To: Freesurfer support list
Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
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Ok, now we know stem2fname is the problem. I can’t reproduce the error
...@nmr.mgh.harvard.edu
On Behalf Of Lawless, Dylan
Sent: Wednesday, October 11, 2023 10:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
I ran
oun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Wednesday, October 11, 2023 9:32 AM
To: Freesurfer support list
Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
Exter
ylan
Sent: Wednesday, October 11, 2023 10:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
Could you point me towards the correct log file? I am unable to loca
Sent: Tuesday, October 10, 2023 10:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
There should be a log for the command you ran.
I’m wondering
...@nmr.mgh.harvard.edu
On Behalf Of Lawless, Dylan
Sent: Tuesday, October 10, 2023 10:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
Sure thing, I have attached
on behalf of Huang, Yujing
Sent: Tuesday, October 10, 2023 9:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration:
if: Expression Syntax. brainmask not found.
External Email - Use Caution
The error that you cut and paste here
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if:
Expression Syntax. brainmask not found.
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Hello,
I am attempting to create a freesurfer v7.2.0 docker container that can run
tracula on the freesurfer outputs
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Hello,
I am attempting to create a freesurfer v7.2.0 docker container that can run
tracula on the freesurfer outputs, however, I am unable to get past the
intra-subject registration step without receiving the following error:
--s sub-01 --mov
...@nmr.mgh.harvard.edu
on behalf of Alexopoulos, Dimitrios
Sent: Monday, March 7, 2022 12:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] error with trac-all -prep in FS7.2 tracula
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Hi all, any comments related to these errors we get with trac-all -prep in FS
7.2
Subject: [Freesurfer] error with trac-all -prep in FS7.2 tracula
* External Email - Caution *
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Hi all,
We are reprocessing some of our data with FS 7.2 to evaluate the new updates to
Tracula, however, we are getting errors from
the trac-all -prep -c configfile
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Hi all,
We are reprocessing some of our data with FS 7.2 to evaluate the new updates to
Tracula, however, we are getting errors from
the trac-all -prep -c configfile step.
The last 20 lines of output are shown below. Anyone have any comments on how
up script of whichever version you
>>> need to use.
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
>>> vinit.k.srivast...@gmail.com>
>>> *
;
Sent: Thursday, September 20, 2018 8:25:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error with trac-all -prep
External Email - Use Caution
Hi Anastasia,
Thanks for your reply. I needed the dev version in order to ut
sday, September 20, 2018 8:25:31 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] error with trac-all -prep
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia,
>>
>> Thanks for your reply. I needed the dev ve
-
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 8:25:31 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error wit
rvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Vinny K
mailto:vinit.k.srivast...@gmail.com>>
Sent: Thursday, September 20, 2018 6:57:02 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error with tra
n behalf of Vinny K <
> vinit.k.srivast...@gmail.com>
> *Sent:* Thursday, September 20, 2018 6:57:02 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] error with trac-all -prep
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
&
K
Sent: Thursday, September 20, 2018 6:57:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error with trac-all -prep
External Email - Use Caution
Hi Anastasia,
A similar post had encountered a similar problem a while back:
https://mail.nmr.mgh.harvard.edu/pipermail
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Hi Anastasia,
A similar post had encountered a similar problem a while back:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html
Should I install the latest stable release of FreeSurfer and run only the
trac-all -prep step
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Hello Anastasia,
Please find attached the trac-all log.
Thanks for your help,
Vinny
On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia
wrote:
> Hi Vinny - This error is during the diffusion-to-structural registration.
> Can you send the entire
Hi Vinny - This error is during the diffusion-to-structural registration. Can
you send the entire log file (scripts/trac-all.log)?
Best,
a.y
On Sep 19, 2018 8:39 PM, Vinny K wrote:
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Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I
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Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I get the following error when running the command: trac-all -prep -c
dmrirc.
Any help would be greatly appreciated.
Thanks,
Vinny
du
Subject: [Freesurfer] Error from trac-all prep: data and bvals/bvecs do not
contain the same number of entries
Hello:
I followed the tutorial for tracula, because of the tutorial data that you give
dont have the T1 image, so I use on of my own diffision data and the
reconall-ed T1 image, and I
Hi Jon - The command that fails is trying to multiply 2 volumes and
complains that they have different sizes. Have you checked if these 2
volumes exist and what their dimensions are?
a.y
On Wed, 27 Mar 2013, Jon Wieser wrote:
i ran
trac-all -prep -c dmrirc_single_subject
and got the error
@nmr.mgh.harvard.edu
Sent: Thursday, March 28, 2013 10:13:19 AM
Subject: Re: [Freesurfer] error during trac-all -prep
Hi Jon - The command that fails is trying to multiply 2 volumes and
complains that they have different sizes. Have you checked if these 2
volumes exist and what
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