[Freesurfer] longitudinal tracula error

[Francesco Siciliano]

Hi,

I have been unsuccessful in getting longitudinal tracula to run. I have been 
directing my dmrirc file to skip the registration-based B0-inhomogeneity 
compensation (by setting it to 0). However, when I try to run trac-all prep, I 
get an error message asking to specify a field map for each input. I also tried 
running the step and specifying appropriate field maps, yet still got the same 
error. Any help with this would be appreciated.

Best,


Francesco Siciliano, B.A.
Research Assistant
Department of Child and Adolescent Psychiatry
The New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646) 774-5703
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[Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

From the mailing list, it seems a similar issue has been fixed in previous 
updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

From what I understand, the base is not necessary to run any analysis, but it 
has to be there anyhow (?): 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe 
I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal tracula error

[Anastasia Yendiki]

Hi Francesco - Please attach your dmrirc, and also the tracula log file of 
your subject (scripts/trac-all.log). It's hard to guess what went wrong 
without looking at the complete output.


Thanks,
a.y

On Thu, 29 Jan 2015, Francesco Siciliano wrote:


Hi,
I have been unsuccessful in getting longitudinal tracula to run. I have been 
directing my dmrirc file to skip the registration-based B0-inhomogeneity 
compensation (by setting it to 0).
However, when I try to run trac-all prep, I get an error message asking to 
specify a field map for each input. I also tried running the step and 
specifying appropriate field maps, yet
still got the same error. Any help with this would be appreciated.

Best,


Francesco Siciliano, B.A. Research Assistant
Department of Child and Adolescent Psychiatry
The New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646) 774-5703

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

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia  wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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



trac-all.local-copy
Description: trac-all.local-copy
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Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia  wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://ma

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

From the mailing list, it seems a similar issue has been fixed in previous 
updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, i

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S000

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach t

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bárbara Avelar Pereira 
mailto:barbara.avelar.pere...@ki.se>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy f

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Thanks again — it was a huge help!

On 31 Jan 2017, at 18:25, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bárbara Avelar Pereira 
mailto:barbara.avelar.pere...@ki.se>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but

[Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Emad Ahmadi]

Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all 
-prep & -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu


trc_.e11258806
Description: application/applefile


trc_.o11258806
Description: Binary data


trc_0001.e11258808
Description: application/applefile


trc_0001.o11258808
Description: Binary data
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#_
setenv SUBJECTS_DIR /cluster/guptagp/Emad/3LT/subjDir
setenv RAW_DATA /cluster/guptagp/Emad/3LT/rawData
#_

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
#set dtroot = /path/to/tracts/of/ducks

# Subject IDs (one per time point per subject)
#_
set subjlist = ( 2a \
 2b \
 3a \
 3b )
#_

# Longitudinal base template subject IDs (one for each time point above)
#_
set baselist = ( 2tem \
 2tem \
 3tem \
 3tem )
#_

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
#set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#_
set dcmroot = $RAW_DATA
set dcmlist = ( 2a/Diffusion/IM-0001-0001.dcm \
2b/Diffusion/IM-0001-0001.dcm \
3a/Diffusion/IM-0001-0001.dcm \
3b/Diffusion/IM-0003-0001.dcm )
#_

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# 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 = (/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt)
#_

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#_
#set bvecfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt
#_

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#_
set bvalfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bval.txt
#_

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
#set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0mlist = ( huey/year1/fmag/XXX-1.dcm \
huey/year2/fmag/XXX-1.dcm \
dewey/year1/fmag/XXX-1.dcm \
dewey/year2/fmag/XXX-1.dcm \
louie/year1/fmag/XXX-1.dcm \
louie/year2/fmag/XXX-1.dcm )

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = ( huey/year1/fphas/XXX-1.dcm \
huey/year2/fphas/XXX-1.dcm \
dewey/year1/fphas/XXX-1.dcm \
dewey/year2/fphas/XXX-1.dcm \
louie/year1/fphas/XXX-1.dcm \
   

Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please 
send me the entire trac-all.log of one of your subjects? Thank you!


a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - I believe that it's not finding your freesurfer recons. They 
should be under the $SUBJECTS_DIR and have the same names for time points 
and longitudinal template as what is under your tracula output directory 
(if the latter is different from SUBJECTS_DIR).


Best,
a.y

On Fri, 1 Apr 2016, Emad Ahmadi wrote:


Hi Anastasia,

I’ve attached the log files. The cases are:

1. Case #2; time points: 2a, 2b; base template: 2tem
2. Case #3; time points: 3a, 3b; base template: 3tem

Thank you again for your help,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu



On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki  
wrote:


Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please send 
me the entire trac-all.log of one of your subjects? Thank you!

a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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

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