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Dear freesurfer team
I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -
248...@163.com>
Reply-To: FS Help
Date: Monday, July 8, 2019 at 2:07 AM
To: FS Help
Subject: [Freesurfer] Skull Strip
External Email - Use Caution
Dear Freesurfer group：
just tried recon-all with the -use-gpu flag from the current development
version of freesurfer (freesurfer
External Email - Use Caution
Dear Freesurfer group：
just tried recon-all with the -use-gpu flag from the current development
version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0),
but it fail with the message that is cannot open libcudart.so.5.0.
I
I believe I already answered this. I don't understand what amplified
noise you mean. The brainmask.mgz can be used with mri_mask to apply to
any input volume you want.
cheers
Bruce
On Sun, 7 Jul 2019, Admin wrote:
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Dear Freesurfer group： Now,I wan
External Email - Use Caution
Dear Freesurfer group：
Now,I want generated a brain mask including the brain but excluding the
amplified noise regions after skull strip, but I can't find the corresponding
command line, so I send this email to you, hoping to get your help.
My Engli
you can apply the brainmask to any volume using mri_mask, including the
orig if you want. The skull stripping shouldn't amplify noise though. What
amplified noise regions do you mean? Maybe you can send a picture?
cheers
Bruce
On Thu, 4 Jul
2019, Admin wrote:
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Dear Freesurfer：
I am a graduate student of Northeastern University in China, and I do brain
image analysis . Now,I want generated a brain mask including the brain but
excluding the amplified noise regions after skull strip, but I can't find the
cor
Hi Douglas,
I am not sure why my previous message (posted Dec 22) did not get posted.
I have reported many problems with the skull stripping and resulting issues
in freesurfer. To summarize:
1. For our structural scans, we have significant pial matter/dura matter
remaining for > 50% of subjects
Dear experts,
I recently finished processing a subject for whom I had performed a skull-strip
on the brainmask.mgz volume. I decreased the watershed parameter and re-examined
the brainmask and the portion of the skull was gone, although some dura was
left over. I did a recon-all using the fol
Hi Uli
that looks like a pretty dramatic failure for the surfaces even without
considering the skull stripping problem. There are some expert options that
can improve this a ton (e.g. mris_make_surfaces -wlo and such). If you
would prefer you can upload the whole subject (tarred and gzipped ) a
Hi,
I am learning to use the program.
I have some questions about how to edit skull strip manually. In this
procedure is correct to remove only the residual skull or even other
non-cerebral elements (eg meninges)? So far I have never found remaining
skull but small residual portions of meninges. A
Hi Salil
have you checked the talairach.xfm to make sure it's accurate? There are
options to recon-all to strip less - check out the help.
cheers
Bruce
On Fri, 5 Jul 2013,
Salil Soman wrote:
> Hi,
> I have a study for which the original T1 looks good, was obtained
> identically to dozens of ot
Hi Rashimi,
please read
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
it should explain everything.
The clean way would be to edit the brainmask in the cross sectional
runs, complete them, run the base and the longs. Optimally no edits
should be necessary in the base and longs if cr
Hello FreeSurfer expets,
Our study requires our subjects to be scanned 3-4 times and then I use
FreeSurfer Tool to generate their voulumetrics. Since I do several time
points on a subjects also perform the longitudinal runs and then take the
volumetrics information from longitudinal run output fo
hi FS users;
have two questions which i am having issue across ss and pial/wm/orig surf
boundaries
1- it has happened that sometimes the sagittal view of individual was flipped
from left to right. but the pial/wm boundaries look good. was wondering why
this happened only for countable ppl? i t
Hi,
I have an image that is completing the skull strip with a lot of skull/dura
remaining and it is affecting the surfaces. I've tried lowering the
watershed threshold as low as 5 and I've tried adding the -gcut option, but
the low threshold by itself does not eliminate the skull and gcut not onl
Why don't you upload the subject and we'll take a look
On Mar 21, 2012, at 8:24 PM, Vincent wrote:
> Hi,
>
> I have an image that is completing the skull strip with a lot of skull
> remaining and it is have a large effect on the surfaces. I've tried lowering
> the watershed threshold as lo
Hi,
I have an image that is completing the skull strip with a lot of skull
remaining and it is have a large effect on the surfaces. I've tried
lowering the watershed threshold as low as 5 and I've tried adding the
-gcut option, but the low threshold by itself does not eliminate the skull
and gcut
Hi Vincent
is it affecting the surfaces? If not you can ignore it. Otherwise you
might try the graph cuts skull stripping and/or changing the preflooding
heights
cheers
Bruce
On Wed, 21 Mar 2012, Vincent wrote:
Hi,
I am having an issue where some dura remains behind after the skull strip
a
Hi,
I am having an issue where some dura remains behind after the skull strip
and is being mistakenly classified as white matter. Since it is just dura,
and not skull, would it be better to edit the white matter volume or should
I start by adjusting the skull strip since occurs earlier in the rec
Hi Douglas,
Thanks for your reply.
I think I have solved the problem -- I made a silly mistake myself.
Best,
Xiaoying
2011/5/24 Douglas N Greve
> what do you mean that the result is not good? Does the freesurfer analysis
> look ok?
>
> Xiaoying Tang wrote:
>
>> Hi Bruce and Douglas,
>>
>>
what do you mean that the result is not good? Does the freesurfer
analysis look ok?
Xiaoying Tang wrote:
> Hi Bruce and Douglas,
>
> After I ran through the FS, I ran the following two commands:
>
> bbregister --s T1_0145 --mov T2_0145_file1.nii --reg register.dat
> --init-fsl --t2 --o outvol
>
Hi Bruce and Douglas,
After I ran through the FS, I ran the following two commands:
bbregister --s T1_0145 --mov T2_0145_file1.nii --reg register.dat --init-fsl
--t2 --o outvol
mri_vol2vol --mov T1_0145/mri/brain.mgz --reg register.dat --o
T1_mappedToT2.nii
T1_0145 is the directory for analyzing
I see.
Thanks a lot.
Xiaoying
2011/5/22 Bruce Fischl
> yes, bbregister uses the surfaces generated by recon-all, so run it through
> to the end, then use bbregister.
>
> cheers
> Bruce
>
> On Sun, 22 May 2011, Xiaoying Tang wrote:
>
> Hi Douglas,
>>
>> Thanks for your reply!
>>
>> bbregister
yes, bbregister uses the surfaces generated by recon-all, so run it
through to the end, then use bbregister.
cheers
Bruce
On Sun, 22 May 2011, Xiaoying Tang
wrote:
> Hi Douglas,
>
> Thanks for your reply!
>
> bbregister succeeded in running now. But I still have another question.
>
> You mentio
Hi Douglas,
Thanks for your reply!
bbregister succeeded in running now. But I still have another question.
You mentioned that "If you have a T1 that you've run through FS".What do you
mean by "run through"? I just ran autorecon1 to get the skullstripped T1. Do
you mean that I also have to run au
Do you still have version 4.1 in your path? It looks like it is calling
an old version of fslregister.
doug
On 5/22/11 1:26 AM, Xiaoying Tang wrote:
Hi Douglas and Bruce,
I have updated my freesurfer version to 5.0.0. But I still have error
when I tried to run bbregister. The error informatio
Hi Douglas and Bruce,
I have updated my freesurfer version to 5.0.0. But I still have error when I
tried to run bbregister. The error information is as follows"
My command: bbregister --s bert --mov T2_0145_file1.nii --reg register.dat
--init-fsl --t2 --o outvol
Error information:
FREESURFER_HO
The full name on my machine is: freesurfer-centos4_x86_64-v4.1.0
So I think the version is 4.1.0
Best,
Xiaoying
2011/5/22 Bruce Fischl
> No, it's not the same what version are you running?
>
>
>
> On May 21, 2011, at 11:26 PM, Xiaoying Tang wrote:
>
> Hi Douglas,
>
> Thanks a lot for your sug
No, it's not the same what version are you running?
On May 21, 2011, at 11:26 PM, Xiaoying Tang wrote:
> Hi Douglas,
>
> Thanks a lot for your suggestion.
>
> It is really strange that I don't find bbregister in the file foler of the
> freesurfer on my machine. But I find a program named "f
Hi Douglas,
Thanks a lot for your suggestion.
It is really strange that I don't find bbregister in the file foler of the
freesurfer on my machine. But I find a program named "fslregister". Is that
the same?
If they are different, is it that I need to update my version of freesurfer
so that I can
If you have a T1 that you've run through FS and are happy with the skull
strip, then you can register your T2 with the FS anatomical (with
bbregister), then map the skull stripped T1 into the T2 space
(mri_vol2vol), then apply it to the T2 (mri_mask).
doug
On 5/21/11 7:27 PM, Bruce Fischl wrot
Hi Xiaoying,
unfortunately there isn't. I would recommend BET (from the FSL).
cheers
Bruce
On Sat, 21 May 2011,
Xiaoying Tang wrote:
> Hi All,
>
> I am wondering whether there is any way to skull strip a T2 image using
> freesurfer. I tried to use the same way as for skullstripping T1 image, bu
Hi All,
I am wondering whether there is any way to skull strip a T2 image using
freesurfer. I tried to use the same way as for skullstripping T1 image, but
always failed.
I would be most grateful if someone can give me some suggestion.
Best,
Xiaoying Tang
sure, you can try it, but it won't work as well. Just run mri_watershed
directly
cheers
Bruce
On Thu, 5 Aug 2010, Zhang, Yuning wrote:
> hi,experts,
>
> is there a way to use -skullstrip of freesurfer on my raw data (.mgz format)
> without any correction,i.e , intensity correction , normaliz
hi,experts,
is there a way to use -skullstrip of freesurfer on my raw data (.mgz format)
without any correction,i.e , intensity correction , normalization ?
thanks a lot
yuning
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https://mai
I have a question regarding the skull stripping process.
I ran my data through recon-all but still had much skull intact. I then
followed the recommended process per the freesurfer wiki to change the
watershed threshold levels on the recon process. I did so at the 20, 15,
10, 5, and 0 threshold w
W. Moore
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] skull strip error
try adding -nowsgcaatlas to the end of the recon-all command.
n.
On Tue, 2010-04-13 at 18:59 +, Dana W. Moore wrote:
> Hi everyone,
>
> I am using freesurfer version 4.5.0, and have just gotten
try adding -nowsgcaatlas to the end of the recon-all command.
n.
On Tue, 2010-04-13 at 18:59 +, Dana W. Moore wrote:
> Hi everyone,
>
> I am using freesurfer version 4.5.0, and have just gotten an error
> message that I have never received before. The end of the recon-all
> script is pasted
Hi everyone,
I am using freesurfer version 4.5.0, and have just gotten an error message that
I have never received before. The end of the recon-all script is pasted
below. what does this mean?
#...@# Skull Stripping Mon Apr 5 15:06:52 EDT 2010
/home/fs01/kab2003/FS/133_S_0525/mri
mri_water
Hi:
The tissue located in volume index coordinates (164, 54, 137) approx in the
skull stripped volume that I am sending, could produce an error in the
cortical thickness values for example, or any other parameters that freesurfer
computes ?...
I uploaded the files through your upload web page
Hi Gonzalo,
it's hard to tell from the two slices. The superior one looks like it
only took out dura, not brain. The inferior one is harder to know. Did it
strip cerebellum?
Bruce
On Sun, 29 Nov 2009, Gonzalo Rojas Costa
wrote:
> Hi:
>
> I am sending attached two images with some skull str
the clone tool is useful for copying parts of the unstripped volume back
into the stripped one if parts of the brain are incorrectly removed (it's
part of tkmedit)
Bruce
On Tue, 6 Oct 2009, Gonzalo Rojas wrote:
> Hi:
>
> The command:
> recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgc
Hi:
The command:
recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s
only runs the skullstrip procedure ?...
Which is the "clone" tool ?...
Sincerely,
--
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Te
Hi Lena,
in general you only need to fix the skull stripping if it makes any of
the downstream processing less accurate. If the surfaces and aseg in the
region where the skullstrip leaves are accurate than you don't need to do
anything.
cheers,
Bruce
On Wed, 2 Sep 2009, Lena Palaniyappan
w
I think the brainmask looks fine.
In general, tissue being stripped off or large chunks of skull left
behind should be corrected as explained in the wiki.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But small pieces of skull left is okay as long as
it's not affecting
Hi Ben,
do the images appear in the right orientation in tkmedit? How did you
convert to .mgz? If they are in the correct orientation then feel free to
drop an example that isn't working on our website and we'll take a look.
cheers,
Bruce
On
Tue, 28 Apr 2009, Wilson, Benjamin wrote:
Hi,
Hi,
I am trying to run freesurfer on some SPGR sequences that I have on a few
subjects. I managed to import and convert the DICOM files to .mgz with
success, but when I ran the skull strip I have a significant amount of skull
left in some places and a large chunk of brain missing in other plan
Hi Paul,
Make smart cuts to simplify the normalization and skullstrip steps. This
is done using tkmedit --> tkmedit monkey orig to open the volume, and then
selecting --> Tools > Volume > Smartcut after positioning the cursor (red
cross) at the desired location. Smart cuts are only orthogonal an
Hello All,
I am having a very difficult time getting skullstrip to work on my monkey
anatomical data set. Are there any suggestions on how to get it to work
properly?
Thanks in advance
Paul
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check to see if your talairach is ok
On Wed, 29 Nov 2006, XJ Kang wrote:
Hi,
I got the following message when doing the skull strip:
*WATERSHED**
preflooding height equal to 25 percent
Sorting...
T1-weighted MRI image
modification of the
Hi,
I got the following message when doing the skull strip:
*WATERSHED**
preflooding height equal to 25 percent
Sorting...
T1-weighted MRI image
modification of the preflooding height to 15 percent
Count how many 110 voxels are prese
yes, but it won't be as robust.
On Wed, 10 Aug 2005, Sasha Wolosin wrote:
Is it possible to do skull stripping without motion correction or intensity
normalization?
Disclaimer:
The materials in this e-mail are private and may contain Protected Health
Information. Please note that e-mail is
Yes, skull-stripping is pretty robust.
You can definitely try that on your data.
-Xiao
On Wed, 10 Aug 2005, Sasha Wolosin wrote:
Is it possible to do skull stripping without motion correction or intensity
normalization?
Disclaimer:
The materials in this e-mail are private and may contain
Is it possible to do skull stripping without motion correction or intensity
normalization?
Disclaimer:
The materials in this e-mail are private and may contain Protected Health
Information. Please note that e-mail is not necessarily confidential or secure.
Your use of e-mail constitutes your
Dear experts,
Thank you for answering basic question.
Iam using Linux version of Freesurfer on Pen4 PC, and
trying to run "Process Volume" with my anatomical data
which was acquired by Siemens Allegra 3T maschine and
converted to analyze format.
"conversion" and "normalize intensities" were OK a
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