External Email - Use Caution
Hello,
Just wanted to re-circulate this – thanks again!
Best,
Panos
From: Fotiadis, Panagiotis
Date: Monday, June 10, 2024 at 10:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: TRACULA multiple sessions output question
Hello,
First of all,
External Email - Use Caution
Hello,
First of all, thank you for the fantastic software! I have a cohort of
individuals with multiple DWI sessions each, and I have been using TRACULA with
a configuration file similar to that of Example 3 (“Cross-sectional study,
multiple
The easiest thing is to set up contrasts to pull out the parameters you
want. The next easiest (or maybe the easiest) is to look in the beta
file. It will have a frame for each column in the design matrix. The
value is the regression coefficient.
On 3/5/2024 11:33 AM, Hoskinson, Kristen
External Email - Use Caution
We’re working on a project where we ran 3 groups, 1 covariate, and ran a glm
looking at white matter at cross-sections from TRACULA output, covarying for
functional activation. We’re now wanting to plot out the interaction/slopes per
group, but are
External Email - Use Caution
Hi,
I've been trying to use TRACULA on my data, trying to setup a configuration
file but I am having some difficulty on how to incorporate my data.
I have a DWI scan with 65 volumes (1 b0 image, 64 with b = 1000)
I also have separate volumes for b0
External Email - Use Caution
We'd like to use FS7.2 to generate hi-re surfaces on 0.8mm data on 6yo subject.
However, we'd like to be able to generate the white matter tracts that are
produced with older versions (specifically 6.0), not the new 42 tracts with 7.2.
Can a FS 6.0
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Hi FreeSurfers,
I am attempting to run tracula on longitudinal DTI data however during trac-all
-prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz
from mri_concat.
#-
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Hi FreeSurfers,
I have successfully run trac-all -prep, -bedp, and -path on all of my files.
However on two of my files when i ran trac-all -stat -c
/Users/corpuscallosum/Desktop/TRACULA/RRD/R007A/R007A.txt and trac-all -stat
-c on
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi Lauren.
Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you
corrected?
best regards
Woo-Suk, Tae
On Tue, Oct 31, 2023
t;
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.
: (650)-725-1716
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Woo-Suk Tae
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.
#chage codes from
set cmd = mri_binarize
set cmd =
@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA Error: Subregion Segmentation
aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi FreeSurfers,
I am trying to troubleshoot an error during TRACULA preprocessing and the issue
seems related to the creation of aparc+aseg+thalnuc.nii.gz
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Hello,
The following command
trac-all -c dmrirc.example -bedp
always exits with the following error.
{
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1
External Email - Use Caution
Hi Chiara -
Please ignore the previous email. I set my doB0 = 0, but it gives me this
error message:
copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_4
ERROR: for B0 distortion correction with reverse-polarity DWIs
ERROR: or for
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Hi King-Wai/ Chiara
Thank you for your excellent suggestions.
Chiara: I have made the changes you suggested. Can you please check if the
config file looks workable?
King-Wai - I made the change you suggested. But the problem still persists.
I have
External Email - Use Caution
Hi Alan,
It looks like you have specified the ncpts variable but not the pathlist. If
you do not specify pathlist, TRACULA will include all 42 tracts by default, so
your pathlist and ncpts variables will have different lengths.
If you want to
External Email - Use Caution
Hi King-Wai:
I have been running Tracula on 7T images and it keeps giving me an error.
The error is as follows:
copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
Unmatched '"'.
I have attached my config file. Can you please let me know
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Hi Lauren,
>From the log it actually looks like you have never run "trac-all -c dmrirc
>-path", but "trac-all -c dmrirc -prep" twice.
Chiara
On May 24, 2023, at 11:51 AM, Lauren Stephens
mailto:laure...@stanford.edu>> wrote:
External
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Dear developers,
Does TRACULA perform an intensity normalization of the DWI image, as recon-all
do for the T1?
Thanks,
Silvia
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Hi,
Does Freesurfer / Tracula provide any way to automatically segment a tract
between two arbitrarily selected points?
Christian
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
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Hi, I've been trying to configure Tracula to use different inter-subject
registration methods.
It fails for type #3 (robust cost) and #4 (nonlinear CVS).
From the trac-all script (line #1634), it looks like Tracula points to
different trctrain
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Hi Freesurfer Experts,
I’m attempting to run Tracula and receiving the same error for both Tracula 6.0.
Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which
runs without issue) and then Tracula (which returns the same
External Email - Use Caution
I have a similar question to this unanswer one (see link)
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to apply TRACULA for the reconstruction of white matter pathways
but I am getting an error when running the trac-all command which I haven’t
managed to resolve. The TRACULA is applied on an MRI sample from
Hi Nita,
What is your FREESURFER_HOME points to? It should be set to your Freesurfer
7.3.2 install directory.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Nita Akoh
Sent: Wednesday, January 18, 2023 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer
External Email - Use Caution
Hey, I'm trying to run "trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial" but keep getting this error
: /shared/centos7/freesurfer/7.3.2/bin/free/sources.csh: No such file or
directory.
My colleague ran this step on the same data
External Email - Use Caution
Hi Freesurfer Developers,
I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat,
and I was wondering how to best visualize and interpret the results of the
cluster-wise correction in freeview.
I referenced this page (
Dear FreeSurfer TRACULA experts,
I am new to FreeSurfer and using TRACULA to process DTI data. From the
mail-archive, I understand TRACULA mainly needs the aparc+aseg output from
recon_all in order to run. Using the recon_all output information, I was able
to complete the 3 steps in TRACULA
External Email - Use Caution
Dear Freesurfer experts
I'm attempting to running TRACULA in a two subjects(one visit per
subject and multiple deffusion scans per visit), as described on the
TRACULA tutorial
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DearFreesurfer developers,
when trying to run trac-all -prep I am running into this error
gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c
/Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt
domainname: Command not found.
External Email - Use Caution
Dear FreeSurfer TRACULA team
I have processed subjects using TRACULA on FS6.0 and 7.2.
With both pipelines all the steps are completed without errors but for most
subjects when I checked the pathstats.overall.txt file volume of the tract is
almost
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Hi,
Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt,
I have 2 more questions.
Since my previous 3 questions still have not been answered, I'm including
them here
so that they are all in one place. The 2 new questions are
External Email - Use Caution
Hi,
I have 3 questions on tracula statistics outputs.
1) There are duplicate points in pathstats.byvoxel.txt, is it normal?
I didn't try it on all 42 tractcs. For the few I've looked at, they all
have duplicate points.
I used the default setting in
External Email - Use Caution
Dear Freesurfer experts
I finished TRACULA's trac-all steps. Then I'd like to transform all DTI
pathways to MNI space.
Are there any commands in freesurfer or any external neuroimaging softwares.
My scripts did not provided no transformation to MNI
External Email - Use Caution
Hi,
I have successfully run the preprocessing steps for my DWI data, and I was
wondering how long does bedpostx usually take to process DWI? I am running on
a high-powered computer (cluster) and a multi-shell data 3 b-values of (b=
1000s/mm2, 34
Sent: Friday, August 19, 2022 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA - preprocessing error
External Email - Use Caution
Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop
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Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc
INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c
External Email - Use Caution
Hi,
I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am
getting the following error
ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni
I don’t see the mni folder created in my files… I am trying to only
on behalf of Liliana Wu
Sent: Wednesday, August 17, 2022 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA - custom tracts and path labelling
External Email - Use Caution
Hi,
I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF)
but I am
Sent: Wednesday, August 17, 2022 4:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula - Preproc
External Email - Use Caution
Thank you King Wai and Philip. I am reworking the config file to see if that
works. The earlier Tracula versions were much easier to run.
best
External Email - Use Caution
Hi,
I am trying to reconstruct the inferior frontal occipital fasciculus (IFOF)
but I am seeing that this tract is not included in TRACULA. Does TRACULA enable
manually selecting seed and target ROIs ?
Also, I am trying to access the list of the
External Email - Use Caution
Hi Freesurfer team!
I am having an issue with the -jobs flag for trac-all -bedp in
freesurfer/7.3.0. I ran trac-all -prep with the -jobs flag with no issue, and
submitted the commands as jobs on my cluster without error. However, when I try
to
t; ANTSPATH=/home/afrancis/Imaging/ANTs
>>>>>>
>>>>>> For tcsh
>>>>>> setenv ANTSPATH /home/afrancis/Imaging/ANTs
>>>>>>
>>>>>> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis <
>>>>>> alandarkene...@gmail.
ed this
>>>>>>
>>>>>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>>>>>
>>>>>> but it did not work. Is there a different set path?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>&g
t;>>>> Thanks,
>>>>>
>>>>> Alan
>>>>>
>>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>>> ayend...@mgh.harvard.edu> wrote:
>>>>>
>>>>>> If you want to use ANTs for
gt;>> but it did not work. Is there a different set path?
>>>>
>>>> Thanks,
>>>>
>>>> Alan
>>>>
>>>> On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia <
>>>> ayend...@mgh.harvard.edu> wrote:
>>>>
>>>>> If you w
>> ayend...@mgh.harvard.edu> wrote:
>>>
>>>> If you want to use ANTs for registration, you have to have ANTs
>>>> installed and set ANTSPATH to its location.
>>>> ----------
>>>> *From:* freesurfer-boun...@nmr.mgh.harva
gt;> installed and set ANTSPATH to its location.
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>>> alandarkene...@gmail.com>
>
alandarkene...@gmail.com>
>> *Sent:* Friday, August 12, 2022 4:35 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia and King_Wei :
>>
>&
*Sent:* Friday, August 12, 2022 4:35 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula - Preproc
>
>
> External Email - Use Caution
>
> Hi Anastasia and King_Wei :
>
> Thank you for your suggestions. I have fixed the bet issue by reinst
> On Thu, Aug 11, 2022 at 2:50 PM wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> Hi Alan,
>>>>
>>>>
>>>>
>>>> As Anastasia said, bet is part of FSL.
>
: [Freesurfer] Tracula - Preproc
External Email - Use Caution
Hi Anastasia and King_Wei :
Thank you for your suggestions. I have fixed the bet issue by reinstalling FSL.
But I have one more error:
ERROR: must set ANTSPATH environment variable to use ANTs
I tried setting
set ANTSPATH = 0
>
>>>
>>> Best,
>>>
>>>
>>>
>>> King-Wai
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki,
>>> Anastas
edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
>> *Sent:* Thursday, August 11, 2022 3:42 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Tracula - Preproc
>>
>>
>>
>> Yes that's from
arvard.edu
on behalf of Alan Francis
Sent: Friday, August 12, 2022 12:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula - Preproc
External Email - Use Caution
Hi Anastasia and King wei -
I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is
par
; *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia
> *Sent:* Thursday, August 11, 2022 3:42 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula - Preproc
>
>
>
> Yes that's f
11, 2022 3:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula - Preproc
�
Yes that's from FSL. It's needs to be in $FSLDIR.
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harva
Yes that's from FSL. It's needs to be in $FSLDIR.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alan Francis
Sent: Thursday, August 11, 2022 3:30 PM
To: Freesurfer
Subject: [Freesurfer] Tracula - Preproc
External Email - Use Caution
Hi
External Email - Use Caution
Hi Anastasia, King Wei:
I did as you suggested with the config file and the preprocessing ran for a
bit but then an error occurred. I have attached the run script. It says BET
not found. Is this the Brain Extraction tool?
Could you please shed some
gt;
> *Sent:* Friday, August 5, 2022 5:03 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Config file.
>
>
> External Email - Use Caution
>
> Hi Alan,
>
> In your pathlist, the 1st path is acomm. You have "ac" in your fil
...@nmr.mgh.harvard.edu
on behalf of King-Wai Chu
Sent: Friday, August 5, 2022 5:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hi Alan,
In your pathlist, the 1st path is acomm. You have "ac" in your file.
gt;>>>>> will have the same, correct effect:
>>>>>>
>>>>>> set dcmroot = /home/afrancis/Imaging
>>>>>> set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>>
>>>>>> OR
>>>
ncis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
>>>>>
>>>>> In addition, there are *a lot *of things that you left in there from
>>>>> the example RC file. You should delete them entirely, unless you
>>>>> specifically want to set
: Re: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
cc.bodyt cc.genu cc.rostrum cc.splenium mcp
lh.af<h
>>>
>>>> In addition, there are *a lot *of things that you left in there from
>>>> the example RC file. You should delete them entirely, unless you
>>>> specifically want to set one of those things to something other than the
>>>> default. These are examples tha
; have the minimum necessary for your analysis.
>>>
>>> Best,
>>> Anastasia.
>>>
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu>
han the
>>> default. These are examples that may not give you the default behavior.
>>> Also the field mapping files - delete those lines because you're just using
>>> the example names and they're not going to work. You want your RC file to
>>> have the minimum necessary for yo
st,
>> Anastasia.
>>
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
>> alandarkene...@gmail.com>
>> *Sent:* Thursday, August 4, 20
t; on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 4, 2022 12:23 PM
> *To:* Freesurfer
> *Subject:* [Freesurfer] Tracula Config file.
>
>
> External Email - Use Caution
>
> Hi Anastasia -
>
> Hope you are well. I am running
--
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 4, 2022 12:23 PM
> *To:* Freesurfer
> *Subject:* [Freesurfer] Tracula Config file.
>
>
>
.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alan Francis
Sent: Thursday, August 4, 2022 12:23 PM
To: Freesurfer
Subject: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC
External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file
based on your recommendations. However it is giving me an error message
when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you
of output. Please attach your entire trac-all.log file.
Thanks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Monday, July 25, 2022 3:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error in path
ent:* Monday, August 1, 2022 12:44 AM
> *To:* 'Freesurfer support list'
> *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
>
>
> I thought he wants me to run trac-preproc.sh he
Cc: kingwai@gmail.com
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
There is a change related to that,
Date: Mon Jul 25 21:24:30 2022 -0400
trac-preproc. #BF. Changed expected thalseg version to 1.3; also added an
option to be able
,King-WaiFrom:freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfYendiki,
AnastasiaSent:Monday, August 1, 2022 12:15 AMTo:'Freesurfer support
list' freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer]
TRACULA in FreeSurfer version 7.3Indeed. Doug sent you
support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Anastasia,
I thought he wants me to run trac-preproc.sh he sent to run it directly.
I wasn’t told to replace it with the one in the original 7.3.
After replacing the original
config.file runs w/o problem.
�
Thanks,
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:15 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Indeed. Doug sent you a modified
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of kingwai@gmail.com
Sent: Monday, August 1, 2022 12:10 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Anastasia,
The problem is in 7.3, trac-all -prep
(ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).
�
Thanks,
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Monday, August 1, 2022 12:03 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Hi King-Wai
list'
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
External Email - Use Caution
Hi Douglas,
Thank you for looking into this.
It gives the following error.
trac-preproc.sh -c config.file
intrareg: Undefined variable.
Thanks,
King-Wai
From: freesurfer-boun
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
I don't know; Anastasia is the author. She's busy today and tomorrow, I was
just trying to push it forward. Does it work with the given config file in 7.2?
On 7/25/2022 5:46 PM, kingwai@gmail.com <mailto:king
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:
*External Email - Use Caution *
Hi Douglas,
According to
TRACULA
...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai@gmail.com
.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
are you sure the config file is right? it should be defining the
intrareg variable
On 7/25/2022 2:11 PM, kingwai
�
�
�
�
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 5:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
are you sure the config file is right? it should be defining
: Undefined variable.
Thanks,
King-Wai
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Monday, July 25, 2022 1:55 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Can you copy the attached trac-preproc
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, July 21, 2022 4:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula error in path construction
Could be that you reached a memory limit? If the same
. Greve
Sent: Monday, July 25, 2022 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
�
Can you copy the attached trac-preproc into $FREESURFER/bin and try again
(after removing the link)?
On 7/22/2022 8:36 AM, kingwai@gmail.com
Can you copy the attached trac-preproc into $FREESURFER/bin and try
again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:
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Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all,
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Hi Anastasia,
�
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3
However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
from
To: Freesurfer support list
Subject: [Freesurfer] Tracula error in path construction
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Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file
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Dear Anastasia
I am running tracula on FreeSurfer 7.2.
It worked fine on a linux computer now I am changing to a Cloud workstation.
Attached is my Configuration file. For this person the pipeline worked without
errors until path reconstruction but
--
> *From:* Yendiki, Anastasia
> *Sent:* Saturday, June 4, 2022 1:05 AM
> *To:* Salar Dini, Elaheh ; Freesurfer support
> list
> *Subject:* Re: TRACULA -bedp parallel processing
>
> What kind of cluster are you running the parallel processes on?
>
> ---
!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Steven Meisler
Sent: Thursday, July 7, 2022 12:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [TRACULA] Auto-BIDS Config Variables Question
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Hello,
I am trying out the development dmri-bids-config script
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Hi FreeSurfer experts,
I am planning to use TRACULA and have a question regarding the
configuration file and whether we can start with already processed data.
We have already run some steps involved in the TRACULA configuration
script, which take
uster are you running the parallel processes on?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
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PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
External Email - Use Caution
Thank you for the guidance.
When it tries to run pre.ParallelI , I'll get this:
Copying files to bedpost directory
cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/
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