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I REGISTERED TO THIS MAILING LIST AND HERE IS WHAT HAPPENED:
1.I'M FLOODED WITH EMAILS - I DONT WANT THAT
2 TWICE I ASKED TO BE UNSUBSCRIBED - SEEMS IT DIDN'T WORK - STILL BEING
FLOODED
WHO CAN HELP/WHO DO I EMAIL??
Dr Katarzyna Cieśla-Seifer
The Ba
Hi, sorry for the delay
On 4/23/2025 10:43 PM, Dorian Pustina wrote:
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Hi all, I have some questions regarding failed segmentations on
longitudinal data.
We have large datasets of Huntington's disease with data collected
longitudinally for 3-10 years. Fre
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Forget to mention, we use FS6, not FS7.
On Wed, Apr 23, 2025 at 10:43 PM Dorian Pustina wrote:
> Hi all, I have some questions regarding failed segmentations on
> longitudinal data.
>
> We have large datasets of Huntington's disease with data collect
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Ah, that makes sense, thanks! We hadn’t really considered feeding them all in
at the cross-sectional step, since to this point for these types of analyses we
have been doing all averaging after freesurfer (on the individual extracted
measures). Bu
You are right that using all the scans will bias toward tp2. I think I
would just run the cross for each time point using all the data you
have. This will not bias the base because an average of the images
within each time point will be used to make the base. If possible, you
will want to make
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Here is the tutorial page for longitudinal pipeline -
https://secure-web.cisco.com/1DcUJ0a_skONZSHVRpSGkgbTHuJUYN0f05kxjKkGh8ULxXW5lqtpzszfBoN-Xtfji8oIhv9vRccou8zbWsrBEOjLdmo0rTMcvCMZxYlfgwwj9WhTkMxZjPQXRIllql_rFkKSHG62EwrEuQ-E69bA0inHgOQJ7ZBwMv0T0u6l4
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Hi Jack,
it depends on how different your questions are and how many cases you have in
the cross study vs long study.
If the questions are different or you have a large cohort for the cross
sectional, then it makes sense to keep the two analyses sep
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Hi Yujing,
Thanks for your reply – I have a follow up query (see email thread below):
I have both a cross-sectional aim and a longitudinal aim I am hoping to explore
with FreeSurfer. While they are separate aims, some participants are present in
bot
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Hi Jack,
Longitudinal recon-all pipeline is available in Freesurfer 7.3.2.
To do longitudinal segmentation using the hippocampal subfield pipeline, it is
a requirement that the data have been processed with the longitudinal stream
Freesurfer.
Best,
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For base processing, specify each timepoint with -tp <> (not the nii file).
recon-all -base -tp -tp ... -all
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Atwater, Emanuel R
Sent: Wednesday, July 5, 2023 11:37 AM
To: fre
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Hi Vittal,
please see my response from Nov 30th on this list.
Best,
Kersten.
Am 04.12.2020 um 08:16 schrieb vittal korann
mailto:vittalkor...@gmail.com>>:
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Dear FreeSurfer experts
This is just a gentle remind
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Dear FreeSurfer experts
This is just a gentle reminder of my previous mail.
Diers Kersten has replied to my query. He asked me to send a few details
pertaining to my issue.
I shared all the necessary details with you people and waiting for your
respons
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Hello VIttal,
thanks for the info about the design.
You wrote before that the Matlab variable X (i.e., the design matrix) has a
dimension of 47x6. X is a translation of the study design into a numerical
matrix, which is part of the statistical model
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No problem, thanks!
So I shall send an email only to freesurfer or would it fine if I put you
in cc?
With regards
Vittal
On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE
wrote:
> Hi Vittal,
>
> Sorry, I can only help on the public freesurfer l
By post processing and stats, do you mean mris_preproc, mri_surf2surf,
and mri_glmfit? You can run v6 of those on data reconned with any
version of FS
On 7/28/2020 1:25 PM, Rachel Romeo wrote:
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Hi,
I am working with some longitudinal data that was origina
pport list
> Subject: Re: [Freesurfer] Longitudinal Pipeline
>
> Hi Aaron and Hi Bruce!
> There is code to convert ANTs format to FSL, so you can use that.
> It is part of this tool:
> https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md
>
> I've include
FYI
-- Forwarded message --
Date: Tue, 16 Jan 2018 19:59:38 +
From: Mark Jenkinson
To: Bruce Fischl
Cc: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal Pipeline
Hi Aaron and Hi Bruce!
There is code to convert ANTs format to FSL, so you can use that.
It is
Thank you very much. Your last email gave me a lot to work with.
On Mon, Jan 15, 2018 at 9:18 AM, Bruce Fischl
wrote:
> Hi Aaron
>
> we compute the warp and save it in the mri/transforms/talairach.m3z, but
> don't apply it (so don't require an extra resampling). I know we have some
> tools aroun
Hi Aaron
we compute the warp and save it in the mri/transforms/talairach.m3z, but
don't apply it (so don't require an extra resampling). I know we have some
tools around to convert to ANTS format, but I'm not sure about fnirt. I'll
cc MJ who may know (hi MJ!)
cheers
Bruce
On Mon, 15 Jan 20
Is the warp saved anywhere and where can I find it? Also is the warp
compatible with FNIRT in any way. I am interested in combining warps
together to reduce the number of re-sampling steps.
Thank you so much in advanced
On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl
wrote:
> in the last stage the
in the last stage there is a nonlinear atlas alignment that is specific to
each timepoint. We are working on building a nonlinear base, but it is not
distributed yet.
cheers
Bruce
On Sun, 14 Jan 2018, Aaron
Tanenbaum wrote:
>
> I am interested in knowing what type of alignment goes into the
Hi Theo,
- not sure what test you mean. Have a second person correct the data and
compare ?
- you can run 1.5. and 3 T data in the longitudinal pipeline, however (similar
to cross sectional processing) you will not know if the differences of the
results are due to anatomical changes or due to
Yes, that is why it is experimental.
However, global atrophy will affect the ventricles (they are growing) which is
an effect in the opposite direction, so maybe it cancels out to some extend.
Best, Martin
> On 12 Apr 2017, at 23:55, Arman Eshaghi wrote:
>
> Thanks Martin. Should I be worri
Thanks Martin. Should I be worried about affine transform masking out the
global atrophy if I am using the whole brain (no skull stripping)?
Arman
On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter
wrote:
> Hi Arman,
>
> should be possible by passing the - - affine flag. I think I also
> experiment
Hi Arman,
should be possible by passing the - - affine flag. I think I also experimented
around with a -base-affine flag to recon-all for that (instead of -base). It is
experimental!
Best, Martin
> On 07 Apr 2017, at 13:34, Arman Eshaghi wrote:
>
> Hi,
>
> I wonder if there is a way for m
Thank you so much!
Mihaela
On Tue, Apr 5, 2016 at 4:41 PM, Martin Reuter
wrote:
> Hi Mihaela,
>
> you can use our BrainPrint tool (after running FS) to see how closely the
> brain shape matches:
>
> http://reuter.mit.edu/publications/pid/wachinger-brainprint15
> http://reuter.mit.edu/software/br
Hi Mihaela,
you can use our BrainPrint tool (after running FS) to see how closely
the brain shape matches:
http://reuter.mit.edu/publications/pid/wachinger-brainprint15
http://reuter.mit.edu/software/brainprint/
Best, Martin
On 04/05/2016 12:49 PM, Mihaela Stefan wrote:
Hi Martin,
Just an
Hi Martin,
Just an update on this. It turned out that there was just a DICOM mismatch
for this subject but now that you mentioned it, I wonder what people do to
make sure that the same person returns for follow-up in a longitudinal
study. Even when there is one study coordinator for the entire leng
Wow! I haven't thought about that but it's possible since we had a few
study coordinators along the way. So it could be the case that the study
coordinator didn't know the subject who came at follow-up. Hopefully it
will be just a DICOM mismatch. Will see how it goes.. :)
On Thu, Mar 31, 2016 at 1
I have seen cases where annonymization messed up ID's and individual
time points came from a different subject. That could mess things up
quite bad. (Also if the person sends their sibling or friend, because
they don't have time to come to the follow up themselves, has also
happened - not to me
Hi Martin,
We ran this subject twice but we got the same error. The norm is not
aligned. They almost look like two different brains. I double checked the
exam numbers to make sure that these three exams belong to the same person.
They indeed seem to belong to the same person but I will re-run reco
Hi Mihaela,
does the cross sectional run of that time point, and the base look OK?
Also check if this time point is aligned correctly to the base (e.g.
open norm.mgz from the long and the base, they should be aligned). If
all this is OK, then I would recommend to re-run this long run again,
HI Song,
are you talking about the longitudinal tractography?
If you have longitudinal data, then yes, we recommend the use of longitudinal
processing both for the structural and for the tractography. That's what they
have been developed for.
Best, Martin
On Jan 26, 2015, at 5:50 PM, Inkyung
smartphone, please excuse brevity.
Original message
From: Brianna Damadian
Date:07/03/2014 1:57 AM (GMT+01:00)
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal pipeline + LME question
Hi Martin,
Thanks for the response. What we are trying to do is look
Hi Martin,
Thanks for the response. What we are trying to do is look at changes within the
same subject after a certain date (date of a surgical procedure). Would it make
more sense to run all scans before and after this date in the same longitudinal
pipeline and then look for differences or to
Hi Brianna,
Yes, that is the best option in my opinion. You should include field strength
as a covariate, and maybe other acquisition parameters.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Brianna Damadian
Date:07/02/2014 10:04 PM (
Hi Elijah,
the recon-all command is correct. The error you are getting is something
else. Does the ribbon file exist? I would re-run that base from scratch,
could be an IO problem or disc space etc.
Martin
On 05/30/2014 08:56 AM, Elijah Mak wrote:
Dear FS Experts,
I am running a longitudi
Dear Martin,
thanks for your quick reply.
I am using version 5.1. I only have two timepoints per subject and I
took the snapshots from the independent runs. What bothers me is that
the difference is not present in the 001.mgz images, but seems to appear
later in the workflow.
Thanks again,
Irene
Hi Irene,
both images should be smoothed the same. You only have two time points
in each subject? Which FreeSurfer version are you using? And these
images are from the *.long.base directories (or are they from the
independent runs)?
-Martin
On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli wrot
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