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Sorry, I just realized that I sent a wrong trac-all.log and trac-all.error file.
From: Salar Dini, Elaheh
Sent: Friday, December 3, 2021 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: follow-up on trac-all -prep
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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
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Hello Anastasia,
Thank you so much for your response. It was very useful. I have changed the
config file to the one I'm attaching to this message, but I'm still getting the
same error:
ERROR: for B0 distortion correction with reverse-polarity DWIs
holidays
From: Salar Dini, Elaheh
Sent: Tuesday, December 14, 2021 2:31 PM
To: Freesurfer support list
Subject: Re: trac-all -prep error
Good day Anastasia,
Thank you for replying back. It worked like a charm, I also had to add set
epifactor, but after
d.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
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Dear Anastasia,
I just wanted to follow-up on my previous message with having this in mind:
the inde
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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
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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.
6%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D0tciIgIkPmrifx8r1Fgwmjx3csGNkQXrsSD4p6ZSSeQ%253D%26reserved%3D0>
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Thursday, December
.
Anastasia.
____
From: Salar Dini, Elaheh
Sent: Tuesday, January 4, 2022 3:40 PM
To: Freesurfer support list
Subject: Re: Trac-all -prep -c error
Dear Anastasia,
Honestly, this was just based on our instructor's suggestion, who used to work
with you a few years back, so I just trusted
!
Anastasia.
____
From: Salar Dini, Elaheh
Sent: Sunday, January 9, 2022 8:26 PM
To: Freesurfer support list
Subject: Re: Trac-all -prep -c error
Dear Anastasia,
I just wanted to share with you that after following up with our instructor,
asking him why he recommended FLIRT rather than bb
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Dear Freesurfer developers,
I have a dwi.nii image which I want to co-register on a orig.mgz (produced by
running recon-all on the subject's T1 image) file without any drop in the
quality of image (i.e. without any resolution cost, or changes in the
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Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something
quite similar as volumetric co-registration but for surfaces. To be exact, I
have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1
te.newcoords
____
From: Salar Dini, Elaheh
Sent: Wednesday, March 16, 2022 4:15 PM
To: Freesurfer support list
Subject: lh.white surface co-registration
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something
q
in the exact
opposite direction, so it completely overlays the first brain using freesurfer?
Thank you and all the best,
Ela
From: Salar Dini, Elaheh
Sent: Monday, January 31, 2022 6:46 PM
To: Freesurfer support list
Subject: Recon-all reconstructed image
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Hello,
I just wanted to follow-up on my last message. I will be thankful if you can
respond at the earliest time of your convince.
Thanks and all the best,
Ela
From: Salar Dini, Elaheh
Sent: Wednesday, January 26
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Dear Freesurfer developers,
In the link below, you see two brains belonging to the same subject:
mgz --interp nearest The betmaskvol should be the intensity image
(like orig.mgz) and not a binary mask or segmentation
____
From: Salar Dini, Elaheh
Sent: Wednesday, February 2, 2022 4:05 PM
To: Freesurfer support list
Subject: Re: Recon-all reconstructed image coordin
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Dear Anastasia,
I have run trac -all -prep in 2 different conditions:
a) prerequisite recon-all step was done using freesurfer 7.2.0
b) prerequisite recon-all step was done using freesurfer 6
The first time everything ran smoothly without an error,
____
From: Salar Dini, Elaheh
Sent: Tuesday, January 18, 2022 5:05 PM
To: Freesurfer support list
Subject: Re: TRACULA Question
________
From: Salar Dini, Elaheh
Sent: Tuesday, January 18, 2022 4:55 PM
To: Freesurfer support list
Subject: TRACULA Question
Dear An
?
Anastasia.
____
From: Salar Dini, Elaheh
Sent: Thursday, June 30, 2022 5:08 PM
To: Freesurfer support list
Subject: Re: trac-all -prep -c ERROR
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 bra
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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
the left CST is truncated in this one subject? E.g., if
the top part of the brain was outside the field of view?
Anastasia.
___
____
From: Salar Dini, Elaheh
Sent: Wednesday, June 29, 2022 11:38 AM
To: Freesurfer support list
Subject: trac-all -prep -c ERROR
Dear
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
S
rror.
-Paul
____
From: Salar Dini, Elaheh
Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia ; Freesurfer support list
Subject: Re: TRACULA -bedp parallel processing
That actually helps but not solving all the problems. So, what happens is that
if I create dmri.bed
jjssDiTuI-jnsRNrB4yhpU34pjFC9SMElfpKIsMLQf3kgHKb1CBetp79j8vvZBoIzuUWIEiNjvZLgGeZi3FH6yf9DJxYsWjzDWeny_dgtQvzhshVEqDuPx0EKj8a5R0_968gdibNj_WrxGox87Vc11vKbap28AeyC4OVA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220606>
To: Salar Dini, Elaheh
From: Salar Dini, Elaheh
Sent: Wednesday, June 8, 2022 3:32 PM
To: Yendiki, Anastasia ; Freesurfer support list
Subject: Re: TRACULA -bedp parallel processing
Thanks Paul.
bedpostx_preproc.sh is the first job that is I submit to my cluster. My input
file is attached to this email
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Hello,
I have tried to create a text file with command lines that can be run in
parallel by using trac-all -bedp -c -jobs Parallel.
When I use this command three text files are produced named: pre.Parallel,
post.Parallel, and Parallel. Should I
mgh.harvard.edu%26q%3Ddate%3A20220603>
You run them in that order. First the pre, then the parallel, then the post.
You can queue them that way, so that the parallel jobs wait for the pre to
finish, and the post waits for all the parallel jobs to finish.
________
From: S
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
wers your question ...
____
From: Salar Dini, Elaheh
Sent: Thursday, July 21, 2022 5:26 PM
To: Freesurfer support list
Subject: Understanding ?h.sphere.reg
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to
the
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Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to
them? What I actually mean is I'm using TRACULA which itself use the following
files from mri and surf folder (all created by running recon-all
el
Thanks and all the best,
Ela
____
From: Salar Dini, Elaheh
Sent: Tuesday, July 26, 2022 12:45 PM
To: Freesurfer support list
Subject: Re: Understanding ?h.sphere.reg
Hi Douglas,
It does. Thank you. Can you also help me with something else? If we coregister
bunch of v
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Dear Anastasia,
Thanks for your support in the past few months. I got an error message in -prep
step:
"Exception caught:
itk::ExceptionObject (0x8a1e880)
Location: "unknown"
File:
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Hello dear freesurfer developers,
I am leaving this message on the board to ask about the possibility of resuming
the Boston Freesurfer course in the near future. The last update that I'm
seeing on the Freesurfer official website pertains to the
: Salar Dini, Elaheh
Sent: Friday, October 21, 2022 2:18 PM
To: Freesurfer support list
Subject: A TRACULA Question
Dear Anastasia,
Thanks for your support in the past few months. I got an error message in -prep
step:
"Exception caught:
itk::ExceptionObject (0x8a1e880)
Location: "unk
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