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Hi Simone,
Based on your other recent question, I would recommend running samseg the
way it is documented here:
https://secure-web.cisco.com/1J42u65oQ1VRxZxUyRLQ0WfsPO92xbqHhvftl-50s4v7BtSkaxkqj9Uth8zkhUbE5ltPY6CmgzIx_1mP4ycP1j7W8fDqhKLTDHkGmI-DqSRGDb
External Email - Use CautionHi!I don’t think this email was meant for me, I was struggling to get freesurfer to run on a Mac that was running 14.X and was struggling to get the package that was sent to run. Cheers,AlishaOn Sep 11, 2024, at 4:26 AM, Sravanthi Upadrasta wrote:
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Hi Krzysztof,
Samseg will "eat" anything you throw at it. That doesn't mean that the type
of input data doesn't matter: the higher the contrast-to-noise ratio for
the specific structure(s) you're interested in, the better the results will
be. Note that
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Hi Stefano,
Thank you for your reply and explanation.
The command I'm using to segment FLAIR is as follows:
run_samseg --input T2_FLAIR.nii.gz --output samseg_outputs --threads 8
--lesion --lesion-mask-pattern 1 --threshold 0.3 --save-posteriors
--s
Hi Evie,
--save-probabilities and --save-posteriors will save two different things for
lesions. The former is an initialization of lesions based on intensity and
location constraints, and the latter is a probability map of seg.mgz after we
also introduce lesion shape constraints (Cf Fig.4 of
h
You should not use either T1.mgz as that has been highly processed for
other purposes. The brainmask has also been processed, skull stripped
and bias correction. I have not looked at what has to happen to get the
most correlation between the methods; they are different methods and are
supposed
Hi Gabriel,
These messages look like TensorFlow warnings. They just mean that you're
running it on a system without GPUs. They should not stop the run.
Is this the last message printed by run_samseg, or does the algorithm
continues? Can you provide more details on when the run terminates?
Stef
when you say that it is better cortex segmentation, do you mean better
than the aseg.mgz=aparc+aseg.mgz or better than the aseg.presurf.mgz? Do
you mean in general or just near the WMH? The aseg/aparc+aseg use the
surfaces to refine the gray/white boundary, and usually the surfaces do
a much be
Hi Valentin,
Glad to hear that.
Did you use the command "samseg" with the --recon flag? If yes, there are a
couple of flags that you can add so that the output of SAMSEG ("seg.mgz") is
used in more steps in the recon-all stream:
" --fill : use samseg to create filled.mgz instead of recon-all"
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Hello Jacky,
You can try the procedure listed below, which was posted to the list around
Dec. 12th. It might work for 7.3.1 release, though I have only tried it
on the 7.3.2 release. If it does not work for you on 7.3.1, then I would
download and i
Can you send your command line and log file? In particular, how did you
register the time points?
On 9/26/2022 6:46 AM, Nederpelt, D.R. van (David) wrote:
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Dear SAMSEG developers,
We have a dataset with 55 subjects (MS patients and controls) scanned
on th
On 9/25/2022 5:06 AM, Mikolaj Pawlak wrote:
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On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve
wrote:
On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:
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Would providing better manual segmentations of those
External Email - Use Caution
On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve
wrote:
>
>
> On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:
>
> External Email - Use Caution
> Would providing better manual segmentations of those structures of
> interest help you in building bet
On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:
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Would providing better manual segmentations of those structures of
interest help you in building better solutions?
I can work with the segmentation that is produced now, but I am
interested in improving the res
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Would providing better manual segmentations of those structures of interest
help you in building better solutions?
I can work with the segmentation that is produced now, but I am interested
in improving the results for extracerebral tissues using multim
by template I'm assuming you mean the atlas. There is not an easy way to
create a new atlas or modify the existing one (though we are developing
methods to do both). For the eyes, you could probably just write
something to look at the column index in the eyes. If it is less than
128, then set i
Hi yvg,
It is most likely a memory error problem. You will need to allocate more RAM to
your calls. You probably need at least 32GB or RAM for such big images (might
be even more).
You can process the FLAIR images with mri_robust_template since they are
slighly smaller than your T1 images.
Hi Dilek,
0.2 Dice seems extremely low. Also, in my experience, a threshold of 0.05 on
T1w-FLAIR scans will show up many FP lesions.
We usually reported a Dice in the range of 0.50-0.65 on various datasets (MS
and WMH, default threshold, T1w-FLAIR), so I'm surprised by a such low value.
Can yo
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Hello again,
I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional).
I use the T1 and Flair for this. (just these are inputs) I registered *flair
and t1 to DIR *for every patient. (My manual lesion masks are on DIR
imaging.) I controlled
Hi Dilek, your bug report is incomplete. Please see
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to file
an informative bug report.
On 8/30/2022 12:51 PM, Dilek Özkan wrote:
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Hello dear all,
I use Freesurfer-Samseg for MS lesion segmenta
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Even if I register 2d T1 to 3D Flair? (form low res to higher res; such as
2D T1: 1*1*5, 3D Flair: 1*1*1)
Douglas N. Greve , 30 Ağu 2022 Sal, 17:30 tarihinde
şunu yazdı:
> If you resample the t1 to another space, it might get blurrier.
>
> On 8/30/202
If you resample the t1 to another space, it might get blurrier.
On 8/30/2022 9:46 AM, Dilek Özkan wrote:
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I decided to register T1 and Flair to DIR at the beginning. with this
way, I will get the new mask in already DIR's space which means
manually segment
External Email - Use Caution
I decided to register T1 and Flair to DIR at the beginning. with this way,
I will get the new mask in already DIR's space which means manually
segmented masks' space.
In my case, I will give two inputs to the software. The rule that applies
to every so
If you want to use FSL, you will have to convert to nifit, eg,
mri_convert file.mgz file.nii.gz
On 8/30/2022 7:01 AM, Dilek Özkan wrote:
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Hello dear all,
I want to use Freesurfer-Samseg for MS lesion
segmentation(cross-sectional).
I got the T1 and Flai
Hi Dilek,
I've actually run SAMSEG-lesion on some gadolinium-enhanced scans in the paper.
Look at the top row of Fig. 7 ("T1c") and at the "MSseg" dataset. I did not
check the performance of the method on such data. We also don't distinguish
between enhanced and non-enhanced lesions.
I would p
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Firstly, thanks for your explanation, I didn't know that it would take less
than hours since I used recon-all to run 202 samples, I used parallel to
run 8 images at once and it took almost 13 hours, but at the end , you can
be sure of the results you ha
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I've tested reproducibility of the results either using ASEG (therefore
via recon-all -all) and also SAMSEG (via run_samseg).
The methods are different either in terms of reproducibility of results.
Multiple runs of ASEG (recon-all -all) provide the
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Why you didn't run recon-all directly ?
Le sam. 27 août 2022 à 11:32, Giulio Siracusano
a écrit :
> External Email - Use Caution
>
> Hello,
>
> this is true (i.e. reproducibility) for ASEG (when running recon-all -all).
>
> But, if you use SA
External Email - Use Caution
Hello,
this is true (i.e. reproducibility) for ASEG (when running recon-all -all).
But, if you use SAMSEG (i.e. running run_samseg instead) you get
slightly different results everytime. This is regardless you use
-threads flag or not.
My command li
External Email - Use Caution
I used freesurfer for ADNI data, specifically MRI for AD/CN. Even I run
segmentation many times , I always having the same statistics. Would you
share with us the commend line you used !
Le sam. 27 août 2022 à 09:32, Giulio Siracusano
a écrit :
>
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Hi Douglas,
I've investigated the use of SAMSEG for AD/MCI patients. I'm using the
7.2 version of Freesurfer and I've realized that I get different results
using the same data but when I run the SAMSEG multiple times (on the
same patient).
Differen
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Hi Stefano,
I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2
version of Freesurfer and I've realized that I get different results using
the same data but when I run the SAMSEG multiple times.
Differently from using ASEG, SAMS
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Thanks for the explanation!!
El vie, 12 ago 2022 a las 17:04, Koen Van Leemput ()
escribió:
> External Email - Use Caution
>
> Hi Alberto,
>
> As you already indicated, it's really a combination of an unsupervised
> clustering method with a su
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Hi Alberto,
As you already indicated, it's really a combination of an unsupervised
clustering method with a supervised shape model, so the dichotomy between
the two doesn't neatly apply. When I think about this type of method, I
consider it an unsuperv
intensity constraints,
but it also indirectly leads to better lesion segmentation overall as the model
parameters are better estimated. So in general it's hard to disentangle its
effect.
Hope it helps,
Stefano
From:
Subject: Re: [Freesurfer] SAMSEG (Lesion Mask Pattern) ... ah, [0 0]
To: "
Hi Randy,
"seg.mgz" is the "hard segmentation", with lesion labeled as 99.
You have all the volumes in "samseg.stats".
If you want segmentation maps (values between 0 and 1), you should add the flag
--save-posteriors to run_samseg. They will be saved in the samseg output
directory under the "
? ? )
else:? ? samseg = samseg.Samseg(**samseg_kwargs)
_, _, _, optimizationSummary = samseg.segment(? ? costfile=costfile,? ?
timer=timer,? ? transformFile=args.reg,? ? initTransformFile=args.init_reg,? ?
reg_only=args.reg_only)
# Save a summary of the optimization processwith open(costfile, '
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Hello Randy,
I think the expectation is for users to run “samseg” from the command line.
(The samseg script is a front-end you run with command line options,
e.g., —help, which calls samseg_run that in turn runs the samseg python scripts
in the free
On 2/16/2022 3:35 PM, Martin Kavec wrote:
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Hi all,
previous question from Florent triggered my interest in SAMSEG and I
am running now couple of cases to see what it gives. I would like to ask
* SAMSEG can also output a mesh. How is the mesh stored in
On 2/16/2022 4:12 AM, k3...@free.fr wrote:
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release
> and started to give a try on few subjects were FreeSurfer was having a hard
> time to segment brain
self.imageBuffers, self.transform, self.voxelSpacing,
> self.cropping = readCroppedImages(
> self.imageFileNames,
> os.path.join(self.atlasDir, 'template.nii'),
> self.imageToImageTransformMatrix
> )
>
>
>
> --
self.imageFileNames,
os.path.join(self.atlasDir, 'template.nii'),
self.imageToImageTransformMatrix
)
-Original Message-
From: Douglas N. Greve
To: freesurfer@nmr.mgh.harvard.edu
Sent: Sun, Oct 3, 2021 8:04 am
Subject: Re: [Freesur
Can you compare the template_coreg.mgz to the input image; they should
be mostly aligned. If not, then the initial registration failed.
On 9/28/2021 2:38 PM, daedalu...@aol.com wrote:
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We have recently installed FS-7.1 and have tested a few “ADNI” images
There is not, but you could create your own. By default, it uses this
table to determine which superclass each segment goes into
$FREESURFER/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/sharedGMMParameters.txt
YOu can see that CP is in the CSF glass. You can try creating its own
External Email - Use Caution
Hi Achille,
Great that you managed to solve the cropping issue.
Regarding the small lesions detection problem in the superior part of the brain
(I guess you are looking at juxtacortical lesions?), hard to say without seeing
the data. It might be a m
Not sure. The first step would be to check the affine registration with
freeview template_coregistered.mgz input
where input is the input to samseg
On 8/31/2021 5:27 AM, achille.teil...@chu-lyon.fr wrote:
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Dear experts,
We are working with a large MRI datas
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Hi Achille,
It sounds like the initial affine registration of the template in SAMSEG is
failing for some of your subjects. If that is the case, you will see that
"template_coregistered.nii" is probably not aligned with your original data.
As the a
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Hi Simon,
This could be an issue with the affine registration or the subsequent head
masking step in samseg, both of which have been upgraded/improved in the
development version.
Would you be able to try the dev version and see if this resolves the is
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Hi all,
Just few clarifications:
1) Lesions are segmented in SAMSEG with the label 99.
2) @Paul: The script Koen was talking about is not yet in the repo (hopefully
we will commit it soon)
@Alberto: if you are just interested in *only* the volum
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Hi Alberto, Koen and Stefano,
You can get the behavior you want/expect by counting the number of voxels
> assigned to lesions in the seg.mgz file - there is a ready tool for that in
> FreeSurfer but I don't remember off the top of my head what the corr
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Hi Alberto,
In the current implementation the volume reported in the table is simply
the sum of the lesion posterior probabilities, i.e., it is not affected by
the threshold used to create the crisp segmentation result for the lesions.
A few months ago
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Hi Andrew,
No, I don't think we have seen something like that before.
I'm a bit doubtful about the "enhanced T1 images", though - for sure there
is more information for samseg to work on when you feed it both T1 and
FLAIR, compared to some fused image
On 2/25/2021 9:43 AM, Jayachandra Raghava wrote:
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Hello Douglas,
Thank you for your advice.
As you have suggested, I have now used orig.mgz from the recon-all
longitudinal processing stream as an input to Samseg longitudinal
processing stream. For compa
External Email - Use Caution
Hello Douglas,
Thank you for your advice.
As you have suggested, I have now used orig.mgz from the recon-all
longitudinal processing stream as an input to Samseg longitudinal
processing stream. For comparison, I have the following volumes
1) Left-Hip
On 2/18/2021 7:06 AM, Jayachandra Raghava wrote:
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Hello Freesurfer Experts,
I am using Freesurfer version 7.1.1 to perform longitudinal
Samseg processing (using run_samseg_long) on my T1 longitudinal data.
1) First, I run the mri_robust_template to gene
In principle, yes. But, the atlas was trained using MS, not AD-style,
lesion data, and some recent analyses has shown the segmentation to be
hit-or-miss on leukoaraiosis-like data. Git it a try and give us feedback.
On 2/9/2021 12:15 PM, Steve Petersen wrote:
External Email - Use
External Email - Use Caution
Ahh great, thank you!
From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, June 8, 2020 11:43 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg wi
case when we might have to run samseg2recon
post running samseg?
Thanks,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Monday, June 8, 2020 11:20 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesu
surfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
Oh, sorry, that way of running recon-all will run samseg2recon. Sorry, I lost
track of what you are asking
On 6/8/2020 10:45 AM, Sneha Pandya wrote:
Ex
Thank you,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Monday, June 8, 2020 10:08 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 4:47 PM,
rd.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 4:47 PM, Sneha Pandya wrote:
External Email - Use Caution
Thank you Doug.
it is not run by default
* When I ran “samseg2recon –s subject” after running samseg
t the T1.mgz. file format is unimportant
*
Thank you,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Friday, June 5, 2020 4:05 PM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg w
m: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, June 5, 2020 4:05 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 3:54 PM, Sneha Pandya wrote:
Ex
,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Tuesday, May 5, 2020 11:38 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg with subfields
In theory it is possible, though I don
reesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields
In theory it is possible, though I don't know if it is better or worse. You can
run samseg, then run samseg2recon (this creates a folder that looks like it was
created by recon-all), then run subfields
: Tuesday, May 5, 2020 11:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields
sorry, did not see this before I responded. Ignore what I said
On 5/5/2020 11:13 AM, Iglesias Gonzalez, Juan E. wrote:
Dear Sneha,
We use cortical and white matter parcels in the
://www.jeiglesias.com
*From: * on behalf of Sneha
Pandya
*Reply-To: *Freesurfer support list
*Date: *Tuesday, May 5, 2020 at 10:46
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] samseg with subfields
*External Email - Use Caution *
Dear experts,
I want to
In theory it is possible, though I don't know if it is better or worse.
You can run samseg, then run samseg2recon (this creates a folder that
looks like it was created by recon-all), then run subfields on that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
External Email - Use Cauti
be included as a patch to current release or will it part of next big
release?
Thank you,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Tuesday, May 5, 2020 11:14 AM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] samseg with
: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] samseg with subfields
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg?
If it is possible is it as reliable as from running regular routine with “-a
External Email - Use Caution
Dear experts,
I want to revisit if anyone has ran subfield analysis just by running samseg?
If it is possible is it as reliable as from running regular routine with "-all"
recon-all flag?
Thank you,
Sneha
From: Sneha Pandya
Sent: Thursday, April 3
what is your command line and terminal output?
On 2/24/2020 10:50 AM, Russo, Andrew William wrote:
Hello Freesurfer Developers,
I am trying to use the "samseg" function in /usr/local/freesurfer/dev
but do not have permission to access the directory
/usr/local/freesurfer/dev/subjects/fsaverage
Hi Andrew,
Thanks for pointing this out, it looks like the permissions of our fsaverage
subjects have all changed since yesterday! Will fix this now
Best,
Andrew
From: on behalf of "Russo, Andrew
William"
Reply-To: FS Help
Date: Monday, February 24, 2020 at 10:51 AM
To: FS Help
Subject: [
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