External Email - Use Caution
Hello,
I'm trying to run the second step of TRACULA processing (in bash), which is:
trac-all -bedp -c /path/to/configuration/file
I'm currently using the FreeSurfer version v7.1.4 and I get the following error:
WARN: Running bedbostx locally - this m
External Email - Use Caution
Dear TRACULA experts,
I'm trying to run TRACULA for one subject (multiple scans, longitudinal)
but I'm getting the following error. Is there a way to fix this? I attach
the b-vals and b-vecs.
eddy_openmp
--imain=/home/data/dsf4b/trc/sub-F4B002_2.long.
External Email - Use Caution
Hello all,
Apologies for reposting this. I am still having the same issue and have
unfortunately not found a solution.
I am trying to run trac-all prep longitudinally (testing it on a single subject
for now with three timepoints and 2 scans per time
External Email - Use Caution
Hello all,
I am trying to run trac-all prep longitudinally (testing it on a single subject
for now with three timepoints and 2 scans per time point). I keep getting the
below error. Can't figure out what is causing it and could use some advice.
I've
External Email - Use Caution
Hi FreeSurfers,
I have been running Tracula on a two time point longitudinal data set. I have
successfully ran 95% of my data all the way through -stat. However, with 7 of
my subjects trac-all -path runs for about 24 hours and then gives the follow
External Email - Use Caution
Dear FreeSurfer developer.
I successfully completed the tracula trac-all analysis using freesurfer
7.4.1. ThalamicNuclei.v13.T1.FSvoxelSpace.mgz images were obtained using
segmentThalamicNuclei.sh, and trac-all analyses results were obtained using
both
External Email - Use Caution
Hello,
I am attempting to run white matter tractography using TRACULA, as
described in the tutorial, however, using a brain parcellation acquired
using an external algorithm. I have put the aparc+aseg.mgz file in the
subject directory in folder mri
External Email - Use Caution
Hello,
I am attempting to run white matter tractography using TRACULA, as
described in the tutorial, however, using my own data and brain
parcellation acquired using external algorithm. I have put the
aparc+aseg.mgz file in the subject directory in
External Email - Use Caution
bedpostx, which also uses xfibres, takes a very long time on a single
CPU. It does not seem like xfibres can even use multiple CPUs.
We have GPUs available, and prior work with FSL suggests that using
the GPU cuts processing down from about a day to a
External Email - Use Caution
Hi:
I tried to use trac-all using following syntax:
trac-all -prep -s name -i
SIEMENS_DICOM_256_GRADIENTS_TRACTOGRAPHY_FILES_PATH
and I got the following error message:
"ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for
External Email - Use Caution
Hello everyone,
I am having trouble getting past the very first stages of trac-all -prep.
I am using FreeSurfer 7.3.2. I tried several workarounds based on previous
answers to similar problems in this mailing list, but I am unsuccessful
each time.
Fir
Subject: Re: [Freesurfer] trac-all -prep -c ERROR
External Email - Use Caution
Hi back,
Should be alright now. Please try this link: MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be
https://drive.google.com/dri
External Email - Use Caution
Hi back,
Should be alright now. Please try this link:
https://secure-web.cisco.com/1LYPTJn0s7YjdWTtPFS55k3z-IqjPfKIscsxsCg4qgjYm5i7hgZ47NYZ8BRHgQAtw4DZhP0bO52JhFFLI8LcEH2uXcDPnyyn6mXbi2PEZLkzub2KbFSDNMpQcj-DHyeMAdbjU8od-fcAnsd58VKB5nnYprNNUzbu4SeyZphu
Hi Ela - Can you make the google doc accessible by all?
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Thursday, June 30, 2022 5:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep -c ERROR
External Email - Use Caution
Thank you for the reply. For some reason, when I change the DCM file to nii and
look at them, in majority of our subjects, the cerebellum and lower brain stem
has been cut off, but in this specific subject, I don't think the CST is
truncated or out o
:38 AM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -prep -c ERROR
External Email - Use Caution
Dear experts,
I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I
get the following error in -prep step:
((INFO: Distances between consecutive
External Email - Use Caution
Dear experts,
I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I
get the following error in -prep step:
((INFO: Distances between consecutive points in test subject's space are 10 13
12 13 13 12
WARN: Could not find sati
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trac-all error assistance
External Email - Use Caution
Hello, freesurfer developers
I was running the trac-all command for infant images. But I got an error during
the cst processing. I've already checked the mailbox to
External Email - Use Caution
Hello, freesurfer developers
I was running the trac-all command for infant images. But I got an error
during the cst processing. I've already checked the mailbox to find similar
issues, but it seems that there are several logic errors. I will appreciate
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Kaplan, Elizabeth
Sent: Monday, February 14, 2022 11:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Hello All,
I am attempting to process images using tracula, howev
External Email - Use Caution
Hello freesurfer devs,
Thank you so much for all of your work on Tracula! I have been following this
conversation
(https://secure-web.cisco.com/1Ykw2-j5trx6ExR25illKidIACAuQbQ8aKBMO_GQNJvBetczSCKd1Qag-D73npLMv-T9LQAxWCim4zQwoc6bHCXKZVS5Jd0fTRVxpO4UV
).
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Monday, January 10, 2022 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Thank you for
External Email - Use Caution
Thank you for constantly improving TRACULA. I believe we don't have reverse
polarity scan or a field-map. We might be able to acquire the field-map though
since the MRI has been acquired locally.
Having that in mind, and just for clarification and m
u and your instructor for bringing this to our attention!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Sunday, January 9, 2022 8:26 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all -prep -c
External Email - Use Caution
Dear Anastasia,
I just wanted to share with you that after following up with our instructor,
asking him why he recommended FLIRT rather than bbregister, he clarified that
4-5 years ago when he was using TRACULA for his project,
registration using bbr
rom: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Tuesday, January 4, 2022 3:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Dear Anastasia,
Honestly, this was just based on our instructor'
, Elaheh
Sent: Monday, January 3, 2022 9:09 PM
To: Freesurfer support list
Subject: [Freesurfer] Trac-all -prep -c error
External Email - Use Caution
Dear Freesurfer developers and Anastasia,
Happy new year. I am trying to run trac-all -pep -c dmriEla. dmriEla is my
config file which is
External Email - Use Caution
Dear Freesurfer developers and Anastasia,
Happy new year. I am trying to run trac-all -pep -c dmriEla. dmriEla is my
config file which is also attached to this message. I am also attaching the
trac-all.log file to this email. I am getting the followi
mgh.harvard.edu>
on behalf of Kaplan, Elizabeth
<elizabeth_kap...@brown.edu>Sent: Friday, December 31, 2021 1:56
PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer]
Trac-all -Prep -C
Error External Email - Use
CautionHi All,
harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kaplan, Elizabeth <
> elizabeth_kap...@brown.edu>
> *Sent:* Friday, December 31, 2021 1:56 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Trac-all -Prep -C Error
>
>
>
PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trac-all -Prep -C Error
External Email - Use Caution
Hi All,
I am working to process DWI images using Tracula, however I am running into an
error when attempting to run the "trac-all -prep -c" command line. The error
reads
External Email - Use Caution
Hi All,
I am working to process DWI images using Tracula, however I am running into
an error when attempting to run the "trac-all -prep -c" command line. The
error reads:
"Error when attempting to read --index file".
I have searched through the arch
Glad to hear it worked!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Tuesday, December 21, 2021 6:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
External Email - Use
arvard.edu
on behalf of Salar Dini, Elaheh
Sent: Tuesday, December 21, 2021 1:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
External Email - Use Caution
Dear Anastasia,
I just wanted to follow-up on my previous message with having this in mind:
ay, December 9, 2021 2:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
Hi Ela - Do you know what phase-encode direction your DWIs were collected with
(e.g. AP, PA, LR, etc.)? Then add it to the config file like this: "set pedir =
(AP)"
Otherwise, i
s
6.0.5.1 .
Thank you as always.
Kindly,
Ela
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, December 9, 2021 2:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
Hi Ela - Do you know
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep error
External Email - Use Caution
Dear freesurfer developers and Dr. Yendiki,
I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I
am attaching the config file here. If I perform registration-based c
External Email - Use Caution
Dear freesurfer developers and Dr. Yendiki,
I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I
am attaching the config file here. If I perform registration-based correction
with eddy_correct, doeddy=1, things start to run.
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Friday, December 3, 2021 12:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep -c error
External Email - Use Caution
Hi all,
I am trying to run trac-all -prep -c dmrirc1.txt, with dmrirc1.txt
External Email - Use Caution
Hi all,
I am trying to run trac-all -prep -c dmrirc1.txt, with dmrirc1.txt being the
configuration file. As soon as I attempt, I get the following error:
ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for model-based e
You're running the old version, you should install 7.2 🙂
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Arman Avesta
Sent: Wednesday, December 1, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep
External Email - Use Caution
Hello Arman,
The first error indicates there is a file missing from under fsl/bin,
/usr/local/fsl/bin/eddy_correct: line 95: /usr/local/fsl/bin/imglob: No such
file or directory
- which makes me think something may not be correct with how fsl is
setu
at. Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
juergen.haen...@upd.unibe.ch
Sent: Tuesday, June 29, 2021 8:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep problem (error: corRead(): can't ope
External Email - Use Caution
Dear TRACULA experts
I try to run trac-all -prep using the "Perform registration-based
B0-inhomogeneity compensation“ option, but the following error occurred:
mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/
/Volumes/Dat
External Email - Use Caution
solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors
On Fri, 6 Nov 2020 at 11:38, Michele Valotti
wrote:
> Hi all,
> I am trying t
on behalf of Zeng, Qi
Sent: Wednesday, May 13, 2020 7:36 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all prep error
External Email - Use Caution
Hi,
I have an error message when processing trac-all prep. attached the log file.
error:
"terminate called after throwing
u> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Thursday, April 30, 2020 2:22 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] trac-all -bedp error
>
>
> External Email - Use Caution
>
> Hi,
>
> I run trac-all, the log f
Yes, this is fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Thursday, April 30, 2020 2:22 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -bedp error
External Email - Use Caution
Hi,
I run trac-all, the
External Email - Use Caution
Hi,
I run trac-all, the log file has the following endings.
"Queuing post processing stage"
or
"Queuing post processing stage
59 slices processed
All slices processed
/hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
line 345:
f Hua, Jessica
Sent: Thursday, April 23, 2020 4:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trac-All NaN
External Email - Use Caution
Hi FreeSurfer,
I ran the trac-all -stat command on some of my participants, and I noticed that
some of the values that were outputted cont
External Email - Use Caution
Hi FreeSurfer,
I ran the trac-all -stat command on some of my participants, and I noticed that
some of the values that were outputted contained NaN. Why are the values
coming out as NaN?
fmajor_PP.avg33_mni_bbr.AD_Avg.txt
S11018a_LGI S11019a_LGI S1
External Email - Use Caution
Hi Dr. Yendiki,
Thanks! That fixed the issue I was having.
Jessica
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
___
Freesurfer mai
Hi Jessica - A couple of things to fix. The bvecs file has commas in it. The
bvals file, if you view it with the more command on linux, you'll see that
instead of line changes it has "^M" in between the values. This can happen if
it's saved in a windows text editor. You can open it in a linux te
External Email - Use Caution
Attached are bvecs and bvals.
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
0,0,0
0,0,0
0,0,0
0,0,0
0,0,0
1,
Can you please also send your bvecs and bvals files? I can't see anything else
going wrong, so I'm guessing it has to do with those.
From: Hua, Jessica
Sent: Monday, April 13, 2020 12:10 PM
To: Yendiki, Anastasia ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: Tra
External Email - Use Caution
Hi Dr. Yendiki,
I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed
your work email. Attached is my full configuration file as well as my error
log.
Best,
Jessica
---
Jessica Hua, M.A.
Cognitive and Emotional Control
ehalf of Hua, Jessica
Sent: Sunday, April 12, 2020 12:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trac-all Error
External Email - Use Caution
Hi FreeSurfer,
I am running trac-all prepocessing using a configuration file. I tried
preprocessing a couple of partici
External Email - Use Caution
Hi FreeSurfer,
I am running trac-all prepocessing using a configuration file. I tried
preprocessing a couple of participants, and I keep getting this error:
#-
#@# Tensor fit Sat Apr 11 21:29:36 PDT 2020
dtifit
> nayanw...@gmail.com>
> *Sent:* Tuesday, October 22, 2019 2:32 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] trac-all error
>
>
> External Email - Use Caution
>
> I have attached the log-file from the trac-all command
> Thanks and Regard
y, October 22, 2019 2:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all error
External Email - Use Caution
I have attached the log-file from the trac-all command
Thanks and Regards
Nayan Wadhwani
On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia
ma
Please attach your log file from scripts/trac-all.log.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of nayan wadhwani
Sent: Tuesday, October 22, 2019 1:13 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all error
External
erting it to plain text (if you use mac, from the Format menu of the
> text editor).
>
> Best,
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of nayan wadhwani
>
> Sent: Saturday, October 19, 2019 1:36 AM
> To: Freesurfer@nmr.mgh.h
tasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of nayan wadhwani
Sent: Saturday, October 19, 2019 1:36 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all error
External Email - Use Caution
Hello Freesurfer,
After running recon all script which comp
External Email - Use Caution
Hello Freesurfer,
After running recon all script which completed successfully, I ran trac-all
command which exited with error and tried running it with dicom files.
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Reference
> ddcc2...@gmail.com>
> *Sent:* Thursday, July 4, 2019 8:24:32 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Trac-all error
>
>
> External Email - Use Caution
>
> When running on freesurfer 6.0 I get the following pop-up screen as well.
>
>
on your system and tkregister2 did
not compile?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Thursday, July 4, 2019 8:24:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all error
External Email - Us
er-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
>> ddcc2...@gmail.com>
>> *Sent:* Wednesday, July 3, 2019 2:06:27 PM
>> *To:* Freesurfer support list
>> *Subject:* [Freesurfer] Trac-all error
>>
>>
>> External Email
---
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Wednesday, July 3, 2019 2:06:27 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Trac-all error
>
>
&g
Freesurfer support list
Subject: [Freesurfer] Trac-all error
External Email - Use Caution
Hello,
I am running trac-all preproc with the following code
setenv FREESURFER_HOME /Applications/freesurfer_dev
source $FREESURFER_HOME/SetUpFreeSurfer.csh
#Must set SUBJECTS_DIR to where data
External Email - Use Caution
Hello,
I am running trac-all preproc with the following code
setenv FREESURFER_HOME /Applications/freesurfer_dev
source $FREESURFER_HOME/SetUpFreeSurfer.csh
*#Must set SUBJECTS_DIR to where data is or else uses what was set up when
installing freesu
External Email - Use Caution
Hello Doug,
When running trac-all -prep and including b0 inhomogeneity correction with
epidewarp.fsl I get the following error.
FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X
Looking at the epidewarp.fsl source code I see that the error is occ
External Email - Use Caution
Hello,
After running
trac-all -prep -jobs file -c /homes/dcallow/dmrirc.long.example.parallel.sh
I am trying to submit the jobs for parallel computing.
However, when running the following
#!/bin/tcsh -f
#SBATCH --time=300:00:00
#SBATCH --mem=24000
u <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
>> heidifo...@gmail.com>
>> *Sent:* Wednesday, September 19, 2018 11:06:09 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] trac-all using nifti
>>
>>
&g
r-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Heidi Emmanuel Foo
mailto:heidifo...@gmail.com>>
Sent: Wednesday, September 19, 2018 11:06:09 PM
To: Freesurfer support list
Subject: Re: [Freesurf
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
> heidifo...@gmail.com>
> *Sent:* Wednesday, September 19, 2018 11:06:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] t
What is the trac-all command line that you run?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Heidi Emmanuel Foo
Sent: Wednesday, September 19, 2018 11:06:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti
o <
> heidifo...@gmail.com>
> *Sent:* Monday, September 17, 2018 11:03:47 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] trac-all using nifti
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> It seems like I do. Could the problem be
Sent: Monday, September 17, 2018 11:03:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti
External Email - Use Caution
Hi Anastasia,
It seems like I do. Could the problem be the config.txt?
Thanks!
Best Regards,
Heidi Foo
On Tue, Sep 18, 2018 at 12:47 AM
reate the output directory
> /data_int/heidi/forHeidi/Preprocessed?
>
> a.y
>
> From: on behalf of Heidi
> Emmanuel Foo
> Reply-To: Freesurfer support list
> Date: Monday, September 17, 2018 at 12:55 AM
> To: Freesurfer support list
> Subject: [Freesurfer] trac-all
o:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, September 17, 2018 at 12:55 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all using nifti
External Email - Use Caution
Hi Anastasia,
I am currently trying to run trac-all with my DWI
External Email - Use Caution
Hi Anastasia,
I am currently trying to run trac-all with my DWI data. I do not have the
DICOM but only the Nifti files and I would like to use the same bval and
bvec template for every subject. I created a configiration file as
attached. However, I hav
Sent: Thursday, April 13, 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -stat
Thanks, Anastasia!!
It should be it. I had run the same command before with slightly fewer subjects
in my "set subjlist" and it did work fine. Then I rerun the -path (and added
extra
Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 12, 2017 5:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -stat
Hi Amelia - This means that it can't find any of the tracts that you've
specified (or any tracts period, if you haven't specified a list) for
Hi Anastasia,
I am having some issues with the -stat option. Below is the error. I am not
sure of what's causing the issue. Any idea?
Thanks a lot!! Amelia
-
trac-all -c scripts/dmrirc.stats -stat
INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer
INFO: Diffusion root is /da
a/$subj/dpath/
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia
[versa...@upmc.edu]
Sent: Wednesday, April 12, 2017 5:00 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -stat
Hi Ana
Glad to hear!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Abigail Waters
[awate...@suffolk.edu]
Sent: Tuesday, February 21, 2017 7:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep
behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 15, 2017 4:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – Interesting, this means that it was the update and not the subject.
I’ve never seen
.edu>>
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi - Sorry about that! I was not aware that anything had been updated and was
only checking the freesurfer version in the log. The previously successful
subject failed, I've a
>
Date: Tuesday, February 14, 2017 at 2:55 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Attached are both the successful and failed trac-all logs.
___
ruary 13, 2017 2:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
It's the same. These are all subjects from the same research protocol.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[frees
PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Is the data size different for the new subjects than the old subject? Is the
spatial resolution or number of directions higher? Or is the acquisition
exactly the
behalf of Abigail Waters
[awate...@suffolk.edu]
Sent: Friday, February 10, 2017 8:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
The successfully processed subject was completed using the same FS version
(5.3) in December. We have not
-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Friday, February 10, 2017 4:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hi Abby – When you say you
2017 at 3:05 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
Hello -
I'm attempting to run the -trac-all -prep command with FS 5.3. I am ru
Hello -
I'm attempting to run the -trac-all -prep command with FS 5.3. I am running
into the same memory allocation issues on my Mac that were present in earlier
versions of Freesurfer/Tracula. See below:
MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th
slice
Cannot a
Thanks for the tip, Peter. Someone has had this issue in past. These were
adapted from old FSL scripts and the goal is to phase them out eventually.
Right now trac-all has a new option to print out the commands to be
submitted to a cluster, so that the user can handle that herself. It would
be impr
Hi,
there is a bug in the scripts bedpostx_mgh and fsl_sub_mgh. Both use code that
do not conform to the standard shell syntax and work only with bash. This does
not work in system that do not link /bin/sh to /bin/bash (as is the case in
Ubuntu). Both scripts must use #!/bin/bash as the interpr
[hao.freesur...@hotmail.com]
Sent: Tuesday, December 20, 2016 1:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom
Hello:
More information to give, I think the problem is from the format of the
magnitude and phase image for the
Hello:
More information to give, I think the problem is from the format of the
magnitude and phase image for the registration-based B0-inhomogeneity
compensation, I tried to comment the registration-based B0-inhomogeneity
compensation, and it seems to work, So:
In TRACULA, we can not define t
Hello, FreeSurfer experts:
I know that we are going to have a new version of FS 6.0.0, but with the curent
newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp )
for FS5.3.0, I am working on UBUNTU14.0.
To run tracula in parallel on my machine, here is my config file( for
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