[Freesurfer] Skull strip

[irene saviozzi]

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. Also, I have to correct it
inside and/or outside the red line of brainmask?
I noticed that by removing the small remaining portions of the meninges (
outside of the red line), during the subsequent processing are "cut" pieces
of brain cortex, and also sucortical volumes changes (i.e. callosal
volume).
Thank you,
Irene
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[Freesurfer] Skull strip

[Vincent]

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 only
fails to remove the dura affecting my surfaces but it removes cerebellum as
well.  There is enough skull/dura left that I am hesitant to try manual
edits, but I don't know any other options.  I believe a good source of my
trouble comes from my own confusion about how much remaining dura/skull is
acceptable and how much cerebellum can be missing without affecting the
rest of the data.  I've uploaded the file (AL.zip) to the FTP server.  If
anybody has the time I would greatly appreciate it if I could have it
looked at.  Thank you very much.

--Vincent
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[Freesurfer] Skull Strip

[Admin]

External Email - Use Caution

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 
corresponding command line, so I send this email to you, hoping to get your 
help. 
My English is poor, if I make mistakes , I hope you can understand me. Thank 
for your kind consideration of this request. Looking forward to receiving your 
reply. Thank you very much again. My Email address is:15140248...@163.com.






Sincerely: Meng Nan Lin


Date: 07/04/2019

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[Freesurfer] Skull Strip

[Admin]

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 English is poor, if I make mistakes , I hope you can understand me. Thanks 
for your help！






Sincerely: Meng Nan Lin


Date: 07/04/2019







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[Freesurfer] Skull Strip

[Admin]

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 have the current cuda version install(8.0). Does Freesurfer only work 
with cuda 5.0?
Date: 07/08/2019







 






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[Freesurfer] skull strip...

[Gonzalo Rojas]

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.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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[Freesurfer] skull strip

[Tara Brah]

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 with little improvement to the amount of skull
removed.  I know a similar question has been asked but in that scenario
freesurfer was not including the skull as part of the cortical matter while
in my scenario it is.
Do you have any further suggestions as to how to remove the skull from my
images?
Thank you.
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[Freesurfer] skull strip

[Tetsuya Iidaka]

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 and
COR001-COR256 were written in "orig" and "T1" directory.

but next process failed and following message appeared.

No COR-XXX file is written in "brain" directory.

New mri-watershed" file is in bin/Linux directory as
indicated by mailing list.

Thanks in advance

Tetsuya Iidaka
Nagoya University
Department of Psychology
[EMAIL PROTECTED]


-
/home/XXX/freesurfer//bin/Linux/mri_watershed
/home/XXX/freesurfer/subjects/test01/mri/T1
/home/XXX/freesurfer/subjects/test01/mri/brain



The input file is /home/XXX/freesurfer/subjects/test01/mri/T1
The output file is /home/XXX/freesurfer/subjects/test01/mri/brain
If this is incorrect, please exit quickly the program (Ctl-C)


*WATERSHED**
preflooding height equal to 25 percent
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Find the largest 110-component...
Command Finished
-


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[Freesurfer] skull strip

[Sasha Wolosin]

Is it possible to do skull stripping without motion correction or intensity 
normalization?



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Re: [Freesurfer] Skull strip

[Bruce Fischl]

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 ) and we 
can figure out better options for you
cheers
Bruce


On Wed, 16 Mar 2016, ulrike 
kaunzner wrote:

> Hi,
> We have problems with the skull of one subjects (please see below). We tried 
> adjusting the watershed parameters, but it still did not work.
> What else can we do to change the surface?
>
> Thank you for your help!
>
> Best,
> Uli
>
>
>
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[Freesurfer] Skull strip failure

[Vincent]

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 not only fails to remove the skull but it removes cerebellum as
well.  There is so much skull left that I am hesitant to try manual edits,
but I don't know any other options.  Are there any? By the way, this brain
is from an older individual with pretty substantial atrophy.


--Vincent
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Re: [Freesurfer] Skull Strip

[Bruce Fischl]

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:




External Email - Use Caution

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 corresponding command line, so 
I send this email to
you, hoping to get your help. 
My English is poor, if I make mistakes , I hope you can understand me. Thank 
for your kind
consideration of this request. Looking forward to receiving your reply. Thank 
you very much again.
My Email address is:15140248...@163.com.


                                                                                
                   
                                                                            
Sincerely: Meng Nan Lin
                                                                                
                   
                                                                            
Date: 07/04/2019




 


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Re: [Freesurfer] Skull Strip

[Bruce Fischl]

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:



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 English is poor, if I make mistakes , I hope you can understand me. Thanks 
for your help！


                                                                                
                   
                                                                            
Sincerely: Meng Nan Lin
                                                                                
                   
                                                                            
Date: 07/04/2019




 




 


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Re: [Freesurfer] Skull Strip

[Hoopes, Andrew]

Hi, unless you build the binaries yourself, I believe the stable freesurfer 
versions only support cuda 5. However, cuda support has been completely removed 
in the current development version. The dev version that you’re referencing is 
from 2016.
Andrew


From:  on behalf of Admin 
<15140248...@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-Linux-centos6_x86_64-dev-20161123-bb356e0), 
but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install(8.0). Does Freesurfer only work 
with cuda 5.0?

Date: 07/08/2019
















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[Freesurfer] skull strip problem

[Wilson, Benjamin]

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 planes on the 
same brain.  I am wondering if there is a problem with intensity normalization 
(most of my brain appears to be close to an intensity of 110), but I do not 
know how to fix the problem.  Can anybody offer some suggestions on how to fix 
the problem?

Thanks.

Sincerely,
Ben Wilson


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Re: [Freesurfer] skull strip...

[Bruce Fischl]

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-wsgcaatlas  -s 
>
> only runs the skullstrip procedure ?...
>
>   Which is the "clone" tool ?...
>
>   Sincerely,
>
>
>
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[Freesurfer] skull strip question...

[Gonzalo Rojas Costa]

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...

  Sincerely,



Gonzalo Rojas Costa




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[Freesurfer] skull strip error

[Dana W. Moore]

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_watershed -T1 T1.mgz brainmask.auto.mgz 


Mode:  T1 normalized volume

*
The input file is T1.mgz
The output file is brainmask.auto.mgz
If this is incorrect, please exit with CTL-C


*WATERSHED**
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  20676

  Find the largest 110-component...
 heap usage = 128720 Kbytes.
 removing small segments (less than 1 percent of maxarea).done
  And identify it as the main brain basin...done
  Main component: 6553 voxels
  first estimation of the COG coord: x=124 y=177 z=184 r=110
  first estimation of the main basin volume: 5673266 voxels
mri_watershed Error: 
 Problem with WM_MIN too small
Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 
2009 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Apr  5 15:06:54 EDT 2010

Thanks,
Dana


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[Freesurfer] Skull strip problem

[XJ Kang]

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 present :  71137

 Find the largest 110-component...
heap usage = 113392 Kbytes.
removing small segments (less than 1 percent of maxarea).done
 And identify it as the main brain basin...done
 Main component: 22057 voxels
 first estimation of the COG coord: x=140 y=179 z=122 r=91
 first estimation of the main basin volume: 3160802 
voxelsSegmentation fault


recon-all exited with ERRORS at Wed Nov 29 15:46:36 PST 2006

Seems 71137  in "Count how many 110 voxels are present :  71137" is too 
small compared to other subject's.

Any idea about this "Segmentation fault"? Thanks.

XJ
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Re: [Freesurfer] skull strip

[Xiao Han]

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?



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Re: [Freesurfer] skull strip

[Bruce Fischl]

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?



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Re: [Freesurfer] Skull strip failure

[Bruce Fischl]

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 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 
> only fails to remove the skull but it removes cerebellum as well.  There is 
> so much skull left that I am hesitant to try manual edits, but I don't know 
> any other options.  Are there any? By the way, this brain is from an older 
> individual with pretty substantial atrophy.   
> 
> 
> --Vincent
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] skull strip problem

[Bruce Fischl]

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,

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 planes on the 
same brain.  I am wondering if there is a problem with intensity normalization 
(most of my brain appears to be close to an intensity of 110), but I do not 
know how to fix the problem.  Can anybody offer some suggestions on how to fix 
the problem?

Thanks.

Sincerely,
Ben Wilson


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Re: [Freesurfer] skull strip errors ?...

[Bruce Fischl]

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 strip errors that I got in a
> study... Will I got any error as a result of that skull strip algorithm
> errors, or I must adjust the parameters of the watershed algorithm ?...
>
>  Sincerely,
>
>
>
> Gonzalo Rojas Costa
>
>
>
>
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Re: [Freesurfer] skull strip error

[Nick Schmansky]

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 below.  what does this mean?
> 
> #...@# Skull Stripping Mon Apr  5 15:06:52 EDT 2010
> /home/fs01/kab2003/FS/133_S_0525/mri
> 
>  mri_watershed -T1 T1.mgz brainmask.auto.mgz 
> 
> 
> Mode:  T1 normalized volume
> 
> *
> The input file is T1.mgz
> The output file is brainmask.auto.mgz
> If this is incorrect, please exit with CTL-C
> 
> 
> *WATERSHED**
> Sorting...
>   T1-weighted MRI image
>   modification of the preflooding height to 15 percent
>   Count how many 110 voxels are present :  20676
> 
>   Find the largest 110-component...
>  heap usage = 128720 Kbytes.
>  removing small segments (less than 1 percent of
> maxarea).done
>   And identify it as the main brain basin...done
>   Main component: 6553 voxels
>   first estimation of the COG coord: x=124 y=177 z=184 r=110
>   first estimation of the main basin volume: 5673266 voxels
> mri_watershed Error: 
>  Problem with WM_MIN too small
> Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27
> 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all exited with ERRORS at Mon Apr  5 15:06:54 EDT 2010
> 
> Thanks,
> Dana
> 
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Re: [Freesurfer] skull strip error

[Dana W. Moore]

Hi Nick,

I should have mentioned that this actually was done with the -no-wsgcaatlas
option.  The results I sent you were obtained using that command.

Thanks,
Dana

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
Sent: Tuesday, April 13, 2010 3:09 PM
To: Dana 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 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_watershed -T1 T1.mgz brainmask.auto.mgz 
> 
> 
> Mode:  T1 normalized volume
> 
> *
> The input file is T1.mgz
> The output file is brainmask.auto.mgz
> If this is incorrect, please exit with CTL-C
> 
> 
> *WATERSHED**
> Sorting...
>   T1-weighted MRI image
>   modification of the preflooding height to 15 percent
>   Count how many 110 voxels are present :  20676
> 
>   Find the largest 110-component...
>  heap usage = 128720 Kbytes.
>  removing small segments (less than 1 percent of
> maxarea).done
>   And identify it as the main brain basin...done
>   Main component: 6553 voxels
>   first estimation of the COG coord: x=124 y=177 z=184 r=110
>   first estimation of the main basin volume: 5673266 voxels
> mri_watershed Error: 
>  Problem with WM_MIN too small
> Linux compute-3-14.v4linux 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27
> 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all exited with ERRORS at Mon Apr  5 15:06:54 EDT 2010
> 
> Thanks,
> Dana
> 
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Re: [Freesurfer] Skull strip problem

[Bruce Fischl]

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 preflooding height to 15 percent
Count how many 110 voxels are present :  71137

Find the largest 110-component...
   heap usage = 113392 Kbytes.
   removing small segments (less than 1 percent of maxarea).done
And identify it as the main brain basin...done
Main component: 22057 voxels
first estimation of the COG coord: x=140 y=179 z=122 r=91
first estimation of the main basin volume: 3160802 voxelsSegmentation 
fault


recon-all exited with ERRORS at Wed Nov 29 15:46:36 PST 2006

Seems 71137  in "Count how many 110 voxels are present :  71137" is too small 
compared to other subject's.

Any idea about this "Segmentation fault"? Thanks.

XJ
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[Freesurfer] skull strip for monkeys

[Paul Aparicio]

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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[Freesurfer] Skull strip and white matter

[Vincent]

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 recon-all
processing stream?

--Vincent
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[Freesurfer] skull strip on raw data

[Zhang, Yuning]

  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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Re: [Freesurfer] skull strip for monkeys

[Reza Rajimehr]

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 and
calculated as follow: if the cursor is in the upper half of the volume,
everything above the cursor will be removed; if the cursor is in the right
half of the volume, everything to the right will be removed, etc.  It is
not necessary to strip all the skull (and may not be necessary to strip
any of the skull); the point is only to disrupt the skull to make the
strip process more effective.

Reza


> 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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Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]

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Re: [Freesurfer] Skull strip and white matter

[Bruce Fischl]

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
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 recon-all
processing stream?

--Vincent


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[Freesurfer] Skull-strip issues: commands not working

[Arsenije Subotic]

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 following command as the troubleshooting 
tutorial suggested to regenerate the surfaces based on the new brainmask.mgz 
volume:


recon-all  -autorecon-pial -subjid 



However, after the subject finished processing the surfaces were 
generated/outlined on the dura as well. I tried performing a g-cut command but 
it did not get rid of the dura. I also had issues with the subcortical 
segmentation as the ventricles were not completely segmented.


Thank you for your help.


Best,

Arsenije

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[Freesurfer] Skull strip t1 in recon-all

[Julie Ottoy]

External Email - Use Caution

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 -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used and
for what?)

Any recommendations?

Thank you!
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[Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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
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Re: [Freesurfer] skull strip on raw data

[Bruce Fischl]

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 , normalization ?
>
> thanks a lot
>
> yuning
>
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[Freesurfer] FreeSurfer Skull Strip issue and longitudinal runs

[Rashmi Singh]

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 for each time point
subject wise.
 To do the ccros sectional time point runs I performed run recon all on my
subjects T1 Mparge data as follows:
recon-all -s SUBjid -use-mritotal -all  outFSSubjid &

I examined the output data for skull stripping and I am finding errors.
What do you suggest: shall I try to correct the skull stripping on the
cross sectional out put before performing the base and longitudinal run or
shall I complete all the runs and do skull strip editing in the output of
the longitudinal run data.
Please advise.
Thanks,
Rashmi.


I am 

On 3/2/12 8:02 AM, "Bruce Fischl"  wrote:

>Hi Rashmi
>
>what version of FS are you using? And what sequence are you using? There
>will of course be noise-induced variation across scans, which in the best
>case is around 2%. But that only occurs if you use multi-echo (high
>bandwidth sequence) and are careful about subject positioning to minimize
>differential gradient nonlinearity distortions.  You should also make
>sure 
>that your outlier measurements aren't significantly more motion corrupted
>than your other scans. Finally, it can also help to control for hydration
>status and time-of-day.
>
>cheers
>Bruce
>
>
>
>On Thu, 1 Mar 2012, Rashmi Singh wrote:
>
>> Hello,
>>  I am finding differences  in hippocampus  voulme of same subject when
>>scanned at different times . Our study requires our subjects to be
>>scanned 3-4 times (T0-T3)  within a
>> period of 1 month. We have performed MRI Scanning on all our subjects
>>with same sequence using 3T GE scanner.
>> Please suggest the reason behind this difference and how would I go
>>about correcting it.
>> For example following are the hippocampal  values for two subjects ( A
>>and AA ) calculated by freesurfer from different scans. Surprisingly
>>for these two subjects T3 and T2
>> Hipp-values  for A and AA respectively that are differing from the
>>other timepoints  are  same.
>> 
>> Left-Hippocampus
>>   Right-Hippocampus
>> A.T0
>> 3537
>> 3632
>> A.T1
>> 3629
>> 3796
>> A.T2
>> 3536
>> 3782
>> A.T3
>> 3096
>> 3671
>> AA.T1
>> 4245
>> 4667
>> AA.T2
>> 3096
>> 3671
>> AA.T3
>> 4341
>> 4491
>> 
>> 
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[Freesurfer] skull strip / pial issues on many scans

[Michelle VanTieghem]

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 or more (of a dataset of 350 scans). I
have tested using freesurfer's gcut and other options, as well as AFNI
skull strip, FSL with many options, and even ANTS.

2. We gave up on trying to use surfaces with this dataset, due to the sheer
amount of manual intervention that would be needed to edit the brains. A
colleague suggested that Freesurfer v 6 may work better than 5.3 , which we
had been using. Do you think that would make sense?

3. The aseg almost always labels the remaining skull as gray matter, which
then influences the icv and wbv measurements. 4. Recently we have decided
to try the longitudinal pipeline. Another problem appears: if a
cross-sectional scan does not have any pial matter (as in, it is one of the
few that as successfully skull stripped -  we call these the "clean" scans)
but a template is made from multiple scans from this subject. If one of
those other tp scans from this subject has any pial mater remaining, then
the (a) the template will include all of the pial matter and (b) the
longitudinal version of the "clean" scan now has extra pial matter that
gets erroneously labeled as gray matter, or sometimes white matter.

I have been trying to solve this for over a year, and I also sent data to
freesurfer over the ftp on December 1st using the directions on the
freesurfer wiki, if you want to take a look at a single representative scan
with this skull strip issue.

Thanks!

Michelle

-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Bruce Fischl]

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, but
> always failed.
>
> I would be most grateful if someone can give me some suggestion.
>
> Best,
> Xiaoying Tang
>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Douglas Greve]

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 wrote:
> 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, but
>> always failed.
>>
>> I would be most grateful if someone can give me some suggestion.
>>
>> Best,
>> Xiaoying Tang
>>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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 have the program bbregister?

Thanks a lot.

Best,
Xiaoying

2011/5/21 Douglas Greve 

> 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 wrote:
> > 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,
> but
> >> always failed.
> >>
> >> I would be most grateful if someone can give me some suggestion.
> >>
> >> Best,
> >> Xiaoying Tang
> >>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[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 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 have the program bbregister?
> 
> Thanks a lot.
> 
> Best,
> Xiaoying
> 
> 2011/5/21 Douglas Greve 
> 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 wrote:
> > 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, but
> >> always failed.
> >>
> >> I would be most grateful if someone can give me some suggestion.
> >>
> >> Best,
> >> Xiaoying Tang
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> ___
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> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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 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 have the program bbregister?
>
> Thanks a lot.
>
> Best,
> Xiaoying
>
> 2011/5/21 Douglas Greve < 
> gr...@nmr.mgh.harvard.edu>
>
>> 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 wrote:
>> > 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,
>> but
>> >> always failed.
>> >>
>> >> I would be most grateful if someone can give me some suggestion.
>> >>
>> >> Best,
>> >> Xiaoying Tang
>> >>
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> ___
>> Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>>  
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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_HOME
/usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
$Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
reading from T2_0145_file1.nii...
TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999276, 0, 0.0380414)
j_ras = (-0.00161026, 0.999104, -0.0422986)
k_ras = (0.0380073, 0.0423292, 0.998381)
writing to ./tmp.bbregister.16142/template.nii...
fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg
./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.16142/fslregister --dof 6
*ERROR: Flag --niters unrecognized.*

I am not sure about the reason since the Flag --niters seems to be created
during the process, but not in my original command.

I would be most grateful if you could help me solve this problem.

Thanks in advance.

Best,
Xiaoying


2011/5/22 Xiaoying Tang 

> 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 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 have the program bbregister?
>>
>> Thanks a lot.
>>
>> Best,
>> Xiaoying
>>
>> 2011/5/21 Douglas Greve < 
>> gr...@nmr.mgh.harvard.edu>
>>
>>> 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 wrote:
>>> > 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, but
>>> >> always failed.
>>> >>
>>> >> I would be most grateful if someone can give me some suggestion.
>>> >>
>>> >> Best,
>>> >> Xiaoying Tang
>>> >>
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> ___
>>> Freesurfer mailing list
>>>  Freesurfer@nmr.mgh.harvard.edu
>>>  
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>>  
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Douglas Greve]

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 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_HOME 
/usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0

mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
$Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
reading from T2_0145_file1.nii...
TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999276, 0, 0.0380414)
j_ras = (-0.00161026, 0.999104, -0.0422986)
k_ras = (0.0380073, 0.0423292, 0.998381)
writing to ./tmp.bbregister.16142/template.nii...
fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg 
./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 
--nobetmov --tmp ./tmp.bbregister.16142/fslregister --dof 6

*ERROR: Flag --niters unrecognized.*

I am not sure about the reason since the Flag --niters seems to be 
created during the process, but not in my original command.


I would be most grateful if you could help me solve this problem.

Thanks in advance.

Best,
Xiaoying


2011/5/22 Xiaoying Tang mailto:xta...@jhu.edu>>

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 mailto:fis...@nmr.mgh.harvard.edu>>

No, it's not the same what version are you running?



On May 21, 2011, at 11:26 PM, Xiaoying Tang mailto:xta...@jhu.edu>> 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 "fslregister". Is that the same?

If they are different, is it that I need to update my version
of freesurfer so that I can have the program bbregister?

Thanks a lot.

Best,
Xiaoying

2011/5/21 Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>

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 wrote:
> 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, but
>> always failed.
>>
>> I would be most grateful if someone can give me some
suggestion.
>>
>> Best,
>> Xiaoying Tang
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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 autorecon2 and autorecon3 if I want to use
bbregister?

Best,
Xiaoying

2011/5/22 Douglas Greve 

>  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 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_HOME
> /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
> reading from T2_0145_file1.nii...
> TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.999276, 0, 0.0380414)
> j_ras = (-0.00161026, 0.999104, -0.0422986)
> k_ras = (0.0380073, 0.0423292, 0.998381)
> writing to ./tmp.bbregister.16142/template.nii...
> fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg
> ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov
> --tmp ./tmp.bbregister.16142/fslregister --dof 6
> *ERROR: Flag --niters unrecognized.*
>
> I am not sure about the reason since the Flag --niters seems to be created
> during the process, but not in my original command.
>
> I would be most grateful if you could help me solve this problem.
>
> Thanks in advance.
>
> Best,
> Xiaoying
>
>
> 2011/5/22 Xiaoying Tang 
>
>> 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 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 have the program bbregister?
>>>
>>>  Thanks a lot.
>>>
>>>  Best,
>>> Xiaoying
>>>
>>> 2011/5/21 Douglas Greve 
>>>
 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 wrote:
 > 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, but
 >> always failed.
 >>
 >> I would be most grateful if someone can give me some suggestion.
 >>
 >> Best,
 >> Xiaoying Tang
 >>
  > ___
 > Freesurfer mailing list
 > Freesurfer@nmr.mgh.harvard.edu
 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 >
 >
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom
 it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.


>>>   ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>
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Re: [Freesurfer] skull strip T2 image in Freesurfer

[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 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 autorecon2 and autorecon3 if I want to use
> bbregister?
>
> Best,
> Xiaoying
>
> 2011/5/22 Douglas Greve 
>
>>  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 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_HOME
>> /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
>> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
>> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
>> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
>> reading from T2_0145_file1.nii...
>> TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.999276, 0, 0.0380414)
>> j_ras = (-0.00161026, 0.999104, -0.0422986)
>> k_ras = (0.0380073, 0.0423292, 0.998381)
>> writing to ./tmp.bbregister.16142/template.nii...
>> fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg
>> ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov
>> --tmp ./tmp.bbregister.16142/fslregister --dof 6
>> *ERROR: Flag --niters unrecognized.*
>>
>> I am not sure about the reason since the Flag --niters seems to be created
>> during the process, but not in my original command.
>>
>> I would be most grateful if you could help me solve this problem.
>>
>> Thanks in advance.
>>
>> Best,
>> Xiaoying
>>
>>
>> 2011/5/22 Xiaoying Tang 
>>
>>> 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 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 have the program bbregister?

  Thanks a lot.

  Best,
 Xiaoying

 2011/5/21 Douglas Greve 

> 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 wrote:
>> 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, but
>>> always failed.
>>>
>>> I would be most grateful if someone can give me some suggestion.
>>>
>>> Best,
>>> Xiaoying Tang
>>>
> > ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
   ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>>
>>
>
_

Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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 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 autorecon2 and autorecon3 if I want to
>> use
>> bbregister?
>>
>> Best,
>> Xiaoying
>>
>> 2011/5/22 Douglas Greve 
>>
>>   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 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_HOME
>>> /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
>>> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
>>> mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
>>> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
>>> reading from T2_0145_file1.nii...
>>> TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-0.999276, 0, 0.0380414)
>>> j_ras = (-0.00161026, 0.999104, -0.0422986)
>>> k_ras = (0.0380073, 0.0423292, 0.998381)
>>> writing to ./tmp.bbregister.16142/template.nii...
>>> fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg
>>> ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov
>>> --tmp ./tmp.bbregister.16142/fslregister --dof 6
>>> *ERROR: Flag --niters unrecognized.*
>>>
>>> I am not sure about the reason since the Flag --niters seems to be
>>> created
>>> during the process, but not in my original command.
>>>
>>> I would be most grateful if you could help me solve this problem.
>>>
>>> Thanks in advance.
>>>
>>> Best,
>>> Xiaoying
>>>
>>>
>>> 2011/5/22 Xiaoying Tang 
>>>
>>>  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 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 have the program bbregister?
>
>  Thanks a lot.
>
>  Best,
> Xiaoying
>
> 2011/5/21 Douglas Greve 
>
>  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 wrote:
>>
>>> 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, but
>>
>>> always failed.

 I would be most grateful if someone can give me some suggestion.

 Best,
 Xiaoying Tang

  > ___
>>
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>  ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you
>> in error
>> but does not contain patient information, please contact the sende

Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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 my T1 image with freesurfer,
T2_0145_file1.nii is my T2 image.

The result is not good. I am not sure whether there is some problem with my
above two commands. Do you have any suggestion?

Thanks a lot.

Best,
Xiaoying

2011/5/23 Xiaoying Tang 

> 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 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 autorecon2 and autorecon3 if I want to
>>> use
>>> bbregister?
>>>
>>> Best,
>>> Xiaoying
>>>
>>> 2011/5/22 Douglas Greve 
>>>
>>>   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 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_HOME
 /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
 mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
 mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii
 $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
 reading from T2_0145_file1.nii...
 TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-0.999276, 0, 0.0380414)
 j_ras = (-0.00161026, 0.999104, -0.0422986)
 k_ras = (0.0380073, 0.0423292, 0.998381)
 writing to ./tmp.bbregister.16142/template.nii...
 fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg
 ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov
 --tmp ./tmp.bbregister.16142/fslregister --dof 6
 *ERROR: Flag --niters unrecognized.*

 I am not sure about the reason since the Flag --niters seems to be
 created
 during the process, but not in my original command.

 I would be most grateful if you could help me solve this problem.

 Thanks in advance.

 Best,
 Xiaoying


 2011/5/22 Xiaoying Tang 

  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 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 have the program bbregister?
>>
>>  Thanks a lot.
>>
>>  Best,
>> Xiaoying
>>
>> 2011/5/21 Douglas Greve 
>>
>>  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 wrote:
>>>
 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, but
>>>
 always failed.
>
> I would be most grateful if someone can give me some suggestion.
>
> Best,
> Xiaoying Tang
>
>  > ___
>>>
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.m

Re: [Freesurfer] skull strip T2 image in Freesurfer

[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,
>
> 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 my T1 image with freesurfer, 
> T2_0145_file1.nii is my T2 image.
>
> The result is not good. I am not sure whether there is some problem 
> with my above two commands. Do you have any suggestion?
>
> Thanks a lot.
>
> Best,
> Xiaoying
>
> 2011/5/23 Xiaoying Tang mailto:xta...@jhu.edu>>
>
> 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 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 autorecon2 and autorecon3
> if I want to use
> bbregister?
>
> Best,
> Xiaoying
>
> 2011/5/22 Douglas Greve  >
>
>  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 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_HOME
> 
> /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
> mri_convert T2_0145_file1.nii
> ./tmp.bbregister.16142/template.nii
> mri_convert T2_0145_file1.nii
> ./tmp.bbregister.16142/template.nii
> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58
> nicks Exp $
> reading from T2_0145_file1.nii...
> TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.999276, 0, 0.0380414)
> j_ras = (-0.00161026, 0.999104, -0.0422986)
> k_ras = (0.0380073, 0.0423292, 0.998381)
> writing to ./tmp.bbregister.16142/template.nii...
> fslregister --s bert --mov
> ./tmp.bbregister.16142/template.nii --reg
> ./tmp.bbregister.16142/reg.init.dat --niters 1
> --maxangle 90 --nobetmov
> --tmp ./tmp.bbregister.16142/fslregister --dof 6
> *ERROR: Flag --niters unrecognized.*
>
> I am not sure about the reason since the Flag --niters
> seems to be created
> during the process, but not in my original command.
>
> I would be most grateful if you could help me solve
> this problem.
>
> Thanks in advance.
>
> Best,
> Xiaoying
>
>
> 2011/5/22 Xiaoying Tang  >
>
> 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
> mailto:xta...@jhu.edu>> 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 "fslregister". Is
> that the same?
>
>  If they 

Re: [Freesurfer] skull strip T2 image in Freesurfer

[Xiaoying Tang]

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,
>>
>> 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 my T1 image with freesurfer,
>> T2_0145_file1.nii is my T2 image.
>>
>> The result is not good. I am not sure whether there is some problem with
>> my above two commands. Do you have any suggestion?
>>
>> Thanks a lot.
>>
>> Best,
>> Xiaoying
>>
>> 2011/5/23 Xiaoying Tang mailto:xta...@jhu.edu>>
>>
>>
>>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 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 autorecon2 and autorecon3
>>if I want to use
>>bbregister?
>>
>>Best,
>>Xiaoying
>>
>>2011/5/22 Douglas Greve >>
>>
>>
>> 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 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_HOME
>>
>>  /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0
>>mri_convert T2_0145_file1.nii
>>./tmp.bbregister.16142/template.nii
>>mri_convert T2_0145_file1.nii
>>./tmp.bbregister.16142/template.nii
>>$Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58
>>nicks Exp $
>>reading from T2_0145_file1.nii...
>>TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00
>>i_ras = (-0.999276, 0, 0.0380414)
>>j_ras = (-0.00161026, 0.999104, -0.0422986)
>>k_ras = (0.0380073, 0.0423292, 0.998381)
>>writing to ./tmp.bbregister.16142/template.nii...
>>fslregister --s bert --mov
>>./tmp.bbregister.16142/template.nii --reg
>>./tmp.bbregister.16142/reg.init.dat --niters 1
>>--maxangle 90 --nobetmov
>>--tmp ./tmp.bbregister.16142/fslregister --dof 6
>>*ERROR: Flag --niters unrecognized.*
>>
>>I am not sure about the reason since the Flag --niters
>>seems to be created
>>during the process, but not in my original command.
>>
>>I would be most grateful if you could help me solve
>>this problem.
>>
>>Thanks in advance.
>>
>>Best,
>>Xiaoying
>>
>>
>>2011/5/22 Xiaoying Tang >>
>>
>>
>>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
>>mailto:xta...@jhu.edu>> wrote:
>>
>> Hi Douglas,
>>
>> Thanks a lot for your suggestion.
>>
>> It is really strange that I don't find
>>bbregister in the 

[Freesurfer] skull strip (ss) and pial/wm/orig surf

[Kushal Kapse]

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 tried to look up in forum for anyone 
with similar issue but no clue yet...has anyone come across this issue and if 
yes, how to flip back the orientation in sagittal view

2- how much ss issue should be considered. ss issue= skull pieces left behind, 
or large GM cut. the reason i m asking is because sometimes there would be a 
huge piece of skull remaining but that individual would have perfect visual 
alignment of boundaries and nice inflated surface. sometimes they have mediocre 
skull remaining or GM cut, and that would make pial/wm boundaries go wrong and 
inflation is with holes and droplets. my question is how much of skull 
stripping errors( pieces of skull remaining, gm/wm removed beyond limit or 
orientation flipped) matters to segmentation, inflation and further analysis. 

any help would be appreciated


thanks
kk
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FreeSurfer Skull Strip issue and longitudinal runs

[Martin Reuter]

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 cross are correct.

A potential short cut (depending on how bad the skull strips are) would
be to run cross and base, then edit only the base. This can work if the
skull strip is not too bad and if the asegs in the cross are good.

Best, Martin.

On Thu, 2012-09-27 at 16:04 +, Rashmi Singh wrote:
> 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 for each time point
> subject wise.
>  To do the ccros sectional time point runs I performed run recon all on my
> subjects T1 Mparge data as follows:
> recon-all -s SUBjid -use-mritotal -all  outFSSubjid &
> 
> I examined the output data for skull stripping and I am finding errors.
> What do you suggest: shall I try to correct the skull stripping on the
> cross sectional out put before performing the base and longitudinal run or
> shall I complete all the runs and do skull strip editing in the output of
> the longitudinal run data.
> Please advise.
> Thanks,
> Rashmi.
> 
> 
> I am 
> 
> On 3/2/12 8:02 AM, "Bruce Fischl"  wrote:
> 
> >Hi Rashmi
> >
> >what version of FS are you using? And what sequence are you using? There
> >will of course be noise-induced variation across scans, which in the best
> >case is around 2%. But that only occurs if you use multi-echo (high
> >bandwidth sequence) and are careful about subject positioning to minimize
> >differential gradient nonlinearity distortions.  You should also make
> >sure 
> >that your outlier measurements aren't significantly more motion corrupted
> >than your other scans. Finally, it can also help to control for hydration
> >status and time-of-day.
> >
> >cheers
> >Bruce
> >
> >
> >
> >On Thu, 1 Mar 2012, Rashmi Singh wrote:
> >
> >> Hello,
> >>  I am finding differences  in hippocampus  voulme of same subject when
> >>scanned at different times . Our study requires our subjects to be
> >>scanned 3-4 times (T0-T3)  within a
> >> period of 1 month. We have performed MRI Scanning on all our subjects
> >>with same sequence using 3T GE scanner.
> >> Please suggest the reason behind this difference and how would I go
> >>about correcting it.
> >> For example following are the hippocampal  values for two subjects ( A
> >>and AA ) calculated by freesurfer from different scans. Surprisingly
> >>for these two subjects T3 and T2
> >> Hipp-values  for A and AA respectively that are differing from the
> >>other timepoints  are  same.
> >> 
> >> Left-Hippocampus
> >>   Right-Hippocampus
> >> A.T0
> >> 3537
> >> 3632
> >> A.T1
> >> 3629
> >> 3796
> >> A.T2
> >> 3536
> >> 3782
> >> A.T3
> >> 3096
> >> 3671
> >> AA.T1
> >> 4245
> >> 4667
> >> AA.T2
> >> 3096
> >> 3671
> >> AA.T3
> >> 4341
> >> 4491
> >> 
> >> 
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> >>_
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Re: [Freesurfer] skull strip - how lenient can one be?

[Sita Kakunoori]

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 the surfaces.



Sita.



On Wed, 2 Sep 2009, Lena Palaniyappan wrote:


Hi all

I am not grasping the concept of skull strip correction full, Im afraid. I
have attached a brainmask ­ 128th slice sagittal of which shows some uneven
stripping (I couldn¹t attach the huge T1 image to overlay) - is this degree
of tissue separation acceptable?

Where does one set a limit? The example set in tutorial data shows some very
obvious stripping errors, but the data I have shows really minor stuff ­ and
I am always unsure whether to continue auto recon 2 or correct them. Any
help?

Many thanks in advance

Cheers
LKP

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Re: [Freesurfer] skull strip - how lenient can one be?

[Bruce Fischl]

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 
wrote:



Hi all

I am not grasping the concept of skull strip correction full, Im afraid. I
have attached a brainmask ­ 128th slice sagittal of which shows some uneven
stripping (I couldn¹t attach the huge T1 image to overlay) - is this degree
of tissue separation acceptable?

Where does one set a limit? The example set in tutorial data shows some very
obvious stripping errors, but the data I have shows really minor stuff ­ and
I am always unsure whether to continue auto recon 2 or correct them. Any
help?

Many thanks in advance

Cheers
LKP

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Re: [Freesurfer] freesurfer skull strip removes brain except brainstem, and then has retesselation error

[Bruce Fischl]

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 other studies that went through freesurfer without
> problem. For some reason this study keeps getting stripped down to a little
> more than its brainstem. Then the rest of the processing fails with an error
> of retesselation. Log files attached. Any suggestions on how I can properly
> process this data?
> 
> Best wishes,
> 
> Sal
> 
>
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