqZ5yq1uP5wXiNw3DhzB7T38zS6hkKjqpG3kdba6jkk1-l1CZV0szh1pqWBEI58LBpW-vq1pVNBMemaxLJ7AAD6KUIjyzPXn_Pr2m-n_eGFtpQ1W4o8eeo8IMrPKes6mNdFEC-FT_akmSCvMrb-lnxmCIqKcamprmLhGMyLmyWpRJzvLMPcBxo7yWj9QSM5K0gi-cuCCmHb9/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>> 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 Mass General
>> Brigham Compliance HelpLine at *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1XnKj3m5Ngz3XQ8OLo8siTLorw07cBJF2802aEWCwmT10kl86MlMfZaWHXtWQ_xvoSoFe19ETRJ0qeFiEx1Mb5d5yKdu6DBbnmZEJcOC5lR-T_11kBRKJX49sFd8PZcKE0FpVoqGN0-yej4ZPiOXCrL76SHzSJJeeIRhWzLGRkxsDbZIAzxCt4NMorpwX2wHW4YsfzLBVVJeBWw_9eyvedZ4NyJutBZuE8aV595Kp2f8I1v_dv3nbu4juE2mdORcvSqy3unc9oTm0a0dhj85ojssfTY7c2-tEPDUYpltXeCOuJ1WkNMDJCEj9YbkeW7V3/https%3A%2F%2

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Good morning Anastasia -

I made the changes you suggested and removed "extraneous" commands. But the
error message still persists. Could you please shed some light on this?
Attached - latest RC file.

The error message is : unmatched ' " '

Thank you

Alan

On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia 
wrote:

> Hi Alan - dcmroot is the root directory under which the dicom files are
> saved. It's actually optional. In your case, either of the following will
> have the same, correct effect:
>
> set dcmroot = /home/afrancis/Imaging
> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>
> OR
>
> set dcmlist =
> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>
> In addition, there are *a lot *of things that you left in there from the
> example RC file. You should delete them entirely, unless you specifically
> want to set one of those things to something other than the default. These
> are examples that may not give you the default behavior. Also the field
> mapping files - delete those lines because you're just using the example
> names and they're not going to work. You want your RC file to have the
> minimum necessary for your analysis.
>
> Best,
> Anastasia.
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 4, 2022 12:23 PM
> *To:* Freesurfer 
> *Subject:* [Freesurfer] Tracula Config file.
>
>
> External Email - Use Caution
>
> Hi Anastasia -
>
> Hope you are well. I am running tracula on FS 7.2. I created the RC file
> based on your recommendations. However it is giving me an error message
> when I run it. The error is : Unmatched ' " "
>
> I have attached the RC file. Could you please see where I have made an
> error.
>
> Thanks so much,
>
> Best regards,
>
> Alan
>
> --
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
> Neuroscience*
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley *
>
> *Texas. *
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>  <
> https://secure-web.cisco.com/11NbjxZ6dgbppOeMge0dBc4t_K0ms2pjFQPjOq8RKuKJ-PXVxWqTemfM1sbdQt2gSD9dSMSEsfOV9cBCV4AKm9vMlmw1RpMAToeqQ9UR8CRAEjsGj33CgEKw-o-lPCtIqckR7_ExS0JYI1z39BoE8vIwI5Fm-HcoNlXHrJQxX3T68h4pOj-Zu1opdph5S34NCWyI5xlOHQQ89ZqTtsecn5_CBA-WyUxDydE-aRGSIaQODCjNcpkhO2xqf-a71gFidjTwCbypPfXALsT-LH9YnqK87leS6PSF24szwID0DFSeW-E8dCr0OrIL1wpbCB4p-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
# FreeSurfer SUBJECTS_DIR

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

setenv SUBJECTS_DIR /home/afrancis/Imaging


# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /home/afrancis/Imaging/109123

# Subject IDs
#
set subjlist = (109123)

# Default: Run analysis on all subjects
#
set runlist = (1)

set dcmroot = /home/afrancis/Imaging

set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)


set bvecfile = /home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP.bvec


set bvalfile = /home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP.bval


# Perform correction for B0 

Re: [Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Hi Anastasia -

Thank you so much. I will do as you suggested.

best wishes

Alan

On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia 
wrote:

> Hi Alan - dcmroot is the root directory under which the dicom files are
> saved. It's actually optional. In your case, either of the following will
> have the same, correct effect:
>
> set dcmroot = /home/afrancis/Imaging
> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>
> OR
>
> set dcmlist =
> (/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>
> In addition, there are *a lot *of things that you left in there from the
> example RC file. You should delete them entirely, unless you specifically
> want to set one of those things to something other than the default. These
> are examples that may not give you the default behavior. Also the field
> mapping files - delete those lines because you're just using the example
> names and they're not going to work. You want your RC file to have the
> minimum necessary for your analysis.
>
> Best,
> Anastasia.
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 4, 2022 12:23 PM
> *To:* Freesurfer 
> *Subject:* [Freesurfer] Tracula Config file.
>
>
> External Email - Use Caution
>
> Hi Anastasia -
>
> Hope you are well. I am running tracula on FS 7.2. I created the RC file
> based on your recommendations. However it is giving me an error message
> when I run it. The error is : Unmatched ' " "
>
> I have attached the RC file. Could you please see where I have made an
> error.
>
> Thanks so much,
>
> Best regards,
>
> Alan
>
> --
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
> * Alan N. Francis PhD Assistant Professor of Neuroscience Institute of
> Neuroscience*
> *University of Texas, School of Medicine*
>
> *Rio Grande Valley *
>
> *Texas. *
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1rnwhqaAvrjIPhTTZ-jS08gtbsEm8Zz0bOLdaaH5aEKGgEP2Yej5Tcc6ASALq0lXEU7WElJGUmjOQQf-L5OISq0IFC6pofPTtjW4N5Fb0kIWvWtDwxhBotQdmSbyzu8_fC2vhe_B_Ok-ItReiZ0-C_Yva2pNOQwsBaGKseZsHj5GAghwturjVOEPp9bJSxi6vU5cusNazrIO4oFOXlc_OXoKL37la7MHeKeBN41-tmO5lOxcke7Chm8y2ugS6zahoR1fs25RgkYv0diJKK01WPh5yGO71W-lSn7erBge1bQDIxBgx1Y7RgyyJZQTGNqYa/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1Y94zrR_0sElA34xaZV95EmcQjtEksdDNW-gZ7Bw651WluReGngUugK5bEoHpuYU3WaG4eKOaOvyEv__JD3BXnvanA98xzQfq0E2Nb5aHJMiLqLETyBeboynKw2gvSXYrgl_upoy__va4MBI4VUn86pmb3P4alRMJE_Tv67x4mACUs58cg-nBXjZyGrFDAqicWTnNGMYD1fmAmooB3_nVMLKwrf0udi1WgMaGMP7zpNaNcLVSiW4aLcxo2xFNVv2sOk6drYMmRJANaBQkVJD4ItmmP7dzJkViurPABAK4bDBgfbTR4-nehvNlwzHnG8mk/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
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>  .
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
___
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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 Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula Config file.

[Yendiki, Anastasia]

Hi Alan - dcmroot is the root directory under which the dicom files are saved. 
It's actually optional. In your case, either of the following will have the 
same, correct effect:

set dcmroot = /home/afrancis/Imaging
set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

OR

set dcmlist = 
(/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)

In addition, there are a lot of things that you left in there from the example 
RC file. You should delete them entirely, unless you specifically want to set 
one of those things to something other than the default. These are examples 
that may not give you the default behavior. Also the field mapping files - 
delete those lines because you're just using the example names and they're not 
going to work. You want your RC file to have the minimum necessary for your 
analysis.

Best,
Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Thursday, August 4, 2022 12:23 PM
To: Freesurfer 
Subject: [Freesurfer] Tracula Config file.


External Email - Use Caution

Hi Anastasia -

Hope you are well. I am running tracula on FS 7.2. I created the RC file based 
on your recommendations. However it is giving me an error message when I run 
it. The error is : Unmatched ' " "

I have attached the RC file. Could you please see where I have made an error.

Thanks so much,

Best regards,

Alan

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.

___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Tracula Config file.

[Alan Francis]

External Email - Use Caution

Hi Anastasia -

Hope you are well. I am running tracula on FS 7.2. I created the RC file
based on your recommendations. However it is giving me an error message
when I run it. The error is : Unmatched ' " "

I have attached the RC file. Could you please see where I have made an
error.

Thanks so much,

Best regards,

Alan

-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*


dmrirc-109123_7T
Description: Binary data
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error in path construction

[Yendiki, Anastasia]

Hi Oshadi - Is this the same subject as before, the one that runs on your 
workstation but not on the cluster? Did the first error message (killed when 
loading the bedpostx samples) get solved?

More generally, it's hard to tell what caused an error just by looking at the 
last few lines of output. Please attach your entire trac-all.log file.

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, July 25, 2022 3:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Hi Anastasia
Thanks so much for the reply.
My trac-path worked until last step-it says dmric path done but it exited 
without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat 
etc for individual tracts
The error I get is:
fslmaths 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/path.pd.nii.gz
 -thr 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/tmp.nii.gz
Error: no output filename specified!
I am not sure if I am supposed to specify a output file name in the 
configuration file ( in addition to output directory)

Also, I have used a similar configuration file for other subjects -their 
pre-processing is done without errors but they miss nodif_brain_mask.nii so I 
can't run bedpostx

Any suggestion on what I can try for both these issue is really appreciated
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[King-Wai Chu]

External Email - Use Caution

Hi Anastasia,

I have posted a solution to the thread "TRACULA -bedp parallel processing"
Maybe you can include it in a future release.

Thanks,

King-Wai

On Mon, Aug 1, 2022 at 12:57 AM Yendiki, Anastasia 
wrote:

> Good to hear, thanks for testing it. We'll implement a permanent solution
> so you won't have to replace anything in the future.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com
> 
> *Sent:* Monday, August 1, 2022 12:44 AM
> *To:* 'Freesurfer support list' 
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
>
>
> I thought he wants me to run trac-preproc.sh he sent to run it directly.
>
> I wasn’t told to replace it with the one in the original 7.3.
>
>
>
> After replacing the original one with the modified one Doug sent, trac-all
> -prep -c config.file runs w/o problem.
>
>
>
> Thanks,
>
>
>
> King-Wai
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
> *Sent:* Monday, August 1, 2022 12:15 AM
> *To:* 'Freesurfer support list' 
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
>
> Indeed. Doug sent you a modified version of trac-preproc, which is a
> script that's called by trac-all. The idea was for you to overwrite
> $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run
> trac-all like before. Did you try that?
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com
> 
> *Sent:* Monday, August 1, 2022 12:10 AM
> *To:* 'Freesurfer support list' 
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
>
> *External Email - Use Caution*
>
> Hi Anastasia,
>
>
>
> The problem is in 7.3, trac-all -prep -c config.file is looking for
> ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which
> doesn’t exist.
>
> Because in v7.3, segmentThalamicNuclei.sh output a new version v13
> (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
>
>
>
> Thanks,
>
>
>
> King-Wai
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
> *Sent:* Monday, August 1, 2022 12:03 AM
> *To:* 'Freesurfer support list' 
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
>
> Hi King-Wai - You are not supposed to run trac-preproc directly. Run
> trac-all -c configfile, like before.
>
>
>
> Anastasia.
>
>
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai@gmail.com
> 
> *Sent:* Monday, July 25, 2022 2:11 PM
> *To:* 'Freesurfer support list' 
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
>
> *External Email - Use Caution*
>
> Hi Douglas,
>
>
>
> Thank you for looking into this.
>
> It gives the following error.
>
>
>
> trac-preproc.sh -c config.file
>
> intrareg: Undefined variable.
>
>
>
> Thanks,
>
>
>
> King-Wai
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
> *Sent:* Monday, July 25, 2022 1:55 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
>
> Can you copy the attached trac-preproc into $FREESURFER/bin and try again
> (after removing the link)?
>
> On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:
>
> *External Email - Use Caution*
>
> Hi Anastasia,
>
>
>
> Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
>
> Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
>
> However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
>  from segmentThalamicNuclei.sh which doesn’t exist.
>
> Because in v7.3, segmentThalamicNuclei.sh output a new version v13
> (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
>
> I worked around this problem by linking
> ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to
> ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
>
> ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
>
>
>
> trac-all finished w/o proble

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Yendiki, Anastasia]

AY did look into it, I just checked in a change on top of that change. Let's go 
with my change for the release. Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Monday, August 1, 2022 12:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: kingwai@gmail.com 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


External Email - Use Caution

There is a change related to that,

Date:   Mon Jul 25 21:24:30 2022 -0400
trac-preproc. #BF. Changed expected thalseg version to 1.3; also added an 
option to be able to spec the thalseg file. AY should look at it.

- in the latest development builds, which are located under,
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/<https://secure-web.cisco.com/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL9k5AAMKLWHm2POf_S0eGJD7LvH-Rx4mlhUvWx6LgQy-q3pHUo6odo2HUzH5uK2pw4hWjukRqykCXncWcvL89U7Ihr1Wy4vWcysi3Yq9UySr4hJBKqO7jh_1gx5bkNy4GVG58Hq8eKCWI8kG1UM8dAm5slogANcs8Hh0lcUCOJcHmo10D2MOEouR8Byjb7CNF0mBxiQcx7v5zXpBfGpqYAp8SlSqB7_L_8uTU7HCxsVAZZlJfNOacSDHlv__n0uWJFLDDcLFPdZHVfrr-BIsETaPpcp5bzQVyMzpRzoFYF35LAXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F>

That and some other changes will make it into the 7.3.2 release.

- R.

On Aug 1, 2022, at 00:44, kingwai@gmail.com wrote:


External Email - Use Caution

Hi Anastasia,

I thought he wants me to run trac-preproc.sh he sent to run it directly.
I wasn’t told to replace it with the one in the original 7.3.

After replacing the original one with the modified one Doug sent, trac-all 
-prep -c config.file runs w/o problem.

Thanks,

King-Wai

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Indeed. Doug sent you a modified version of trac-preproc, which is a script 
that's called by trac-all. The idea was for you to overwrite 
$FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run 
trac-all like before. Did you try that?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
kingwai@gmail.com<mailto:kingwai@gmail.com>mailto:kingwai@gmail.com>>
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

External Email - Use Caution
Hi Anastasia,

The problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which 
doesn’t exist.
Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

Thanks,

King-Wai

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.

Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
kingwai@gmail.com<mailto:kingwai@gmail.com>mailto:kingwai@gmail.com>>
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


External Email - Use Caution

Hi Douglas,

Thank you for looking into this.
It gives the following error.

trac-preproc.sh -c config.file
intrareg: Undefined variable.

Thanks,

King-Wai

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com<mailto:kingwai@gmail.com> wrote:

External Email - Use Caution

Hi Anastasia,

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
However trac-all -prep is l

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[fsbuild]

External Email - Use Caution

There is a change related to that,

Date: Mon Jul 25 21:24:30 2022 -0400
 trac-preproc. #BF. Changed expected thalseg version to 1.3; 
also added an option to be able to spec the thalseg file. AY should look at it.

- in the latest development builds, which are located 
under,https://secure-web.cisco.com/16IqsFJkXTetOby5z7oQ2GGW3ceVlc5mNqOcsSHL9k5AAMKLWHm2POf_S0eGJD7LvH-Rx4mlhUvWx6LgQy-q3pHUo6odo2HUzH5uK2pw4hWjukRqykCXncWcvL89U7Ihr1Wy4vWcysi3Yq9UySr4hJBKqO7jh_1gx5bkNy4GVG58Hq8eKCWI8kG1UM8dAm5slogANcs8Hh0lcUCOJcHmo10D2MOEouR8Byjb7CNF0mBxiQcx7v5zXpBfGpqYAp8SlSqB7_L_8uTU7HCxsVAZZlJfNOacSDHlv__n0uWJFLDDcLFPdZHVfrr-BIsETaPpcp5bzQVyMzpRzoFYF35LAXg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
That and some other changes will make it into the 7.3.2 release.

- R.
On Aug 1, 2022, at 00:44, kingwai@gmail.com 
wrote:External Email - Use 
CautionHi Anastasia,I 
thought he wants me to run trac-preproc.sh he sent to run it directly.I wasn’t 
told to replace it with the one in the original 7.3.After replacing the 
original one with the modified one Doug sent, trac-all -prep -c config.file 
runs w/o 
problem.Thanks,King-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edu
 freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfYendiki, 
AnastasiaSent:Monday, August 1, 2022 12:15 AMTo:'Freesurfer support 
list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
TRACULA in FreeSurfer version 7.3Indeed. Doug sent you a modified version 
of trac-preproc, which is a script that's called by trac-all. The idea was for 
you to overwrite $FREESURFER_HOME/bin/trac-preproc with the version that Doug 
sent, then run trac-all like before. Did you try 
that?From:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf 
ofkingwai@gmail.comkingwai@gmail.comSent:Monday, 
August 1, 2022 12:10 AMTo:'Freesurfer support list' 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in 
FreeSurfer version 
7.3External Email - Use 
CautionHi Anastasia,The 
problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh 
which doesn’t exist.Because in v7.3, segmentThalamicNuclei.sh output a new 
version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).Thanks,King-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfYendiki, AnastasiaSent:Monday, August 1, 2022 12:03 
AMTo:'Freesurfer support list' 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in 
FreeSurfer version 7.3Hi King-Wai - You are not supposed to run 
trac-preproc directly. Run trac-all -c configfile, like 
before.Anastasia.From:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf 
ofkingwai@gmail.comkingwai@gmail.comSent:Monday, 
July 25, 2022 2:11 PMTo:'Freesurfer support list' 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA in 
FreeSurfer version 
7.3External Email - Use 
CautionHi Douglas,Thank 
you for looking into this.It gives the following error.trac-preproc.sh -c 
config.fileintrareg: Undefined 
variable.Thanks,King-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfDouglas N.. GreveSent:Monday, July 25, 2022 1:55 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA 
in FreeSurfer version 7.3Can you copy the attached trac-preproc into 
$FREESURFER/bin and try again (after removing the link)?On 7/22/2022 8:36 
AM,kingwai@gmail.comwrote:External
 Email - Use CautionHi 
Anastasia,Just downloaded FreeSurfer version 7.3 and trying out 
TRACULA.Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3However 
trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from 
segmentThalamicNuclei.sh which doesn’t exist.Because in v7.3, 
segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).I worked around this problem by 
linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz to 
ThalamicNuclei.v13.T1.FSvoxelSpace.mgzln -s 
ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgztrac-all finished w/o 
problem.trac-all -versiontrac-all 7.3.0I seems trac-all in v7.3 
forgets to update the fact that segmentThalamicNuclei.sh output v13 of the 
file.Or it is looking for v12 for a reason?Is my fix 
correct?Thanks,King-Wai___Freesurfer
 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1v-b5JJwuDi1SzLbIsac4ppx7Moeb9XlbmcaO28MpjIUuDqiphObSxY9VDprI-26SInYsgAlhWSshtF0nc4_nZL6wlR0I-H6X64YH7B52izGDToCFFeldeX1ZjGHB37kkEiIsD0HxFwGH0zWTchNYHG4U6eXBOld1mEABg5HX8XrKVGq7jlzrJWsB9pnxqXV4WHoddj8ak6MoUdS-PANYvmCaHpw96f7RHT-HsbmleB2gWUj8IZJTTg8MTnNv9ne16FL8u1DDpQ6PT6yxTW5J6d39_8okyF4e6mgi-HMhYHaTMvrO8HUI6Z

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Yendiki, Anastasia]

Good to hear, thanks for testing it. We'll implement a permanent solution so 
you won't have to replace anything in the future.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of kingwai@gmail.com 

Sent: Monday, August 1, 2022 12:44 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


External Email - Use Caution

Hi Anastasia,



I thought he wants me to run trac-preproc.sh he sent to run it directly.

I wasn’t told to replace it with the one in the original 7.3.



After replacing the original one with the modified one Doug sent, trac-all 
-prep -c config.file runs w/o problem.



Thanks,



King-Wai



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Indeed. Doug sent you a modified version of trac-preproc, which is a script 
that's called by trac-all. The idea was for you to overwrite 
$FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run 
trac-all like before. Did you try that?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com> 
mailto:kingwai@gmail.com>>
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



External Email - Use Caution

Hi Anastasia,



The problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which 
doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).



Thanks,



King-Wai



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.



Anastasia.





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com> 
mailto:kingwai@gmail.com>>
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



External Email - Use Caution

Hi Douglas,



Thank you for looking into this.

It gives the following error.



trac-preproc.sh -c config.file

intrareg: Undefined variable.



Thanks,



King-Wai



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com<mailto:kingwai@gmail.com> wrote:

External Email - Use Caution

Hi Anastasia,



Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz



trac-all finished w/o problem.



trac-all -version

trac-all 7.3.0



I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?



Is my fix correct?



Thanks,



King-Wai



___

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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Hi Anastasia,

 �

I thought he wants me to run trac-preproc.sh he sent to run it directly.

I wasn’t told to replace it with the one in the original 7.3.

 �

After replacing the original one with the modified one Doug sent, trac-all 
-prep -c config.file runs w/o problem.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Indeed. Doug sent you a modified version of trac-preproc, which is a script 
that's called by trac-all. The idea was for you to overwrite 
$FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run 
trac-all like before. Did you try that?

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
kingwai@gmail.com <mailto:kingwai@gmail.com>  mailto:kingwai@gmail.com> >
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 

 �

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

The problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz � from segmentThalamicNuclei.sh which 
doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Yendiki, 
Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.

 �

Anastasia.

 �

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
kingwai@gmail.com <mailto:kingwai@gmail.com>  mailto:kingwai@gmail.com> >
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 

 �

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz 
� to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai

 �




___
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contin

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Yendiki, Anastasia]

Indeed. Doug sent you a modified version of trac-preproc, which is a script 
that's called by trac-all. The idea was for you to overwrite 
$FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run 
trac-all like before. Did you try that?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of kingwai@gmail.com 

Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


External Email - Use Caution

Hi Anastasia,



The problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which 
doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).



Thanks,



King-Wai



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.



Anastasia.





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of kingwai@gmail.com<mailto:kingwai@gmail.com> 
mailto:kingwai@gmail.com>>
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



External Email - Use Caution

Hi Douglas,



Thank you for looking into this.

It gives the following error.



trac-preproc.sh -c config.file

intrareg: Undefined variable.



Thanks,



King-Wai



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com<mailto:kingwai@gmail.com> wrote:

External Email - Use Caution

Hi Anastasia,



Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz



trac-all finished w/o problem.



trac-all -version

trac-all 7.3.0



I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?



Is my fix correct?



Thanks,



King-Wai



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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Hi Anastasia,

 �

The problem is in 7.3, trac-all -prep -c config.file is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh which 
doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.

 �

Anastasia.

 �

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
kingwai@gmail.com <mailto:kingwai@gmail.com>  mailto:kingwai@gmail.com> >
Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 

 �

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz 
� to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai

 �




___
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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 Mass General Brigham 
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<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Yendiki, Anastasia]

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all 
-c configfile, like before.

Anastasia.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of kingwai@gmail.com 

Sent: Monday, July 25, 2022 2:11 PM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3


External Email - Use Caution

Hi Douglas,



Thank you for looking into this.

It gives the following error.



trac-preproc.sh -c config.file

intrareg: Undefined variable.



Thanks,



King-Wai



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3



Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com<mailto:kingwai@gmail.com> wrote:

External Email - Use Caution

Hi Anastasia,



Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz



trac-all finished w/o problem.



trac-all -version

trac-all 7.3.0



I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?



Is my fix correct?



Thanks,



King-Wai



___

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Yes, my original config file works with 7.2

 �

I really appreciate your help.

 �

Thanks.

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 9:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

I don't know; Anastasia is the author. She's busy today and tomorrow, I was 
just trying to push it forward. Does it work with the given config file in 7.2? 

On 7/25/2022 5:46 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

I added it to the config file, then it complains

interreg: Undefined variable.

 �

When I added interreg = 5, then it complains

subj: Undefined variable.

 �

Should I continue fixing it until no more Undefined variable?

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

According to 

TRACULA tutorial

 
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>
 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1zSA_b4ezKCEwgchIiEjJkTpIEBtecsFaamd9vKJ9u9cVmSkAQgnUAuAvI4uXSMMmrEh26h_MAYnwauVVNGcw_oVyzeG7nY4f4TYvyUJszcbvL5b-cNT2d4mQCl-LlqWW-RDYZFsXRUkKcKMPqtGKZp3Dqr-WlgKEC85pfBEmYQv0KLDuoSU6SnwmafZ-Og9_oDVRrW47SZYBDmLTpOZ9f5US6U7H7cfq5fcq90pyh6d6f9Afsp7QX1KObzxlMYnaAXoq4fcvax2sgQF3nWNcyL1jU3-TmppzASKqM6L-nhXvFTBDq2BGxf1pLOVNxwG2l2s-Nv6Maq6oR8gHg8tDCw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula

 �

A very simple configuration file, where only the absolutely necessary inputs 
are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

 �

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a 
mutual information cost), and 3 (bbregister, which uses a boundary-based cost). 
The default is option 3 (bbregister).”

 �

If I don’t specify it in the config file, it should automatically use the 
default setting which is intrareg = 3.

 �

I will add it to the config file and try again.

 �

Thanks,

 �

King-Wai

 �

 �

 �

 �

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

are you sure the config file is right? it should be defining the intrareg 
variable

On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new v

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Douglas N. Greve]

I don't know; Anastasia is the author. She's busy today and tomorrow, I 
was just trying to push it forward. Does it work with the given config 
file in 7.2?


On 7/25/2022 5:46 PM, kingwai@gmail.com wrote:


External Email - Use Caution

I added it to the config file, then it complains

interreg: Undefined variable.

When I added interreg = 5, then it complains

subj: Undefined variable.

Should I continue fixing it until no more Undefined variable?

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Monday, July 25, 2022 5:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Douglas,

According to

TRACULA tutorial

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>

A very simple configuration file, where only the absolutely
necessary inputs are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT
with a mutual information cost), and 3 (bbregister, which uses a
boundary-based cost). The default is option 3 (bbregister).”

If I don’t specify it in the config file, it should automatically
use the default setting which is intrareg = 3.

I will add it to the config file and try again.

Thanks,

King-Wai

*From:*freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

are you sure the config file is right? it should be defining the
intrareg variable

On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Douglas,

Thank you for looking into this.

It gives the following error.

trac-preproc.sh -c config.file

intrareg: Undefined variable.

Thanks,

King-Wai

*From:*freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* freesurfer@nmr.mgh.harvard.edu
    *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Can you copy the attached trac-preproc into $FREESURFER/bin
and try again (after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Anastasia,

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from
segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new
version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to
ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

trac-all finished w/o problem.

trac-all -version

trac-all 7.3.0

I seems trac-all in v7.3 forgets to update the fact that
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

Is my fix correct?

Thanks,

King-Wai





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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

I added it to the config file, then it complains

interreg: Undefined variable.

 �

When I added interreg = 5, then it complains

subj: Undefined variable.

 �

Should I continue fixing it until no more Undefined variable?

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

According to 

TRACULA tutorial

 
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>
 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
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 �

A very simple configuration file, where only the absolutely necessary inputs 
are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

 �

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a 
mutual information cost), and 3 (bbregister, which uses a boundary-based cost). 
The default is option 3 (bbregister).”

 �

If I don’t specify it in the config file, it should automatically use the 
default setting which is intrareg = 3.

 �

I will add it to the config file and try again.

 �

Thanks,

 �

King-Wai

 �

 �

 �

 �

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

are you sure the config file is right? it should be defining the intrareg 
variable

On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz 
� to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai








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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addresse

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Douglas N. Greve]

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:


External Email - Use Caution

Hi Douglas,

According to

TRACULA tutorial

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula 
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>


A very simple configuration file, where only the absolutely necessary 
inputs are specified, intrareg is not there.


and it works on v7.2.0. w/o it explicitly specified.

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT 
with a mutual information cost), and 3 (bbregister, which uses a 
boundary-based cost). The default is option 3 (bbregister).”


If I don’t specify it in the config file, it should automatically use 
the default setting which is intrareg = 3.


I will add it to the config file and try again.

Thanks,

King-Wai

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

are you sure the config file is right? it should be defining the 
intrareg variable


On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Douglas,

Thank you for looking into this.

It gives the following error.

trac-preproc.sh -c config.file

intrareg: Undefined variable.

Thanks,

King-Wai

*From:*freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Can you copy the attached trac-preproc into $FREESURFER/bin and
try again (after removing the link)?

On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Anastasia,

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from
segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version
v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to
ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

trac-all finished w/o problem.

trac-all -version

trac-all 7.3.0

I seems trac-all in v7.3 forgets to update the fact that
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

Is my fix correct?

Thanks,

King-Wai




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Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from
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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Hi Douglas,

 �

According to 

TRACULA tutorial

https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula

 �

A very simple configuration file, where only the absolutely necessary inputs 
are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

 �

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT with a 
mutual information cost), and 3 (bbregister, which uses a boundary-based cost). 
The default is option 3 (bbregister).”

 �

If I don’t specify it in the config file, it should automatically use the 
default setting which is intrareg = 3.

 �

I will add it to the config file and try again.

 �

Thanks,

 �

King-Wai

 �

 �

 �

 �

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

are you sure the config file is right? it should be defining the intrareg 
variable

On 7/25/2022 2:11 PM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>   
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz 
� to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai







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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Douglas N. Greve]

are you sure the config file is right? it should be defining the 
intrareg variable


On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:


External Email - Use Caution

Hi Douglas,

Thank you for looking into this.

It gives the following error.

trac-preproc.sh -c config.file

intrareg: Undefined variable.

Thanks,

King-Wai

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Monday, July 25, 2022 1:55 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Can you copy the attached trac-preproc into $FREESURFER/bin and try 
again (after removing the link)?


On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:

*External Email - Use Caution *

Hi Anastasia,

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from
segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to
ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

trac-all finished w/o problem.

trac-all -version

trac-all 7.3.0

I seems trac-all in v7.3 forgets to update the fact that
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

Is my fix correct?

Thanks,

King-Wai



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Freesurfer@nmr.mgh.harvard.edu

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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Tracula error in path construction

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia
Thanks so much for the reply.
My trac-path worked until last step-it says dmric path done but it exited 
without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat 
etc for individual tracts
The error I get is:
fslmaths 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/path.pd.nii.gz
 -thr 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dpath/acomm_avg16_syn_bbr/tmp.nii.gz
Error: no output filename specified!
I am not sure if I am supposed to specify a output file name in the 
configuration file ( in addition to output directory)

Also, I have used a similar configuration file for other subjects -their 
pre-processing is done without errors but they miss nodif_brain_mask.nii so I 
can't run bedpostx

Any suggestion on what I can try for both these issue is really appreciated
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error in path construction

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30018
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii
set bvecfile = 30018/bvecs.txt
set bvalfile = 30018/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Hi Douglas,

 �

Thank you for looking into this.

It gives the following error.

 �

trac-preproc.sh -c config.file

intrareg: Undefined variable.

 �

Thanks,

 �

King-Wai

 �

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

 �

Can you copy the attached trac-preproc into $FREESURFER/bin and try again 
(after removing the link)? 

On 7/22/2022 8:36 AM, kingwai@gmail.com <mailto:kingwai@gmail.com>  
wrote:

 � � � � � � � �External Email - Use Caution � � � � � � � �

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
�from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz 
� to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai





___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

[Douglas N. Greve]

Can you copy the attached trac-preproc into $FREESURFER/bin and try 
again (after removing the link)?


On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:


External Email - Use Caution

Hi Anastasia,

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from segmentThalamicNuclei.sh 
which doesn’t exist.


Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).


I worked around this problem by linking 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to 
ThalamicNuclei.v13.T1.FSvoxelSpace.mgz


ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz


trac-all finished w/o problem.

trac-all -version

trac-all 7.3.0

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.


Or it is looking for v12 for a reason?

Is my fix correct?

Thanks,

King-Wai


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
#! /bin/tcsh -f

#
# trac-preproc
#
# Tractography pre-processing for a single subject
#
# Original Author: Anastasia Yendiki
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

umask 002

set VERSION = 'trac-preproc @FS_VERSION@';
set ProgName = `basename $0`
set inputargs = ($argv)
set thalseg = ThalamicNuclei.v13.T1.FSvoxelSpace

# Set default options -#

set PrintHelp = 0   # Print help and exit

set debug = 0   # Generate more output

set DoTime = 0  # Time main commands
set fs_time = ()

set rcfile = () # Name of input run command file
set LF = () # Name of log file
set CF = () # Name of command file

set DoIsRunning = 1 # Create a lock file while processing continues

set RunIt = 1   # If 0, do everything but run commands (for debugging)

# Parse input arguments ---#

if ($#argv == 0) goto usage_exit

set n = `echo $argv | egrep -e -help | wc -l`
if ($n != 0) then
  set PrintHelp = 1
  goto usage_exit
endif

set n = `echo $argv | egrep -e -version | wc -l`
if ($n != 0) then
  echo $VERSION
  exit 0
endif

source $FREESURFER_HOME/sources.csh

goto parse_args
parse_args_return:
goto check_params
check_params_return:

# Read configuration file -#

source $rcfile

if ($intrareg == 1 || $intrareg == 2) then
  set reg = flt
else if ($intrareg == 3) then
  set reg = bbr
endif

if ($interreg == 1 || $interreg == 2) then
  set xspace = mni
else if ($interreg == 3) then
  set xspace = rob
else if ($interreg == 4) then
  set xspace = cvs
  set cvstempdir = `dirname $intertrg`  # Assuming ../mri/norm.mgz
  set cvstempdir = `dirname $cvstempdir`
  set cvstemp= `basename $cvstempdir`
  set cvstempdir = `dirname $cvstempdir`
  set cvswarp = final_CVSmorph_to$cvstemp
else if ($interreg == 5) then
  set xspace = syn
  setenv MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT
else if ($interreg == 6) then
  set xspace = fnt
endif

if ($DoTime) then
  fs_time ls >& /dev/null
  if (! $status) set fs_time = fs_time
endif

printf '\n\n' >> $LF
echo "New invocation of $ProgName"  >> $LF
printf '\n\n' >> $LF
whoami >> $LF
hostname >> $LF
uname -a >> $LF
limit >> $LF
if (-e /usr/bin/free) then
  echo "" >> $LF
  /usr/bin/free >> $LF
  echo "" >> $LF
endif
if ("`uname -s`" == "Darwin") then
  echo "" >> $LF
  /usr/bin/top -l 1 | grep PhysMem >> $LF
  echo "" >> $LF
endif

#-- Is this a longitudinal base template? ---#

set dobase = 0

if ($?tplist) then
  if ($#tplist > 0) set dobase = 1
endif

#-- Create output directories ---#

set dtdir = $dtroot/$subj
set fsdir = $SUBJECTS_DIR/$subj
set dwidir = $dtdir/dmri
set xfmdir = $dwidir/xfms
set labdir = $dtdir/dlabel
set touchdir = $dtdir/touch

mkdir -p $dwidir $xfmdir $labdir

#-- Handle run status files -#

# Delete the error file. This is created when error_exit is run.
set ErrorFile = $dtdir/scripts/trac-all.error
rm -f $ErrorFile

# Delete the done file. This is created when the program exits normally.
set DoneFile = $dtdir/scripts/$ProgName.done
rm -f $DoneFile

if ($DoIsRunning) then
  set IsRunningFile = $dtdir/scripts/IsRunning.trac

  if (-e $IsRunningFile) then
echo ""
echo "ERROR: it appears 

[Freesurfer] TRACULA in FreeSurfer version 7.3

[kingwai.chu]

External Email - Use Caution

Hi Anastasia,

 �

Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
from segmentThalamicNuclei.sh which doesn’t exist.

Because in v7.3, segmentThalamicNuclei.sh output a new version v13 
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  
to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz 
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

 �

trac-all finished w/o problem.

 �

trac-all -version

trac-all 7.3.0

 �

I seems trac-all in v7.3 forgets to update the fact that 
segmentThalamicNuclei.sh output v13 of the file.

Or it is looking for v12 for a reason?

 �

Is my fix correct?

 �

Thanks,

 �

King-Wai

___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tracula error in path construction

[Yendiki, Anastasia]

Could be that you reached a memory limit? If the same analysis runs fine on 
your computer, then it's probably a cloud issue, not a TRACULA issue.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Thursday, July 21, 2022 3:58 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula error in path construction


External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


___
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Tracula error in path construction

[Shanika Jayakody]

External Email - Use Caution

Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without 
errors until path reconstruction but exists saying the following
I have checked my bvecs and bvals in the subjects directory and also in dmri
Any suggestion for me to try would be great-thanks so much! I tried to attach 
the trac-all log file but then the email is too big to be posted.
Oshadi

Loading DWIs from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri/data.nii.gz
Loading mask from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from 
/gs/gsfs0/users/helena_blumen_lab/TRACULA//30018/dmri.bedpostX
Killed
Linux sjayakody 4.18.0-348.el8.x86_64 #1 SMP Mon Oct 4 12:17:22 EDT 2021 x86_64 
x86_64 x86_64 GNU/Linux


setenv SUBJECTS_DIR  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dtroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set subjlist = 30018
set runlist = 1
set dcmroot =  /gs/gsfs0/users/helena_blumen_lab/TRACULA/
set dcmlist = 30018/30018_WIP_110_DTI66d_2mm_SF3_SENSE_20190520152420_1201.nii
set bvecfile = 30018/bvecs.txt
set bvalfile = 30018/bvals.txt
set dob0 = 0
set doeddy = 0
set intrareg = 3
set intradof = 9
set intrarot = 90
set interreg = 5
set intertrg =  
/public/apps/freesurfer/7.2.0/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
set segname = aparc+aseg
set usethalnuc = 0
set usemaskanat = 1
set thrbet = 0.3
set trainfile =  /public/apps/freesurfer/7.2.0/trctrain/hcp/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA -bedp parallel processing

[King-Wai Chu]

hows up in the "not a directory"
> error)?
> --
> *From:* Salar Dini, Elaheh 
> *Sent:* Tuesday, June 7, 2022 11:46 AM
> *To:* Yendiki, Anastasia ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
>
> External Email - Use Caution
>
> *Hi Anastasia,*
>
>
> *FSL version is 6.0.5.1*
>
>
> *Thanks,*
>
>
> *Ela *
>
>
>
>
>
> *From:* Yendiki, Anastasia
> <https://secure-web.cisco.com/1gMhd-NtfGQoo4sxXlV5w2SPV4n_Xtg7gFkKUX8CyfIQwAn4-G1nOI0ITlaiQWxefvTnqTHnA-6vk79vZCjSWSy1KCMT_-MwPWEFuwhkyc2dz-PgJLgbqp3JaH-7jrpNxtc1HR0CeUVCEsSUa66xNn5ZECBZQIDcLNngonv7k259pMbYb5noKJsvD0-IkWR6z1vft9vCm_kjpLgCcF6CHsMOW5crdjpKmYHEDqm_GyYpNJq2IBXxv8nB26Y6mK738_pdUMiFBZSv6cikz3yPkmKchzvveAndce4soVa9DIu0hL6T15aJRA9KY_FXOu7yWwjIKRuXxGqprVQLUEFm7nPtvw5szvaKBFgTQSegCrj0/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1hjYaRQ7IoVBQWPddYegWDBTN53vXlBeQHNhe3Bi5HppHR0gq6LIuV4XGy4IS5Tpq8kTOGEgh7qmRZCAonXnVmDmmMHuIq9hHRs8H1uARdoYBvhOmHwqr37Aq_1_pNjH11X0MOXTbh_qNah0f88oGiq4JqracaGbTOkCJrcQYtHrK5lG5VkResx7NDiAElWs23nqCHPOGUV1WlVs8vBKNig0vk1fqs4MPzqx6cb-TK3coYNutw718WC_BSCkCTnqM_4W9KJr3x8w-gN74tO2ekUXxDL9mhUTNJNcjOiAxAbGsMu-hMNHRqDAnV6JtJ1y5aey5xUu0j9jNW2CesCgo-g%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Dfrom%25253A%25252522Yendiki%2525252C%25252BAnastasia%25252522%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252BFlNdHFAkB2YqWdzEtpZNqMkw2J4plyDuHqB1gqyJJ8%253D%26reserved%3D0>
>
> Sent: Mon, 06 Jun 2022 20:17:47 -0700
> <https://secure-web.cisco.com/1hIh3BL11gmgVBTk8xY-63vXTjASmE7KTXnal24JHbAwq-CzcQ5-4e_ro2Jjwt-v5v3MYMO2xmdcbeTpZlE2Q8dy92smW7NwHdkbEsgZ7YFmPOzANViTjOjwWHy_6Xc7C6nMq_tl_LODu8pRKCpGwb3gJ6443qZ6gBG38_lsXsl3M98zzTsyEamnKgQJK-07yiLoi-1_5i4-6UYufuku3iFS8KpGGpo_9oOeK6xRcETIIVTcAy6Fsajz5F9_G7R1qd3Zd3d9r8AudiFrk_eSvxL1_vavtgklbDlfQrNoJGbTmqmn8Bsg04OBMnO1Hye4I-a9qAzdxLdLCol_eou6EPACjSPUmd_sCrnPiGs0_O4I/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11YTHE-9SnX_d-1PQ1yyK7EQYy82okQBAj3-aNpNvl-kJp3dN1G0QO8yztwo24IehLoqbE2gQ5JGCUFPjW6OE2T4RUxK5mY_WuSdC8Ue2dm5d1AI14zEzhbEnoH2wGcaNwmtL3nenG_qHdKlN8qkHjRZ4nU3njkcFajT4valovVZnht7U-peLk4QVCqIzRR3RvYd6vodHNFqPwl3ATlbX3K3dbofDxEC-a4Sn2dutAOC3g_eaOsE2xGmuaALZsSorg81MF_6V-T87knaRRfrG7iiWb-SF0r5wvo_-8AzTyg6VpgSudF4_rFltDEUU3VtoK1OfkbMTczhhRKQvIGphpw%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Ddate%25253A20220606%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DzMpmkQAaTcNySHOkozbk0Y6iqtZuuMKsFmFZ7c%252FKgmE%253D%26reserved%3D0>
>
> *To:* Salar Dini, Elaheh ; Freesurfer support
> list 
>
> *Subject:* Re: TRACULA -bedp parallel processin
>
> Hi Ela - Which version of FSL are you using?
>
> Anastasia.
>
>
>
> --
> *From:* Salar Dini, Elaheh 
> *Sent:* Monday, June 6, 2022 5:26 PM
> *To:* Yendiki, Anastasia ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
> Thanks for the reply. I'm not sure if you are looking for this: we use a
> small cluster with 40 nodes, 512 CPU cores. We are still using PBS.
>
>
> Thanks,
> Ela
> --
> *From:* Yendiki, Anastasia 
> *Sent:* Saturday, June 4, 2022 1:05 AM
> *To:* Salar Dini, Elaheh ; Freesurfer support
> list 
> *Subject:* Re: TRACULA -bedp parallel processing
>
> What kind of cluster are you running the parallel processes on?
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <
> elaheh.salard...@yale.edu>
> *Sent:* Friday, June 3, 2022 7:44 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] TRACULA -bedp parallel processing
>
>
> External Email - Use Caution
>
> Thank you for the guidance.
>
>
> When it tries to run pre.ParallelI , I'll get this:
>
> Copying files to bedpost directory
> cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX'
> is not a directory
> /home1/es2263/fsl//bin/bedpostx_preproc.sh: line

Re: [Freesurfer] [TRACULA] Auto-BIDS Config Variables Question

[Yendiki, Anastasia]

Hi Steven - Indeed you are right that the values from your scanner protocol are 
the ones to use. In this case it sounds like what it finds in the json files 
does not agree with the scanner protocol, and this is good to know. I will look 
into this. Glad to hear it worked well otherwise!

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Steven Meisler 

Sent: Thursday, July 7, 2022 12:03 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] [TRACULA] Auto-BIDS Config Variables Question


External Email - Use Caution

Hello,

I am trying out the development dmri-bids-config 
script<https://secure-web.cisco.com/1w--1vLn2hIhDzN_sQmBI1_PGZkHehc5IsuQS_9ZRqntOosEohjdkyIFCVKGApczWeVr9OI3T4SCrGz69YaLoLGHAMvVm4IR5AcEKAObvLLu31o982_GqN642-HWAmJJOiMJEwfEgspYOdlGbIGoUjEF6p0LUNHZsS8078o-ZKttsF21celYWQb9xQtiilQ30aASxohOLgfShtHnDD4V4jOSusTBWE9Tz9Z-oXbEQbIWe8uCK9mv6XzRusE80TZTO5XHnPiZJyiUeVLZH-R8bjuTfofQRLHfovd6ZrU45DHf1bARkrJd6Y3pKRBGgeq0ukCS8J8kVrMD7gIDYPl-Buw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmri_bids_config>
 to set up my BIDS-formatted data for TRACULA. It runs fine without error, but 
I have some concerns about the automatically generated protocol variables.

1) For “echospacing”, should we be using the echo spacing as found in the 
scanner protocol, or effective echo spacing (as parsed from the BIDS json 
sidecar)? These values are fairly different from each other. It is also not 
clear what units the config file expects (I assume “ms” based on some of the 
examples and protocols I have looked at).
2) “epifactor” seems to be generated by a mathematical operation on the total 
readout time as parsed from the BIDS json file. The value I get from this 
operation is off by a few orders of magnitude. In my case, the predicted value 
from the BIDS json file is 127001, while the protocol epifactor is 128. What I 
imagine is happening here is that the script assumes the TotalReadoutTime is in 
different units, because it does some division by (0.001) and then adds 1 to 
the result. So if the units matched mine, then I would have ended up with 127+1 
= 128 (which matches the protocol).

In either case, I am happy to see this being configured for BIDS and am excited 
to see it deployed in 7.3!

Best,
Steven
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<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail. 

[Freesurfer] [TRACULA] Auto-BIDS Config Variables Question

[Steven Meisler]

External Email - Use Caution

Hello,

I am trying out the development dmri-bids-config script 

 to set up my BIDS-formatted data for TRACULA. It runs fine without error, but 
I have some concerns about the automatically generated protocol variables.

1) For “echospacing”, should we be using the echo spacing as found in the 
scanner protocol, or effective echo spacing (as parsed from the BIDS json 
sidecar)? These values are fairly different from each other. It is also not 
clear what units the config file expects (I assume “ms” based on some of the 
examples and protocols I have looked at).
2) “epifactor” seems to be generated by a mathematical operation on the total 
readout time as parsed from the BIDS json file. The value I get from this 
operation is off by a few orders of magnitude. In my case, the predicted value 
from the BIDS json file is 127001, while the protocol epifactor is 128. What I 
imagine is happening here is that the script assumes the TotalReadoutTime is in 
different units, because it does some division by (0.001) and then adds 1 to 
the result. So if the units matched mine, then I would have ended up with 127+1 
= 128 (which matches the protocol).

In either case, I am happy to see this being configured for BIDS and am excited 
to see it deployed in 7.3!

Best,
Steven___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] TRACULA Configuration Question

[Daliah Ross]

External Email - Use Caution

Hi FreeSurfer experts,

I am planning to use TRACULA and have a question regarding the
configuration file and whether we can start with already processed data.

We have already run some steps involved in the TRACULA configuration
script, which take several hours per subject to complete. Specifically, we
already ran topup to handle B0 distortions and already processed eddy
distortion corrections. Could this be bypassed when configuring TRACULA so
we are not redoing these hours, or does it have to be run within TRACULA?

Thank you,
Daliah

-- 
*Daliah Ross, M.A.* | dro...@mail.yu.edu
Ph.D. Candidate, Clinical Psychology with Health Emphasis
Neuropsychology Concentration
Ferkauf Graduate School of Psychology, Yeshiva University
Albert Einstein College of Medicine
*pronouns: she/her/hers*
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] TRACULA -bedp parallel processing

[Yendiki, Anastasia]

K3coYNutw718WC_BSCkCTnqM_4W9KJr3x8w-gN74tO2ekUXxDL9mhUTNJNcjOiAxAbGsMu-hMNHRqDAnV6JtJ1y5aey5xUu0j9jNW2CesCgo-g%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Dfrom%25253A%25252522Yendiki%2525252C%25252BAnastasia%25252522%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252BFlNdHFAkB2YqWdzEtpZNqMkw2J4plyDuHqB1gqyJJ8%253D%26reserved%3D0>

Sent: Mon, 06 Jun 2022 20:17:47 
-0700<https://secure-web.cisco.com/1kixNktHZqVoDiwzPGH0_SQ74i4gW0m2P1a9d0QXRBeEN-CJAtcbnqTuT_KGDGRbC5UN9rx79WDrWQpv40ltRbitQztIx_Pl8Gdy7vegGkRVZGzFOY2nKQE1Udx_0AReFgFusO0aX2kMOBlASf9rPC0yQqVCWcO0EFSFrqCjjh4ZGbAYFn1iYbSbupsaczgXXpkxxoxhiahs3dOoZHE2SyaRvuNoDMx1SU7ImRr3kC_xKM1Dl6q6IOi3vElIIJkWA_bDjSb7_IM-Pe5jthfUA0xqgtv0wVdPOkp_qr6mVw8k7M0NcTZmmW3gFtJAqhLAlQIJrfh6lV-DWadz5VHg0rg/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11YTHE-9SnX_d-1PQ1yyK7EQYy82okQBAj3-aNpNvl-kJp3dN1G0QO8yztwo24IehLoqbE2gQ5JGCUFPjW6OE2T4RUxK5mY_WuSdC8Ue2dm5d1AI14zEzhbEnoH2wGcaNwmtL3nenG_qHdKlN8qkHjRZ4nU3njkcFajT4valovVZnht7U-peLk4QVCqIzRR3RvYd6vodHNFqPwl3ATlbX3K3dbofDxEC-a4Sn2dutAOC3g_eaOsE2xGmuaALZsSorg81MF_6V-T87knaRRfrG7iiWb-SF0r5wvo_-8AzTyg6VpgSudF4_rFltDEUU3VtoK1OfkbMTczhhRKQvIGphpw%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Ddate%25253A20220606%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DzMpmkQAaTcNySHOkozbk0Y6iqtZuuMKsFmFZ7c%252FKgmE%253D%26reserved%3D0>

To: Salar Dini, Elaheh ; Freesurfer support list 


Subject: Re: TRACULA -bedp parallel processin

Hi Ela - Which version of FSL are you using?

Anastasia.



From: Salar Dini, Elaheh 
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

Thanks for the reply. I'm not sure if you are looking for this: we use a small 
cluster with 40 nodes, 512 CPU cores. We are still using PBS.


Thanks,
Ela

From: Yendiki, Anastasia 
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

Thank you for the guidance.


When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is 
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected
Done


This happens for all subjects.


After this, when I check the subject 57 folder in subjects_dir, there is a file 
named "dmri.bedpostX.nii.gz".


However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log: No 
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No 
such file or directory

...


If I run trac-all -bedp -c  , and not try to process parallelly, 
it runs without any errors to the end.


Do you have any thoughts what goes wrong?


Thanks again,

Ela




From:Yendiki, 
Anastasia<https://secure-web.cisco.com/1Kkgu18O71-DcKUzW7ldCef0cCpxrnQZGaKxOq21FMHj_UrfM7YaQp9jZE4vPANLGyNnKxZqji0rXTCL90SSxVgByPTdYKrU1gfqprG17K-JNx4xy2Nwlkodi86RsFrPPmve7T2PvI5p8N4YlKw_XZksugXyvFTcGnS7bBJEjeHSoOy1u2foVrXCdtaGR32TopeUzjlHzGGgtwIQwXKCnxkPGvMhaefzhZFxv40N7SGS3kKV9sWq9Kq5eAALpMTwrOau4xOdfNqwFCbx6jgUp33smzry8FZy4k0loJp6SJg8/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13C1JAwso_YuO5y9tMvPeX2Y5QGVzJPHKFw48WPzGirv3xqXaE8lnYxUF5YaNpJD-UZY_cUKxwHv4zjCqlZ5cs6OWOpVh0T7syTmN22KmXw5IFlmDxw09yZuYznZgJ9w_Qr41N29l88aKVQbiZXJt3zGjH4uAyG1B94DgOWjlOxY-SCFvNh6IlxUFomOwVJdhHZkpLY28J-SJFxxZZdMuG_L_iRpg7OHwOPOvLSvOzyG-bA0ieiRd9RGAzx14jp5Wv38KZu1zNLWoiuoh5UXPdAjxX18Y8uY-3oh8R_5LE2yd9QYXWY9buODXtppSgUn_3YHjQkypQzagyqDAzdVTcQ%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.o

Re: [Freesurfer] TRACULA -bedp parallel processing

[Salar Dini, Elaheh]

reesurfer%252540nmr.mgh.harvard.edu%252526q%25253Dfrom%25253A%25252522Yendiki%2525252C%25252BAnastasia%25252522%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3D%252BFlNdHFAkB2YqWdzEtpZNqMkw2J4plyDuHqB1gqyJJ8%253D%26reserved%3D0>

Sent: Mon, 06 Jun 2022 20:17:47 
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To: Salar Dini, Elaheh ; Freesurfer support list 


Subject: Re: TRACULA -bedp parallel processin

Hi Ela - Which version of FSL are you using?

Anastasia.



From: Salar Dini, Elaheh 
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

Thanks for the reply. I'm not sure if you are looking for this: we use a small 
cluster with 40 nodes, 512 CPU cores. We are still using PBS.


Thanks,
Ela

From: Yendiki, Anastasia 
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

Thank you for the guidance.


When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is 
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected
Done


This happens for all subjects.


After this, when I check the subject 57 folder in subjects_dir, there is a file 
named "dmri.bedpostX.nii.gz".


However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log: No 
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No 
such file or directory

...


If I run trac-all -bedp -c  , and not try to process parallelly, 
it runs without any errors to the end.


Do you have any thoughts what goes wrong?


Thanks again,

Ela




From:Yendiki, 
Anastasia<https://secure-web.cisco.com/1-yWhuVTBvU0ipygFGOqpnutc2Jb8xnuJeVfcsaMDUedHZvLxF46H7ez8w803E1qWE9-PQ9O7_xUtKR19mN5EMsYNi58wrPEj_DrNr9-KAmJUNqev7dphL8BKZQmPc8B1BCQj_3Akuqa5giyC-7XeUUBmAiOy_RuUOmeEcHOyA9RuGIvBA-sucP0uCV-2evtSkaEBSLRCq2JsuE2B1iWhEuo1AfOKk0Trw8Wk2005XBNZwjDjhwyoF6h9r1_bO18M0fAD6Q5eEIWwRV65YPhbKXkUC482BlAImfEtB-4fpoA/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13C1JAwso_YuO5y9tMvPeX2Y5QGVzJPHKFw48WPzGirv3xqXaE8lnYxUF5YaNpJD-UZY_cUKxwHv4zjCqlZ5cs6OWOpVh0T7syTmN22KmXw5IFlmDxw09yZuYznZgJ9w_Qr41N29l88aKVQbiZXJt3zGjH4uAyG1B94DgOWjlOxY-SCFvNh6IlxUFomOwVJdhHZkpLY28J-SJFxxZZdMuG_L_iRpg7OHwOPOvLSvOzyG-bA0ieiRd9RGAzx14jp5Wv38KZu1zNLWoiuoh5UXPdAjxX18Y8uY-3oh8R_5LE2yd9QYXWY9buODXtppSgUn_3YHjQkypQzagyqDAzdVTcQ%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1G98lOaD7jG4iq2WjhE3v9

Re: [Freesurfer] TRACULA -bedp parallel processing

[Salar Dini, Elaheh]

Mon, 06 Jun 2022 20:17:47 
-0700<https://secure-web.cisco.com/1GCA6MWuKt1VcdDa_5zNx1_IJIImSX5TLU0kAlZFw-c_ua0qZzrsMiTD6JfM9fOpAaYqsZPXyK1TQksuGD9I6A0frHNlnAWrhJeWQ8c4cq5ADmmn7QwvAQBR3NVOTM2japE-_ltq4CwNWBWpD8fAdIWgBDLZZhSu_o0OHLM3cGxDo8SYu5lkgGbxRZuat1-5W6MKIPmyZTpp7JpRZdiQ0cwyDqdQyWffU7mKOIGJwJoB3PBFQRMIL2ZEIStQc444pLf4-oFONszS7378ssthy66lW94y4cXtNnOBSJgnDbT7-HFComnMBLpNJX82D_9l2ZE_Th4YriFjqcpMn-Ov_-Q/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11YTHE-9SnX_d-1PQ1yyK7EQYy82okQBAj3-aNpNvl-kJp3dN1G0QO8yztwo24IehLoqbE2gQ5JGCUFPjW6OE2T4RUxK5mY_WuSdC8Ue2dm5d1AI14zEzhbEnoH2wGcaNwmtL3nenG_qHdKlN8qkHjRZ4nU3njkcFajT4valovVZnht7U-peLk4QVCqIzRR3RvYd6vodHNFqPwl3ATlbX3K3dbofDxEC-a4Sn2dutAOC3g_eaOsE2xGmuaALZsSorg81MF_6V-T87knaRRfrG7iiWb-SF0r5wvo_-8AzTyg6VpgSudF4_rFltDEUU3VtoK1OfkbMTczhhRKQvIGphpw%252Fhttps%25253A%25252F%25252Fwww.mail-archive.com%25252Fsearch%25253Fl%25253Dfreesurfer%252540nmr.mgh.harvard.edu%252526q%25253Ddate%25253A20220606%26data%3D05%257C01%257Celaheh.salardini%2540yale.edu%257C64067fcf096a4c4c5ada08da48b617fd%257Cdd8cbebb21394df8b4114e3e87abeb5c%257C0%257C0%257C637902244183106888%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DzMpmkQAaTcNySHOkozbk0Y6iqtZuuMKsFmFZ7c%252FKgmE%253D%26reserved%3D0>

To: Salar Dini, Elaheh ; Freesurfer support list 


Subject: Re: TRACULA -bedp parallel processin

Hi Ela - Which version of FSL are you using?

Anastasia.



From: Salar Dini, Elaheh 
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

Thanks for the reply. I'm not sure if you are looking for this: we use a small 
cluster with 40 nodes, 512 CPU cores. We are still using PBS.


Thanks,
Ela

From: Yendiki, Anastasia 
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

Thank you for the guidance.


When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is 
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected
Done


This happens for all subjects.


After this, when I check the subject 57 folder in subjects_dir, there is a file 
named "dmri.bedpostX.nii.gz".


However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log: No 
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No 
such file or directory

...


If I run trac-all -bedp -c  , and not try to process parallelly, 
it runs without any errors to the end.


Do you have any thoughts what goes wrong?


Thanks again,

Ela




From:Yendiki, 
Anastasia<https://secure-web.cisco.com/1VYHNzOIeSCkEHQ3tNQrFynLaEkzVA31bYmNlQU4a7sr5WbQX47ZBpeBNyAyBSKJ2odknkB293O_oDAtHpjZlP4nusV38VIYhkNql2YJsqeIvrI3jeV_eJdUUdgNVaF3DmGGaPeZ-7uGKQY9fpOv7DgksXHsuJEXUdz8OBr6-GPqQHhFETxJyt18AW2x9S2JPDiEliLiYPMCgDWnW7_dIxdMguhPbk4-8h-AHw5xo5e3g0V2BilC8SKLRxoj-VGQN3mUiOnIe7PSlcrNZnM294gWRUA168NGE1RuptMLJ7Vc/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F13C1JAwso_YuO5y9tMvPeX2Y5QGVzJPHKFw48WPzGirv3xqXaE8lnYxUF5YaNpJD-UZY_cUKxwHv4zjCqlZ5cs6OWOpVh0T7syTmN22KmXw5IFlmDxw09yZuYznZgJ9w_Qr41N29l88aKVQbiZXJt3zGjH4uAyG1B94DgOWjlOxY-SCFvNh6IlxUFomOwVJdhHZkpLY28J-SJFxxZZdMuG_L_iRpg7OHwOPOvLSvOzyG-bA0ieiRd9RGAzx14jp5Wv38KZu1zNLWoiuoh5UXPdAjxX18Y8uY-3oh8R_5LE2yd9QYXWY9buODXtppSgUn_3YHjQkypQzagyqDAzdVTcQ%252Fhttps%25253A%25252F%25252Fnam12.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1G98lOaD7jG4iq2WjhE3v99As-QgUtMchD9KHZnXE856VPloJEJudQYJSktQvjbe3mj5zEABWY69ORy-E8CDVgclUx9YsdRIfflLP65rQJy59lQgsEF1hGeLoEMYYRqDTV67OUdihog0Nnh_Do2yaKbrGKJJLm2Eit2g-sAMRdrEICAyqi1PTydY_vN2riFdamFcpjYp9DA8Y2gWGC-Z3mBXh28v-uHYJZB1uK15w9cYUm9uutMsKCR9p7xJGcF9ZHyTO-Kzkk8ulOYkXE1RjXy6VxvEw-ZSGRItT-3jswRjK4lgWE_ZDvGIvLQzOmnSv7hTYvLO2lXCX2AKLsOGuww%2525252Fhttps%252525253A%252525252F%252525252Fwww.mail-archive.com%252525252Fsearch%252525253Fl%252525253Dfreesurfer%2525252540nmr.mgh.harvard.edu%2525252526q%252525253Dfrom%252525253A%252525252522Yendiki%25252525252C%252525

Re: [Freesurfer] TRACULA -bedp parallel processing

[Wighton, Paul]

Hi Ela,

It looks to me like line 79 of bedpostx_preproc.sh is:

if [ ${gflag} -eq 1 ]; then

Which is consistent with the error:

-eq: unary operator expected

What this error is saying is that the variable `gflag` has not been set, so the 
script does not know how to perform the comparison.

`gflag` is set a few lines above to the second parameter passed when executing 
`bedpostx_preproc.sh`.  I would investigate how `bedpostx_preproc.sh` is being 
invoked to chase down the cause of this error.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

That actually helps but not solving all the problems. So, what happens is that 
if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target 
'/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a 
directory). However, the second error still exists: a.k.a. 
(home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And 
when I try to run Parallel lines, I still get the error 
(dmri.bedpostX/logs/log: No such file or directory). So, my guess is, it 
still doesn't copy the whole needed package for some reason. So, what we end up 
having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.

I can always manually copy all needed file from fsl folder to our subjects 
folder, but I am curious why we get the error and why everything is not copied 
automatically. I also don't know what files we need to manually copy.

Thanks again,
Ela

From: Yendiki, Anastasia 
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What if you create the directory (that shows up in the "not a directory" error)?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
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Sent: Mon, 06 Jun 2022 20:17:47 
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