Dear TRACULA experts,
I wonder if you could please assist me in extracting tract values from an
image I transferred to diffusion space.
I ran TRACULA on my DTI dataset, however from other structural images I aim
to extract values for tracts as well.
I also extracted DTI derived measures from the
A,
> MD, etc stats that are produced by default by trac-all, you'd threshold
> path.pd.nii.gz to 20% of its max value before using it as an ROI.
>
> Hope this helps,
> a.y
>
> On Mon, 16 Feb 2015, Barbara Kreilkamp wrote:
>
> Dear TRACULA experts,
>
> I wond
hat are outliers with a very high value it won't take them into
> account, which is probably a good idea here). Then use 20% of that robust
> maximum as your lower threshold and voila, you have your ROI.
>
> Best,
> a.y
>
>
> On Wed, 18 Feb 2015, Barbara Kreilkamp wrote:
Dear TRACULA experts and developers,
I am wondering whether TRACULA will allow usage of eddy, the newer
eddy-correction tool from FSL in a newer version?
Alternatively, it seems it would be possible to use the eddy corrected
nifti plus bvec and bval as the original input to TRACULA and turn off
ectors to tracula, and turn off the default eddy correction (then it
> won't rotate anything, either). I'll probably make it an option in the
> upcoming version to use eddy.
>
> Best,
> a.y
>
> On Tue, 25 Aug 2015, Barbara Kreilkamp wrote:
>
>> Dear TRACULA exp
Dear FSL experts,
I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5.
Could you please help me with this error message? I think it relates to the
library, this is what it states in talairach_avi.log.
But I am unsure how to solve this issue.
Any help is greatly appreciated,
Than
Forwarded Message
Subject:ERROR: mpr2mni305 failed
Date: Sat, 28 May 2016 14:27:29 +0200
From: Barbara Kreilkamp
To: Freesurfer support list
Dear FSL experts,
I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5.
Could you please help me with
do
> with the subfield stuff), but we exclude it from our analyses so you should
> be fine
>
> cheers
> Bruce
>
> On Wed, 6 Jul 2016, Barbara Kreilkamp
> wrote:
>
>> Dear Freesurfers,
>>
>> Unfortunately I am having a problem with recon-all segmentation in s
Dear Freesurfers,
I am looking for a way to add a colorbar to my p-value tract cores
generated through TRACULA.
When I load up the images as described in the tutorial here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
I only get a colorbar from 0 to 28.5 which cannot r
Hi Rito,
I just read this today myself "Select a few control points around your
trouble areas, space them out throughout the brain and on different
slices. You want to pick points in a region where the wm intensity is
lower than it should be (that is, having a voxel value less than 110)."
fro
Dear Freesurfers,
How would I be able to use a different colormap under point sets please?
I can only find "solid color" and "heatmap" but a blue to red colorbar
would suit my needs more.
Any assistance is greatly appreciated.
Thank you,
Best wishes,
Barbara
27;s what you're
> trying to display). We should definitely add it in the future.
>
> Best,
> a.y
>
> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers,
>>
>> I am looking for a way to add a colorbar to my p-value tract cores
>> genera
ying values that go all the way from negative to
> positive (which is what I suspect you have).
>
> I'll submit this request to freeview headquarters :) Hopefully we can get
> it in there quickly. Thanks for your patience!
>
> a.y
>
> On Sun, 10 Jul 2016, Barbara Kreil
Dear Anastasia,
As we are analyzing DTI data acquired in patients with epilepsy we are
especially interested in the fornix.
I've come across the mri_cc -f option for fornix segmentation (native
space) but I've also read that manual tracing/labeling of the tracts
would be needed in the 33 contr
Dear Freesurfers,
I've got data pertaining to patients with left and right-sided temporal
lobe epilepsy (TLE).
My aim is to group those tracts according to side of epilepsy for
waypoint comparisons.
Basically for patients with right TLE I'd like to look at right tracts
and at the same time for
without renaming
> the directories.
>
> Hope this helps,
>
> a.y
>
> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers,
>>
>> I've got data pertaining to patients with left and right-sided temporal
>> lobe epilepsy (TLE).
>>
labeling for it.
>
> Best,
>
> a.y
>
> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Anastasia,
>>
>> As we are analyzing DTI data acquired in patients with epilepsy we are
>> especially interested in the fornix.
>> I've come across the mri_c
Dear Freesurfers and TRACULA experts,
Thank you for your help so far. I am trying to map the endpoints of the
tract probability distributions onto the cortical surface (as mentioned
in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
I've somehow gathered that I need to do this (example one
Dear all,
If you have some suggestions I'd greatly appreciate them.
Thank you very much,
Best wishes,
Barbara
Forwarded Message
Subject:TRACULA tract endpoints on cortical surface
Date: Fri, 5 Aug 2016 12:03:02 +0200
From: Barbara Kreilkamp
To: Frees
with --surf-fwhm 6. There are other options in
> mri_vol2surf, I'd recommend playing with the settings to see what works
> better for your data.
>
> Best,
>
> a.y
>
>
> On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers and TRACULA experts,
Hi Emily,
I've never tried to use unpacksdcmdir but you may try the Osirix tool,
it allows you to read in a dicom folder and save a new folder with
subfolders according to the sequences that were run. At the same time
you can also anonymize your data.
Does this help?
Best wishes,
Barbara
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Barbara
Kreilkamp
*Sent:* Sunday, September 18, 2016 3:21:00 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Unpacking DWI Data
Hi Emily,
I've never tried t
Hi Scott,
This previous post might help you.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41439.html
Best wishes,
Barbara
On Sun, Nov 8, 2015 at 10:43 PM, Scott Quadrelli wrote:
> Hi,
>
> Tracula outputs the SNR for each volume in a txt file. I was wondering if
> anyone can p
all details about this position via this link:
http://www.findaphd.com/search/ProjectDetails.aspx?PJID=70289&LID=3417
*Deadline:* Friday, January 22, 2016 - apply ASAP!
Best wishes and a Happy New Year!
Barbara Kreilkamp
PhD researcher
University of Liver
Dear Freesurfer experts,
How may I get Freesurfer v 6 ?
Thank you very much,
Best wishes,
Barbara
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
.
>
> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>> Dear Freesurfer experts,
>>
>> How may I get Freesurfer v 6 ?
>>
>> Thank you very much,
>> Best wishes,
>> Barbara
>> ___
&
now where I got this link from
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
but it does not seem to point anywhere anymore.
Thank you very much,
Barbara
On 17/02/2016 14:30, Barbara Kreilkamp wrote:
> Dear Douglas,
>
> Thanks a lot, I found the version.
> Best
t; is using the 6.0-beta version
> released several months ago, which has been significantly modified since
> its beta release.
>
> -Zeke
>
> On 02/17/2016 11:45 AM, Barbara Kreilkamp wrote:
>> Dear all,
>>
>> Sorry to bother you again. I am a bit confused as
Dear all,
I've been reading the manuscript on version 6 freesurfer hippocampal
subfield segmentation "A computational atlas of the hippocampal
formation using ex vivo, ultra-high resolution MRI: application to
adaptive segmentation of in vivo MRI"
Can you please tell me if the type of sequence
Dear all,
Would you please help me on this one?
Thank you,
best wishes,
Barbara
Forwarded Message
Subject:hippo subfield segmentation new beta version (version 6)
Date: Wed, 20 Apr 2016 11:45:02 +0100
From: Barbara Kreilkamp
To: Freesurfer support list
Hi Joëlle,
Which scanner was used to acquire the images? I have used Osirix light
in the past to anonymize my dicom images, maybe you'd like to try that?
Best wishes,
Barbara
On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:
Hi Anastasia,
Yes, I use dicom images as input f
Dear Freesurfers,
I am trying to run trac-all with many subjects through a configuration file.
The first subject gets processed without error, but after that I keep
getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found.
This is my command with the output (below configuration fi
Dear all,
Is there a way to output the N3's (non-parametric normalization step)
output?
I am interested in the bias field that was computed to correct the image
intensities.
Thank you for your help,
Barbara
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so that you can work with the volumes.
>
> 3) if you do 2), you also get hold of the low-intensity voxel mask that
> N3 operates within. You can use this to constrain the division mentioned
> in 1).
>
> Best,
> Christian
>
> On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
g it will
> show the exact inputs and outputs of nu_correct.
>
> cheers
> Bruce
>
>
> On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:
>
>> Dear Christian,
>>
>> Thanks a bunch for this answer. I ran all the steps you mentioned
>> (except for the one
Dear Michele,
I cannot find anything wrong with your bvec and bval files.
Seeing as you had an errormessage related to the dwi (the one about the
dwi_frame.nii.gz): Did you check that your dwi data have the same amount
of volumes as entries in bvec and bval?
Good luck,
Barbara
On 28/08/2014
like to be sure.
Thank you very much,
Barbara
On Thu, Aug 28, 2014 at 3:27 PM, Barbara Kreilkamp
wrote:
> Dear Bruce and Christian,
>
> I found the easy way of simply writing 'set cleanup = 0' at the beginning
> of mri_nu_correct.mni and then I run this command
> mri_n
ery same dicoms and bval/bvec.
> Any suggestion?
> Thanks
>
>
> On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp
> wrote:
> Dear Michele,
>
> I cannot find anything wrong with your bvec and bval files.
> Seeing as you had an errormessage related to the dwi (the one
2 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443
0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025
You are ending up with multiple columns in the second row, please make sure
they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp
wrote:
> Hi Michele,
>
Dear all,
Robby, are you still having the problem? Did you solve it?
I am really having the same problem, just that I am using nifti files
instead of dicoms. I am using the same version as Robby. Please find my
command+output, trac-all.log and configuration file in the attachment.
I would also app
p 2014, at 12:22, Barbara Kreilkamp <mailto:bakk@googlemail.com>> wrote:
Dear all,
Robby, are you still having the problem? Did you solve it?
I am really having the same problem, just that I am using nifti files
instead of dicoms. I am using the same version as Robby. Please find
i
And attached are the log files of both tracula pre-processing (with
errors) and recon-all (apparently without errors).
Any help/suggestions?
Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp
mailto:bakk@googlemail.com>> wrote:
Hi Michele,
This might be the solutio
tly without errors).
Any help/suggestions?
Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp
mailto:bakk@googlemail.com>> wrote:
Hi Michele,
This might be the solution - try the command 'more' in unix
on your column bvec and
Hi Robby,
Thanks for sharing this and making me aware of the update (great that
this one will give you the motion parameters as well!).
So also for me it works now!
Have fun with your tracts of many subjects then :)!
Barbara
On 05/09/2014 09:22, Robby De Pauw wrote:
Hi Anastasia and Barbara
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they w
(e.g. system('mycommand') .)
>
> Best,
> Markus
>
> 2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp :
>
>> Dear Freesurfers,
>>
>> Is there a way of calling freesurfer-scripts from within MATLAB?
>> I know there are some setups needed to make MATLAB und
Dear all,
I would like to make amendments to the FSL dtifit call during trac-preproc.
In which way can I edit the call in trac-preproc?
# LS tensor estimation
set cmd = dtifit
set cmd = ($cmd -k $dwidir/dwi.nii.gz)
set cmd = ($cmd -m $brainmask)
set cmd = ($cmd -r $dwidir/bvecs)
set cm
Hi Michele,
Don't think there is anything wrong with the attached dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path to your
configuration file.
Right now it reads the path to your file as a flag, which is of course
not what you want.
Best,
Barbara
On 11/09/
Dear Freesurfers,
I would like to alter the trac-preproc to include an EPI to T2 registration
(diffeomorphic) as I do not have a field map, is there a way of doing this?
I saw that bbregister actually only uses 6 doF.
Thank you very much,
Barbara
___
Fr
the bottom).
>>> Any further suggestion?
>>> Thanks.
>>>
>>> [image: Inline image 2]
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari <
>>> cavallari.mich...@gmail.com> wrote:
Dear Freesurfers,
I am looking for information on how exactly the b-table gets rotated.
1. It seems that eddy_correct runs once with 12 doF, and then the
bmatrix gets updated based on this registration. Would you please confirm?
2. I know that my data has negative eigenvalues (most of them seem
Dear all,
Would you please explain why TRACULA is flipping the data so often? And
what does the flip4fsl command do? The data I have is already in the
right (radiological) orientation. fslswapdim does not seem to have an
effect either, as the parameters are just set to 'x y z'.
Are these comman
Dear all,
Do you have suggestions/ideas for me please?
Thank you,
Barbara
Original Message
Subject:TRACULA preprocessing: bvector rotation, negative eigenvalues
Date: Tue, 07 Oct 2014 19:09:00 +0100
From: Barbara Kreilkamp
To: Freesurfer support list
Dear
Thank you Anastasia.
Best wishes,
Barbara
On 21/11/2014 21:45, Anastasia Yendiki wrote:
> Hi Barbara - It's converting to LAS orientation. If it the images are
> already in LAS orientation, that command will have no effect, as you say.
>
> a.y
>
> On Fri, 17 Oct 2014,
External Email - Use Caution
Dear Chris,
We're actually working on control points in our group as well - on Mac
you have to press the 'fn' (very left bottom key) along with the up-down
arrow keys.
Hope that helps,
Cheers,
Barbara
On 11/12/2018 18:36, Ruopeng Wang wrote:
> Wh
External Email - Use Caution
Dear all,
I noticed FastSurfer also seems to run with a 7.1.0 FS version.
Or is there any reason not to do this?
Thank you,
Kind wishes,
Barbara
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