[Freesurfer] recon failed with aseg.mgz

[Xiaomin Yue]

Hi All,
The recon-all stopped at the step of mri_normalize.  The command is: 
mri_normailze -mprage -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz 
brain.mgz.  The error massege:  assuming input volume is MGH (Van der Kouwe) 
MP-RAGE.  not interpolating and embedding volume to be 256^3…  using 
segmentation for initial intensity normalization, using MR volume brainmask.mgz 
to mask input volume.  reading from norm.mgz,  reading from aseg.mgz,  
mdi_normalize: aseg volume aseg.mgz must be conformed.
The aseg.mgz is conformed to minimum voxel size with matrix size: 320 X 320 X 
320.  Also, the aseg.mgz looks right.   any suggestions?
thanks in advance.
Xiaomin
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[Freesurfer] Register.dof

[Xiaomin Yue]

Hi,
I like to transfer a epi file to a T1 space.  Is it possible?
Thanks,

Xiaomin




On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve" 
 wrote:

We don't have anything to do this directly. However, we do have this tool:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
See if that meets your needs.

doug

On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> Hello,
> I am performing clustering ofer data sampled to the fsaverage5 surfaces.
> I would now like to be able to do color matchign and other processes that 
> require a vertex correspondence across both surfaces.
>
> I have noticed that the vertices do not correspond directly (vertex 25 of lh 
> is not the homologous of vertex 25 in rh)
> As both hemispheres have the same number of vertices I guess this has 
> probably already been done, but I have not been able to find this information.
>
> Is there any lookup-table or any easy method to calculate vertex 
> correspondence across hamispheres for fsaverage5 surfaces?
>
> Thank you in advance
>
> David Moreno-Dominguez
> Research Group: Neuroanatomy and Connectivity
> Methods & Development Unit: Cortical Networks and Cognitive Functions
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A, 04103 Leipzig, Germany
> Phone: +49 341 9940-2580
> Email: mor...@cbs.mpg.de
> http://www.cbs.mpg.de/~moreno
>
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>

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Re: [Freesurfer] Register.dof

[Xiaomin Yue]

Hi Doug,


Thanks for your response.  I did run bbregister to register the EPI to T1, but 
it did not resample the EPI to T1 space, just generated a register.dof6.dat 
file, which is expected according to the help document.  Also, the help 
document of bbregister doesn’t indicate resampling or sort, unless I missed 
something.  I did try mri_vol2vol to resample the EPI to T1 space, using the 
registration file generated by bbregister.  When I loaded the T1 and EPI in 
freeview, the two doesn’t match well, unless I loaded the EPI with the 
registration file.  Did I do something wrong?  Or I shouldn’t expect T1 and EPI 
line up after mri_vol2vol?






Xiaomin





From: Douglas Greve
Sent: ‎Wednesday‎, ‎February‎ ‎18‎, ‎2015 ‎1‎:‎35‎ ‎PM
To: Freesurfer support list





Yes, if you've run the T1 through recon-all, then you can use bbregister to 
create a registration between the two. It will also resample to the T1 space, 
but you can also use mri_vol2vol to do so too.
doug



On 2/18/15 5:43 PM, Xiaomin Yue wrote:



Hi,




I like to transfer a epi file to a T1 space.  Is it possible?




Thanks,


Xiaomin 





On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve" 
 wrote:





We don't have anything to do this directly. However, we do have this tool:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
See if that meets your needs.

doug

On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> Hello,
> I am performing clustering ofer data sampled to the fsaverage5 surfaces.
> I would now like to be able to do color matchign and other processes that 
> require a vertex correspondence across both surfaces.
>
> I have noticed that the vertices do not correspond directly (vertex 25 of lh 
> is not the homologous of vertex 25 in rh)
> As both hemispheres have the same number of vertices I guess this has 
> probably already been done, but I have not been able to find this information.
>
> Is there any lookup-table or any easy method to calculate vertex 
> correspondence across hamispheres for fsaverage5 surfaces?
>
> Thank you in advance
>
> David Moreno-Dominguez
> Research Group: Neuroanatomy and Connectivity
> Methods & Development Unit: Cortical Networks and Cognitive Functions
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A, 04103 Leipzig, Germany
> Phone: +49 341 9940-2580
> Email: mor...@cbs.mpg.de
> http://www.cbs.mpg.de/~moreno
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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[Freesurfer] Lta_convert

[Xiaomin Yue]

Hi,
Is it possible to download lta_convert?
Thanks,

Xiaomin




On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson"  
wrote:
ok, great.

so let's say I have a linear transformation or a full warp field to go
between the freesurfer processed image and the unprocessed brain. is there
a way that I can propagate onto the unprocessed image the entire freesurfer
contents including the "mri" and "label" and everything else, using the
warp? The processed image has extensive manual edits, so I basically just
want to transfer everything over.

Thanks Bruce!

-David

On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl 
wrote:

> Hi David
>
> yes, you can use bbregister to do the rigid alignment, then use it as
> initialization for mri_nl_align. I would think you are better off doing the
> surface recons and using cvs though. It's only computer time
>
> cheers
> Bruce
>
> On Wed, 25 Feb 2015, David Grayson wrote:
>
> > Hey Bruce,
> > Thanks for responding. I would actually prefer nonlinear. I did not
> mention
> > it, but the aseg data that I have is on a distortion-corrected T1 image,
> > whereas the unprocessed image I want to warp onto is the same scan but
> not
> > corrected for distortion. The distortions are nonlinear. I was hoping
> there
> > might be a way to get a warp field to go between the two images without
> > running both images through the recon-all pipeline. Are there any other
> > possible tools?
> >
> > Thanks!
> > -David
> >
> > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   Is there any reason you need it to be nonlinear? I would think
> >   bbregister and mri_vol2vol would do the trick
> >   Cheers
> >   Bruce
> >
> >
> >
> >   > On Feb 25, 2015, at 11:18 PM, David Grayson
> >wrote:
> >   >
> >   > Hi freesurfers,
> >   >
> >   > I am hoping to warp an aparc+aseg.mgh file from a subject's
> >   freesurfer-processed image to a separate (unprocessed) T1 image
> >   on the same subject. I would like to use a purely
> >   intensity-based nonlinear volumetric registration to do this, to
> >   save time and complication. I understand I can do this if I have
> >   a .m3z warp file.
> >   >
> >   > My question is, how can I get this warp file? I have tried
> >   using mri_cvs_register with the --step3 option, but that appears
> >   to only work after the surface-based registrations have been
> >   carried out. I haven't found another tool to do this yet.
> >   >
> >   > Are there any ideas? Thank you very much for your time.
> >   >
> >   > -David
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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[Freesurfer] freeview registration

[Xiaomin Yue]

Hi All,
After using freeview to manually adjust the registration between a functional 
and T1.mgz generated by bbregister, I saved the registration file in freeview 
as lta format, which seems the only option.  However, the registration file has 
same file name for source and target volume.  So, when loading it again to 
freeview, the registration is totally wrong.   In order to avoid the problem, I 
converted the register.dof6.dat to lta formation, where the lta file has 
correct source and target volume name.  Then, I loaded the lta file generated 
from register.dof6.dat, did manual adjustment, and then saved adjusted 
registration as a lta file.  the final lta file has same problem.   I am using 
freesurfer 5.3.  Any suggestion is appreciated.
Thanks,Xiaomin___
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Re: [Freesurfer] freeview registration

[Xiaomin Yue]

Hi Doug,
thanks for your response.  You are right that the freeview in v5.3 doesn't 
generate the registration file correctly.   However, the newest development 
version of freeview can generate a lta registration file correctly with correct 
source and target volume.  then, a registration file in reg format can be 
generated using lta_convert included in the development version of freesurfer.  
It is much easier and precise to manually adjust the registration using 
freeview than tkregister.   It might be useful to include a tool using freeview 
to manually adjust registration in the next freesurfer release. 
Xiaomin

Date: Sun, 1 Mar 2015 13:57:52 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freeview registration


  

  
  


I think that freeview does not correctly generate the registration
file. You can use it to check the regsitration, but us tkregister
if  you need to edit  it.

doug





On 2/27/15 10:18 AM, Xiaomin Yue wrote:



  
  Hi All,



After using freeview to manually adjust the registration
  between a functional and T1.mgz generated by bbregister, I
  saved the registration file in freeview as lta format, which
  seems the only option.  However, the registration file has
  same file name for source and target volume.  So, when loading
  it again to freeview, the registration is totally wrong.   In
  order to avoid the problem, I converted the register.dof6.dat
  to lta formation, where the lta file has correct source and
  target volume name.  Then, I loaded the lta file generated
  from register.dof6.dat, did manual adjustment, and then saved
  adjusted registration as a lta file.  the final lta file has
  same problem.   I am using freesurfer 5.3.  Any suggestion is
  appreciated.



Thanks,
Xiaomin
  
  

  
  

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Re: [Freesurfer] Lta_convert

[Xiaomin Yue]

Thanks

Xiaomin




On Mon, Mar 2, 2015 at 11:51 AM -0800, "Douglas N Greve" 
 wrote:

try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert

On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson"
> mailto:dgray...@ucdavis.edu>> wrote:
>
> ok, great.
>
> so let's say I have a linear transformation or a full warp field to go
> between the freesurfer processed image and the unprocessed brain. is
> there a way that I can propagate onto the unprocessed image the entire
> freesurfer contents including the "mri" and "label" and everything
> else, using the warp? The processed image has extensive manual edits,
> so I basically just want to transfer everything over.
>
> Thanks Bruce!
>
> -David
>
> On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi David
>
> yes, you can use bbregister to do the rigid alignment, then use it as
> initialization for mri_nl_align. I would think you are better off
> doing the
> surface recons and using cvs though. It's only computer time
>
> cheers
> Bruce
>
> On Wed, 25 Feb 2015, David Grayson wrote:
>
> > Hey Bruce,
> > Thanks for responding. I would actually prefer nonlinear. I did
> not mention
> > it, but the aseg data that I have is on a distortion-corrected
> T1 image,
> > whereas the unprocessed image I want to warp onto is the same
> scan but not
> > corrected for distortion. The distortions are nonlinear. I was
> hoping there
> > might be a way to get a warp field to go between the two images
> without
> > running both images through the recon-all pipeline. Are there
> any other
> > possible tools?
> >
> > Thanks!
> > -David
> >
> > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> >   Is there any reason you need it to be nonlinear? I would think
> >   bbregister and mri_vol2vol would do the trick
> >   Cheers
> >   Bruce
> >
> >
> >
> >   > On Feb 25, 2015, at 11:18 PM, David Grayson
> >   mailto:dgray...@ucdavis.edu>> wrote:
> >   >
> >   > Hi freesurfers,
> >   >
> >   > I am hoping to warp an aparc+aseg.mgh file from a subject's
> >   freesurfer-processed image to a separate (unprocessed) T1
> image
> >   on the same subject. I would like to use a purely
> >   intensity-based nonlinear volumetric registration to do
> this, to
> >   save time and complication. I understand I can do this if
> I have
> >   a .m3z warp file.
> >   >
> >   > My question is, how can I get this warp file? I have tried
> >   using mri_cvs_register with the --step3 option, but that
> appears
> >   to only work after the surface-based registrations have been
> >   carried out. I haven't found another tool to do this yet.
> >   >
> >   > Are there any ideas? Thank you very much for your time.
> >   >
> >   > -David
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto: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.

Re: [Freesurfer] Register.dof

[Xiaomin Yue]

Thanks.  The new freeview can create correct register file

Xiaomin




On Mon, Mar 2, 2015 at 11:06 AM -0800, "Douglas N Greve" 
 wrote:

On 02/18/2015 09:54 PM, Xiaomin Yue wrote:
> Hi Doug,
>
> Thanks for your response.  I did run bbregister to register the EPI to
> T1, but it did not resample the EPI to T1 space, just generated a
> register.dof6.dat file, which is expected according to the help
> document.  Also, the help document of bbregister doesn’t indicate
> resampling or sort, unless I missed something.
It is the --o option.
> I did try mri_vol2vol to resample the EPI to T1 space, using the
> registration file generated by bbregister.  When I loaded the T1 and
> EPI in freeview, the two doesn’t match well, unless I loaded the EPI
> with the registration file.  Did I do something wrong?  Or I shouldn’t
> expect T1 and EPI line up after mri_vol2vol?
Did you check the registration with tkregister? Look at the last line in
the bbregister log file to get the command line. if that does not look
ok, then vol2vol will surely not work. If it does look ok, then send the
vol2vol command line
doug
>
> Xiaomin
>
> *From:* Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>
> *Sent:* ‎Wednesday‎, ‎February‎ ‎18‎, ‎2015 ‎1‎:‎35‎ ‎PM
> *To:* Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>
>
>
> Yes, if you've run the T1 through recon-all, then you can use
> bbregister to create a registration between the two. It will also
> resample to the T1 space, but you can also use mri_vol2vol to do so too.
> doug
>
>
> On 2/18/15 5:43 PM, Xiaomin Yue wrote:
>
> Hi,
>
> I like to transfer a epi file to a T1 space.  Is it possible?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> We don't have anything to do this directly. However, we do have
> this tool:
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> See if that meets your needs.
>
> doug
>
> On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> > Hello,
> > I am performing clustering ofer data sampled to the fsaverage5
> surfaces.
> > I would now like to be able to do color matchign and other
> processes that require a vertex correspondence across both surfaces.
> >
> > I have noticed that the vertices do not correspond directly
> (vertex 25 of lh is not the homologous of vertex 25 in rh)
> > As both hemispheres have the same number of vertices I guess
> this has probably already been done, but I have not been able to
> find this information.
> >
> > Is there any lookup-table or any easy method to calculate vertex
> correspondence across hamispheres for fsaverage5 surfaces?
> >
> > Thank you in advance
> >
> > David Moreno-Dominguez
> > Research Group: Neuroanatomy and Connectivity
> > Methods & Development Unit: Cortical Networks and Cognitive
> Functions
> > Max Planck Institute for Human Cognitive and Brain Sciences
> > Stephanstraße 1A, 04103 Leipzig, Germany
> > Phone: +49 341 9940-2580
> > Email: mor...@cbs.mpg.de
> > http://www.cbs.mpg.de/~moreno <http://www.cbs.mpg.de/%7Emoreno>
> >
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> >
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[Freesurfer] fs-fast analysis on a group averaged surface

[Xiaomin Yue]

Hi All,
I generated a group averaged surface using make_average_surface successfully.  
Currently, I like to process the fMRI data using this group surface, instead of 
fsaverage, using the fs-fast pipeline.   For doing so, I need to run 
rawfunc2surf-sess with a parameter where I can input this group averaged 
surface before running mkanalysis-sess, mkcontrast-sess, and selxavg3-sess.  
But it seems that rawfunc2surf-sess doesn't accept input other than self or 
fsaverage.  Is there a way to do this in the current fs-fast pipeline?  
Thanks,Xiaomin 


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Re: [Freesurfer] fs-fast analysis on a group averaged surface

[Xiaomin Yue]

Thanks very much.

Xiaomin


> On Apr 13, 2015, at 9:43 AM, Douglas Greve  wrote:
> 
> Use the (undocumented) -trgsubject flag
> 
>> On 4/6/15 9:10 AM, Xiaomin Yue wrote:
>> Hi All,
>> 
>> I generated a group averaged surface using make_average_surface 
>> successfully.  Currently, I like to process the fMRI data using this group 
>> surface, instead of fsaverage, using the fs-fast pipeline.   For doing so, I 
>> need to run rawfunc2surf-sess with a parameter where I can input this group 
>> averaged surface before running mkanalysis-sess, mkcontrast-sess, and 
>> selxavg3-sess.  But it seems that rawfunc2surf-sess doesn't accept input 
>> other than self or fsaverage.  Is there a way to do this in the current 
>> fs-fast pipeline?  
>> 
>> Thanks,
>> Xiaomin 
>> 
>> 
>> 
>> 
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[Freesurfer] mri_vol2vol

[Xiaomin Yue]

Hi Doug,
I like to convert a native functional data into the anatomical space using 
mri_vol2vol with --fstal, so that the resample data has same spatial resolution 
as the original function data.  However, mri_vol2vol give a error: --fstal 
unknown.  I also tried using --fstalres as suggested in the help document, with 
same error.  I am using fs5.3.  the command is: mdi_vol2vol --mov res-001.nii 
--fstarg --fstal 1.5 --o res-001.t1.space.nii --reg register.dof6.dat
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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

Thanks for your response.  The command you gave will generate a new function 
data with the spatial resolution of the anatomical data, which in my case is 
much higher than those of functional data.  What i want is to generate a new 
functional data in the anatomical space, with spatial resolution of the 
original function data. Is it possible?  I thought that --fstalres would give 
me a choice to keep the spatial resolution of the original function data. 
Xiaomin 

Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol


  

  
  
sorry, I don't understand. fstal would imply that you want talairach
space. If you want to map the functional into the anatomical space,
then

mri_vol2vol --mov res-001.nii  --o res-001.t1.space.nii --reg
register.dof6.dat --fstarg







On 4/14/15 11:36 AM, Xiaomin Yue wrote:



  
  Hi Doug,



I like to convert a native functional data into the
  anatomical space using mri_vol2vol with --fstal, so that the
  resample data has same spatial resolution as the original
  function data.  However, mri_vol2vol give a error: --fstal
  unknown.  I also tried using --fstalres as suggested in the
  help document, with same error.  I am using fs5.3.  the
  command is: mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5
  --o res-001.t1.space.nii --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

yes, that's precisely what I want.  the reason is the following.  A subject was 
scanned multiple times across days with slightly different slice position for 
each time.  What I need is to extract a peak response when a stimuli was 
presented.   In order to make the voxels match from one scan to another, I 
thought that all scans have to be in same space, so that the data extracted for 
a voxel from different scans match.   Could there be a better way to do this?
Thanks,Xiaomin

Date: Tue, 14 Apr 2015 21:08:15 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol


  

  
  


So you want it to be in a volume with field of view 256mm in all
three dimensions, but the voxel size to be that of the functional
data? It is possible to do, but not easy to set up. Can you say why
you would want to do that?





On 4/14/15 8:20 PM, Xiaomin Yue wrote:



  
  Thanks for your response.  The command you gave
will generate a new function data with the spatial resolution of
the anatomical data, which in my case is much higher than those
of functional data.  What i want is to generate a new functional
data in the anatomical space, with spatial resolution of the
original function data. Is it possible?  I thought that
--fstalres would give me a choice to keep the spatial resolution
of the original function data. 



Xiaomin 

  

  
Date: Tue, 14 Apr 2015 18:22:00 -0400

From: gr...@nmr.mgh.harvard.edu

To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] mri_vol2vol



sorry, I don't understand. fstal would imply that you want
talairach space. If you want to map the functional into the
anatomical space, then

mri_vol2vol --mov res-001.nii  --o res-001.t1.space.nii
--reg register.dof6.dat --fstarg







On 4/14/15 11:36 AM, Xiaomin
      Yue wrote:



  
  Hi Doug,



I like to convert a native functional data into the
  anatomical space using mri_vol2vol with --fstal, so
  that the resample data has same spatial resolution as
  the original function data.  However, mri_vol2vol give
  a error: --fstal unknown.  I also tried using
  --fstalres as suggested in the help document, with
  same error.  I am using fs5.3.  the command is:
  mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5 --o
  res-001.t1.space.nii --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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Compliance HelpLine at
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Re: [Freesurfer] mri_vol2vol

[Xiaomin Yue]

Because resampling from 1.5 to 0.25 will generate a huge data.  
Xiaomin

Date: Wed, 15 Apr 2015 09:11:10 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol


  

  
  
But why do you need to have the same resolution as the original
functional? 



On 4/14/15 10:30 PM, Xiaomin Yue wrote:



  
  yes, that's precisely what I want.  the reason is
the following.  A subject was scanned multiple times across days
with slightly different slice position for each time.  What I
need is to extract a peak response when a stimuli was presented.
  In order to make the voxels match from one scan to another, I
thought that all scans have to be in same space, so that the
data extracted for a voxel from different scans match.   Could
there be a better way to do this?



Thanks,
Xiaomin

  

  
Date: Tue, 14 Apr 2015 21:08:15 -0400

From: gr...@nmr.mgh.harvard.edu

To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] mri_vol2vol





So you want it to be in a volume with field of view 256mm in
all three dimensions, but the voxel size to be that of the
functional data? It is possible to do, but not easy to set
up. Can you say why you would want to do that?





On 4/14/15 8:20 PM, Xiaomin
      Yue wrote:



  
  Thanks for your response.  The command you
gave will generate a new function data with the spatial
resolution of the anatomical data, which in my case is
much higher than those of functional data.  What i want
is to generate a new functional data in the anatomical
space, with spatial resolution of the original function
data. Is it possible?  I thought that --fstalres would
give me a choice to keep the spatial resolution of the
original function data. 



Xiaomin 

  

  
Date: Tue, 14 Apr 2015
18:22:00 -0400

From: gr...@nmr.mgh.harvard.edu

To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] mri_vol2vol



sorry, I don't understand. fstal would imply that
you want talairach space. If you want to map the
functional into the anatomical space, then

mri_vol2vol --mov res-001.nii  --o
res-001.t1.space.nii --reg register.dof6.dat
--fstarg







On 4/14/15 11:36 AM,
      Xiaomin Yue wrote:



  
  Hi Doug,



I like to convert a native functional data
  into the anatomical space using mri_vol2vol
  with --fstal, so that the resample data has
  same spatial resolution as the original
  function data.  However, mri_vol2vol give a
  error: --fstal unknown.  I also tried using
  --fstalres as suggested in the help document,
  with same error.  I am using fs5.3.  the
  command is: mdi_vol2vol --mov res-001.nii
  --fstarg --fstal 1.5 --o res-001.t1.space.nii
  --reg register.dof6.dat



Thanks,
Xiaomin 
  
  

  
  

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[Freesurfer] a mkanalysis-sess question

[Xiaomin Yue]

Hi, 

 

I have a question related to how to make an appropriate design
matrix using fs-fast 5.3.   Subjects’ eye
movement was collected during an experiment.  Then, the data has been 
transformed to a continuous
variable with a number for each TR.  The
better fixation performance has higher number. 
For example, a number would be 0 if subjects look away from a target
within a TR.  In ideal situation,
subjects should keep his eyes on target all the time, so the variable should be
1 for all TR.  According to
mkanalysis-sess documents, it seems that there are three different ways to take
into account of eye fixation performance: 1) use it as an external task 
regressor;
2) use it as a weight in the paradigm file (the fourth column); 3) use it as a
nuisance regressor.  My question is what’s
the difference between the three methods? 
In my situation, which one is the best choice in my situation?
I hope the question is clear.  Thanks so much for your help.
Xiaomin

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Re: [Freesurfer] a mkanalysis-sess question

[Xiaomin Yue]

Hi Doug,
Thanks for your response.  I want to treat it as a nuisance variable.  If so, 
should the #3 is best choice?
Xiaomin

Date: Sun, 3 May 2015 11:06:01 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] a mkanalysis-sess question


  

  
  


#1 and #3 are basically the same. If used as a task regressor, then
a contrast for it will be created. #2 is a parametric modulation.
Probably not what you want but see
http://freesurfer.net/fswiki/FsFastParametricModulation



Do you want to treat it as  a nuisance variable or task? In any
event, I would probably recode it to make fixation=0 and
non-fixation something else





On 5/2/15 5:34 PM, Xiaomin Yue wrote:



  
  




Hi, 
 
I have a question related to how to make an
  appropriate design
  matrix using fs-fast 5.3.   Subjects’ eye
  movement was collected during an experiment.  Then, the data
  has been transformed to a continuous
  variable with a number for each TR.  The
  better fixation performance has higher number. 
  For example, a number would be 0 if subjects look away from a
  target
  within a TR.  In ideal situation,
  subjects should keep his eyes on target all the time, so the
  variable should be
  1 for all TR.  According to
  mkanalysis-sess documents, it seems that there are three
  different ways to take
  into account of eye fixation performance: 1) use it as an
  external task regressor;
  2) use it as a weight in the paradigm file (the fourth
  column); 3) use it as a
  nuisance regressor.  My question is what’s
  the difference between the three methods? 
  In my situation, which one is the best choice in my situation?



I hope the question is clear.  Thanks so
  much for your help.



Xiaomin

 
  

  
  

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[Freesurfer] out of memory, fast_selxavg3.m

[Xiaomin Yue]

Hi,   
I hope that I can get some answers for the question that has been asked 
previously.   I am analyzing a large dataset, which has 28917 time points.  
Although our server has 128G memory, it is still no enough to process the 
dataset using fsfast 5.3.   One solution I can come up is to process each voxel 
independently using a loop in matlab, which seems could be working with our 
server.  My question is: could this be achievable by using design matrix 
generated by fsfast and matlab regress function?   Or should I use the 
something else other than the design matrix (Xtmp.mat) to do GLM? 
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Re: [Freesurfer] a mkanalysis-sess question

[Xiaomin Yue]

Thanks

Xiaomin




On Sun, May 3, 2015 at 8:55 AM -0700, "Douglas Greve" 
 wrote:
If you just want to exclude those time points then you can use a time
point exclude file. To do this, create a text file with the time in
seconds of the time points you want to exclude (t=0 is first time
point), put this file in the run folder (where the raw data is) then
when making the analysis, specify -tpexclude filename. If you want to
create a nuisance regressor, then create a text file with a value for
each time point and put it in the run folder then run mkanalysis-sess
with -nuisreg filename 1

doug

On 5/3/15 11:17 AM, Xiaomin Yue wrote:
> Hi Doug,
>
> Thanks for your response.  I want to treat it as a nuisance variable.
>  If so, should the #3 is best choice?
>
> Xiaomin
>
> 
> Date: Sun, 3 May 2015 11:06:01 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] a mkanalysis-sess question
>
>
> #1 and #3 are basically the same. If used as a task regressor, then a
> contrast for it will be created. #2 is a parametric modulation.
> Probably not what you want but see
> http://freesurfer.net/fswiki/FsFastParametricModulation
>
> Do you want to treat it as  a nuisance variable or task? In any event,
> I would probably recode it to make fixation=0 and non-fixation
> something else
>
>
> On 5/2/15 5:34 PM, Xiaomin Yue wrote:
>
> Hi,
>
> I have a question related to how to make an appropriate design
> matrix using fs-fast 5.3.   Subjects’ eye movement was collected
> during an experiment.  Then, the data has been transformed to a
> continuous variable with a number for each TR.  The better
> fixation performance has higher number.  For example, a number
> would be 0 if subjects look away from a target within a TR.  In
> ideal situation, subjects should keep his eyes on target all the
> time, so the variable should be 1 for all TR.  According to
> mkanalysis-sess documents, it seems that there are three different
> ways to take into account of eye fixation performance: 1) use it
> as an external task regressor; 2) use it as a weight in the
> paradigm file (the fourth column); 3) use it as a nuisance
> regressor.  My question is what’s the difference between the three
> methods?  In my situation, which one is the best choice in my
> situation?
>
>
> I hope the question is clear.  Thanks so much for your help.
>
>
> Xiaomin
>
>
>
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>
>
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Re: [Freesurfer] out of memory, fast_selxavg3.m

[Xiaomin Yue]

Thanks for your suggestion.  That doesn't work.

Xiaomin




On Sun, May 3, 2015 at 8:50 AM -0700, "Arman Eshaghi"  
wrote:
Does this happen with all parts your analysis (lh, rh, and mni305)? or only
mni305 volumetric analysis? Because if it happens with only the volumetric
part, you can resample with 3 mm (instead of 2 or 1mm).

On Sun, May 3, 2015 at 7:57 PM, Xiaomin Yue  wrote:

> Hi,
>
> I hope that I can get some answers for the question that has been asked
> previously.   I am analyzing a large dataset, which has 28917 time points.
> Although our server has 128G memory, it is still no enough to process the
> dataset using fsfast 5.3.   One solution I can come up is to process each
> voxel independently using a loop in matlab, which seems could be working
> with our server.  My question is: could this be achievable by using design
> matrix generated by fsfast and matlab regress function?   Or should I use
> the something else other than the design matrix (Xtmp.mat) to do GLM?
>
> Thanks for your help!
> Xiaomin
>
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Re: [Freesurfer] a mkanalysis-sess question

[Xiaomin Yue]

I am having another problem with mkanalysis-sess, here is my command: 
mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native -paradigm 
human_curv.par -event-related -gammafit 2.25 1.25 -refeventdur 16 -polyfit 2 
-TR 2 -nconditions 8 -fsd bold -per-run -tpexclude xy_tpexclude.
it got erros as running selxxavg3-sess.   It turns out that the analysis.info 
under volanalysis directory has the following "nurisreg mcextreg 3".  Since the 
data was processing as per run, there is no mcextreg, but mcprextreg file.  The 
analysis file generated for surface based analysis has correct analysis.info 
with mcprextreg.   I am using fs5.3.  Did I do anything wrong with the 
mkanalysis-sess command?
Thanks,Xiaomin




On Sun, May 3, 2015 at 8:55 AM -0700, "Douglas Greve" 
 wrote:




If you just want to exclude those time points then you can use a time point 
exclude file. To do this, create a text file with the time in seconds of the 
time points you want to exclude (t=0 is first time point), put this
 file in the run folder (where the raw data is) then when making the analysis, 
specify -tpexclude filename. If you want to create a nuisance regressor, then 
create a text file with a value for each time point and put it in the run 
folder then run mkanalysis-sess
 with -nuisreg filename 1



doug



On 5/3/15 11:17 AM, Xiaomin Yue wrote:



Hi Doug,



Thanks for your response.  I want to treat it as a nuisance variable.  If so, 
should the #3 is best choice?



Xiaomin





Date: Sun, 3 May 2015 11:06:01 -0400

From: 
gr...@nmr.mgh.harvard.edu

To: 
freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] a mkanalysis-sess question





#1 and #3 are basically the same. If used as a task regressor, then a contrast 
for it will be created. #2 is a parametric modulation. Probably not what you 
want but see

http://freesurfer.net/fswiki/FsFastParametricModulation



Do you want to treat it as  a nuisance variable or task? In any event, I would 
probably recode it to make fixation=0 and non-fixation something else





On 5/2/15 5:34 PM, Xiaomin Yue wrote:




Hi, 
 
I have a question related to how to make an appropriate design matrix using 
fs-fast 5.3.   Subjects’ eye movement was collected during an experiment.  
Then, the data has been transformed to a continuous variable with a number for 
each
 TR.  The better fixation performance has higher number.  For example, a number 
would be 0 if subjects look away from a target within a TR.  In ideal 
situation, subjects should keep his eyes on target all the time, so the 
variable should be 1 for all TR.  According
 to mkanalysis-sess documents, it seems that there are three different ways to 
take into account of eye fixation performance: 1) use it as an external task 
regressor; 2) use it as a weight in the paradigm file (the fourth column); 3) 
use it as a nuisance regressor. 
 My question is what’s the difference between the three methods?  In my 
situation, which one is the best choice in my situation?



I hope the question is clear.  Thanks so much for your help.



Xiaomin



 

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[Freesurfer] beta value

[Xiaomin Yue]

Hi,
During the processing of functional data, can fsfast generate outputs of the 
significants for each beta values modeled in the design matrix?
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Re: [Freesurfer] beta value

[Xiaomin Yue]

Do you mean by contrasting a condition vs fixation?

Xiaomin




On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve" 
 wrote:
Yes, but you have to set up the contrasts, it won't do it automatically

On 5/16/15 10:48 PM, Xiaomin Yue wrote:
> Hi,
>
> During the processing of functional data, can fsfast generate outputs
> of the significants for each beta values modeled in the design matrix?
>
> Thanks,
> XIaomin
>
>
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Re: [Freesurfer] beta value

[Xiaomin Yue]

Thanks

Xiaomin




On Mon, May 18, 2015 at 9:15 AM -0700, "Douglas Greve" 
 wrote:
yes

On 5/18/15 10:38 AM, Xiaomin Yue wrote:
> Do you mean by contrasting a condition vs fixation?
>
> Xiaomin
>
>
>
>
> On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Yes, but you have to set up the contrasts, it won't do it automatically
>
> On 5/16/15 10:48 PM, Xiaomin Yue wrote:
>> Hi,
>>
>> During the processing of functional data, can fsfast generate outputs
>> of the significants for each beta values modeled in the design matrix?
>>
>> Thanks,
>> XIaomin
>>
>>
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[Freesurfer] fast_selxavg3.m

[Xiaomin Yue]

Hi,

I am using v5.3 fsfast to analyze a function data.  The sexlavg3-sess had this 
error: ConList=splitstring('XXX') Error: A matlab string constant is not 
terminated properly (where 'XXX represents contrasts generated using 
mkcontrast-sess).; | Error: unexpected matlab expression; Error: the input 
character is not valid in matalb statements or expressions.  The analysis went 
on to next step, but it ended with error ConList is undefined variable.  My 
analysis has a lot of contrasts (more than 900).  Any suggestions?  

Thanks,
Xiaomin 
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Re: [Freesurfer] fast_selxavg3.m

[Xiaomin Yue]

Thanks for responding.  There is no contrast name with space in them.  I will 
test if there is a critical number causing fail.   

Xiaomin 

_
From: Douglas N Greve 
Sent: Tuesday, July 14, 2015 1:15 PM
Subject: Re: [Freesurfer] fast_selxavg3.m
To:  


   not sure what to tell you. Is there a critical number that 
causes it to
 fail? Eg, 400? Or a particular contrast name? I assume that none of the
 contrast names have a space in them.   

 On 07/09/2015 10:06 AM, Xiaomin Yue wrote:   
 > Hi,   
 >   
 > I am using v5.3 fsfast to analyze a function data.  The sexlavg3-sess
 > had this error: ConList=splitstring('XXX') Error: A matlab string
 > constant is not terminated properly (where 'XXX represents contrasts
 > generated using mkcontrast-sess).; | Error: unexpected matlab
 > expression; Error: the input character is not valid in matalb
 > statements or expressions.  The analysis went on to next step, but it
 > ended with error ConList is undefined variable.  My analysis has a lot
 > of contrasts (more than 900). Any suggestions?   
 >   
 > Thanks,   
 > Xiaomin   
 >   
 >   
 > ___   
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 gr...@nmr.mgh.harvard.edu   
 Phone Number: 617-724-2358   
 Fax: 617-726-7422   

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[Freesurfer] Fafast and matlab question

[Xiaomin Yue]

Dear all,  
I loaded the t.nii under a contrast directory in freeview, and then loaded the 
t.nii to matlab using MRIread.  When I checked the t value for a point, such as 
32, 38, 32, the value is 3.96.  Then I got value from the same point (32, 38, 
32) in matlab,  I got a different t value.  I also tried value from (38, 32, 
32) in matlab, the value is different from the value displayed in freeview.  
Should the value displayed in the freeview be the same as it loaded in matlab?  
Any ideas?
Thanks, 
Xiaomin 

_
From: Park, Jung Mi 
Sent: Monday, July 27, 2015 6:30 PM
Subject: [Freesurfer] recon-all error_cannot find or read   
transforms/talairach.m3z
To:  


 Hello Freesurfer expert

Running recon-all abruptly stopped with this error message at NMR 
center;   
   mri_ca_register -invert-and-save transforms/talairach.m3z    
   
   Loading, Inverting, Saving, Exiting ...  Reading 
transforms/talairach.m3z   ERROR: cannot find or read 
transforms/talairach.m3z  ERROR: mri_ca_register with non-zero 
status 0recon-all -s AD0701IB exited with ERRORS   
1) subjectname 
autofs/cluster/catanagp/users/jumi/subjects/anat/AD0701IB   2) Env: 
source /usr/local/freesurfer/nmr-stable53-env   
    JMi___
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[Freesurfer] mkanalysis-sess, timewindow

[Xiaomin Yue]

Hi, 

I set timewindow to 10 in the mkanalysis-sess.  When I loaded Xtmp.mat in to 
maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 
points, which is corrected because of psdwin is [0 40 2].   Should the psdwin 
be [0 10 2]?  No matter what value I put in to timewindow, the psdwin is alway 
[0 40 2].  Is it correct?  If so, what aspect of design matrix does the 
timewidow have effect on? 

thanks very much for your help.  

Xiaomin
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Re: [Freesurfer] mkanalysis-sess, timewindow

[Xiaomin Yue]

if it is useful,  i can upload the Xtmp.mat file.

thanks,
Xiaomin

> Date: Thu, 6 Aug 2015 10:36:50 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mkanalysis-sess, timewindow
> 
> it would be helpful to have your mkanalysis-sess command
> 
> On 08/05/2015 04:17 PM, Xiaomin Yue wrote:
> > Hi,
> >
> > I set timewindow to 10 in the mkanalysis-sess.  When I loaded Xtmp.mat 
> > in to maltlab, then plot(flac.ev(2).Xirf), the size of the 
> > flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is 
> > [0 40 2].   Should the psdwin be [0 10 2]?  No matter what value I put 
> > in to timewindow, the psdwin is alway [0 40 2].  Is it correct?  If 
> > so, what aspect of design matrix does the timewidow have effect on?
> >
> > thanks very much for your help.
> >
> > Xiaomin
> >
> >
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> -- 
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> 
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Re: [Freesurfer] mkanalysis-sess, timewindow

[Xiaomin Yue]

Hi, Doug,

Thanks for your response.  Here is my command:  mkanalysis-sess -fsd bold 
-paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 
-timewindow 10 -TER 2 -no-inorm -delay 0 -polyfit 3 -gammafit 0 8 -gammaexp 0.3 
-nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. 
-ncondition 940 -funcstem f.mc.perrun.so.nativespace.nii -abcbins 3 -analysis 
perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native -force 
-tpexclude xy_eye_tpe -runlistfile xyrunlist

After running selxavg3-sess, I loaded Xtmp.mat into matlab.  The psdwin under 
flac.ev(2) is [0 40 2].  I also tried to change the timewindow to 20 in the 
mkanalysis-sess, the psdwin is still [0 40 2].  If I changed the TER to 0.5 , 
the psdwin is [0 40 0.5] no matter timewindow is 10 or 20.  

Thanks for looking into this,
Xiaomin

> Date: Thu, 6 Aug 2015 10:36:50 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mkanalysis-sess, timewindow
> 
> it would be helpful to have your mkanalysis-sess command
> 
> On 08/05/2015 04:17 PM, Xiaomin Yue wrote:
> > Hi,
> >
> > I set timewindow to 10 in the mkanalysis-sess.  When I loaded Xtmp.mat 
> > in to maltlab, then plot(flac.ev(2).Xirf), the size of the 
> > flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is 
> > [0 40 2].   Should the psdwin be [0 10 2]?  No matter what value I put 
> > in to timewindow, the psdwin is alway [0 40 2].  Is it correct?  If 
> > so, what aspect of design matrix does the timewidow have effect on?
> >
> > thanks very much for your help.
> >
> > Xiaomin
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mkanalysis-sess, timewindow

[Xiaomin Yue]

The second number in the psdwin parameter is set as 40 in the flac_ev_parse.m 
for 'spmhrf', 'gamma', 'fslgamma'.  It seems that timewindow has no effect on 
hrf?   why is psdwin 40?

Thanks,
Xiaomin

From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 6 Aug 2015 15:17:04 -0400
Subject: Re: [Freesurfer] mkanalysis-sess, timewindow




if it is useful,  i can upload the Xtmp.mat file.

thanks,
Xiaomin

> Date: Thu, 6 Aug 2015 10:36:50 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mkanalysis-sess, timewindow
> 
> it would be helpful to have your mkanalysis-sess command
> 
> On 08/05/2015 04:17 PM, Xiaomin Yue wrote:
> > Hi,
> >
> > I set timewindow to 10 in the mkanalysis-sess.  When I loaded Xtmp.mat 
> > in to maltlab, then plot(flac.ev(2).Xirf), the size of the 
> > flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is 
> > [0 40 2].   Should the psdwin be [0 10 2]?  No matter what value I put 
> > in to timewindow, the psdwin is alway [0 40 2].  Is it correct?  If 
> > so, what aspect of design matrix does the timewidow have effect on?
> >
> > thanks very much for your help.
> >
> > Xiaomin
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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> 
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] mkanalysis-sess, timewindow

[Xiaomin Yue]

  

  
  
The psd window is only really relevant for FIR analyses. You are
assuming a shape to the HRF (a gamma function), and so FSFAST hard
codes the psdwin. If you really want to force it to change, put
-timewindow after -gammafit

On 8/6/15 4:38 PM, Xiaomin Yue wrote:


  
  The second number in the psdwin parameter is set as
40 in the flac_ev_parse.m for 'spmhrf', 'gamma', 'fslgamma'.  It
seems that timewindow has no effect on hrf?   why is psdwin 40?

Thanks,
Xiaomin


  From: yu...@hotmail.com
  To: freesurfer@nmr.mgh.harvard.edu
  Date: Thu, 6 Aug 2015 15:17:04 -0400
  Subject: Re: [Freesurfer] mkanalysis-sess, timewindow
  
  
  if it is useful,  i can upload the Xtmp.mat
file.

thanks,
Xiaomin

 Date: Thu, 6 Aug 2015 10:36:50 -0400
   From: gr...@nmr.mgh.harvard.edu
   To: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] mkanalysis-sess, timewindow
   
   it would be helpful to have your mkanalysis-sess
  command
   
   On 08/05/2015 04:17 PM, Xiaomin Yue wrote:
Hi,
   
I set timewindow to 10 in the mkanalysis-sess.
  When I loaded Xtmp.mat 
in to maltlab, then plot(flac.ev(2).Xirf), the
  size of the 
flac.ev(2).Xirf is 20 points, which is corrected
  because of psdwin is 
[0 40 2]. Should the psdwin be [0 10 2]? No
  matter what value I put 
in to timewindow, the psdwin is alway [0 40 2].
  Is it correct? If 
so, what aspect of design matrix does the
  timewidow have effect on?
   
thanks very much for your help.
   
Xiaomin
   
   
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   -- 
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   MGH-NMR Center
   gr...@nmr.mgh.harvard.edu
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   Fax: 617-726-7422
   
   Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
   FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
   www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
   
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[Freesurfer] selxavg3-sess, -svres

[Xiaomin Yue]

Hi Doug,
In order to understand my data better, I did the following analysis.  First, I 
did a full model analysis with all stimuli conditions included in the analysis 
using: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par 
-event-related -refeventdur 1 -no-inorm -delay 0 -polyfit 3 -gammafit 0 8 
-gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 
1 -TR 2. -nconditions 940 -funcstem f.mc.perrun.so.nativespace -acfbins 3 
-analysis perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native 
-force -tpexclude xy_eye_tpe -runlistfile xyrunlist.  Then I run: selxavg3-sess 
-s beck -d . -analysis  perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier 
-no-preproc -no-con-ok -overwrite -svres
second, I did a analysis without the stimuli conditions: mkanalysis-sess -fsd 
bold -paradigm xy_mky_category_eye_weights.par -notask -no-inorm -delay 0  
-nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. 
-funcstem f.mc.perrun.so.nativespace -acfbins 3 -analysis 
NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native -force 
-tpexclude xy_eye_tpe -runlistfile xyrunlist.  Then, I runselxavg3-sess -s beck 
-d . -analysis  NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier 
-no-preproc -no-con-ok -overwrite -svres
After that, I loaded the residuals (res-00x.nii under the res directories) 
generated from the full model analysis and those from the no task analysis into 
the matlab.  I expected that the results should be different, but the residuals 
from the two analysis are almost identical (correlation is 0.98) for a voxel 
where the stimuli from different conditions should cause significant response 
difference.   Then, I tried to generated the residual from the full model 
analysis by  real signal -  design matrix (loaded from X.mat) *beta values 
(loaded into matlab from beta.nii).  This residual is different from the 
residual of the NO task analysis.  My question is why the residual from the two 
different analysis generated by fsfast are same?  Are my commands wrong?  Or 
the model is wrong?  Second, it is possible to generate raw residuals without 
some kind of normalization?
Thanks very much for your help!
Xiaomin   ___
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Re: [Freesurfer] selxavg3-sess, -svres

[Xiaomin Yue]

Hi Doug,
thanks for the response.  The residual from unwhittening data is the same as 
those produced by the full model.  One more question.  I transferred the 
functional data from functional space to the anatomical space using mri_vol2vol 
without resample: mri_vol2vol --reg register.dof6.dat --mov f.nii --o 
test.noresample.nii --fstarg orig.1p5.mgz --no-save-reg --no-resample.  From 
the wiki, i know that resample parameter will change vox2ras only without 
touching the raw data.  When selxavg3-sess processes the functional data, does 
it resample test.nosample.nii so that voxles from a run to another would 
matches?  The reason I am asking is that my functional data has slight 
different slice position, I like to resample the raw data as little as possible.
Thanks,Xiaomin

Date: Mon, 17 Aug 2015 11:12:35 -0400
From: gr...@nmr.mgh.harvard.edu
To: yu...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess, -svres


  

  
  
They are not the "same". As you point out they have a correlation of
.98, not 1.0. What you are discovering is the inconvenient truth
that task signal accounts for a very small proportion of variation.
Welcome to fMRI:). I think the reason why the residual does not
equal y - X*beta is that they are whitened. Try it with whitening
turned off and see if you get the same (identical) result.

doug



On 8/9/15 10:50 PM, Xiaomin Yue wrote:



  
  Hi Doug,




In order to understand my data better, I did the following
  analysis.  First, I did a full model analysis with all stimuli
  conditions included in the analysis using: mkanalysis-sess
  -fsd bold -paradigm xy_mky_category_eye_weights.par
  -event-related -refeventdur 1 -no-inorm -delay 0 -polyfit 3
  -gammafit 0 8 -gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg
  eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. -nconditions
  940 -funcstem f.mc.perrun.so.nativespace -acfbins 3 -analysis
  perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run
  -native -force -tpexclude xy_eye_tpe -runlistfile xyrunlist.
   Then I run: selxavg3-sess -s beck -d . -analysis  
perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-no-preproc -no-con-ok -overwrite -svres


  
second, I did a analysis without
  the stimuli conditions: mkanalysis-sess
-fsd bold -paradigm xy_mky_category_eye_weights.par -notask
-no-inorm -delay 0  -nuisreg mcprextreg 3 -nuisreg
eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. -funcstem
f.mc.perrun.so.nativespace -acfbins 3 -analysis
NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-per-run -native -force -tpexclude xy_eye_tpe -runlistfile
xyrunlist.  Then, I runselxavg3-sess
-s beck -d . -analysis  
NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier
-no-preproc -no-con-ok -overwrite -svres


  
After that, I loaded the residuals
(res-00x.nii under the res directories) generated from the
full model analysis and those from the no task
  analysis into the matlab.  I expected that the results should
  be different, but the residuals from the two analysis are
  almost identical (correlation is 0.98) for a voxel where the
  stimuli from different conditions should cause significant
  response difference.   Then, I tried to
generated the residual from the full model analysis by  real
signal -  design matrix (loaded from X.mat) *beta values
(loaded into matlab from beta.nii).  This residual is
different from the residual of the NO task analysis.  My
question is why the residual from the two different analysis
generated by fsfast are same?  Are my commands wrong?  Or
the model is wrong?  Second, it is possible to generate raw
residuals without some kind of normalization?


  
Thanks very much for your help!


  
Xiaomin
  



  


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[Freesurfer] mri_glmfit-sim error

[Xiaomin Yue]

Hi,
I got this error when run mri_glmfit-sim: missing name for redirect.  I am 
running freesurfer 5.3.  the command is: mri_glmfit --glmdir ces.nii --cache 2 
--sim-sign .  The ces.nii was generated from group level analysis 
(isxconcat-sess).  
Thanks for your help.
Xiaomin   ___
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Re: [Freesurfer] mri_glmfit-sim error

[Xiaomin Yue]

Thanks

Xiaomin




On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve" 
 wrote:
Use "abs" not ""

On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
>  I am running freesurfer 5.3.  the command is: mri_glmfit --glmdir
> ces.nii --cache 2 --sim-sign .  The ces.nii was generated from
> group level analysis (isxconcat-sess).
>
> Thanks for your help.
>
> Xiaomin
>
>
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[Freesurfer] Retinotopy questions

[Xiaomin Yue]

Hi,
I am running a retinotopy analysis using fsfast 5.3.  The design has 15 TR 
blank before and after wedge presented for 30 TR with 7 repeats, and ring 
presented  for 24 TR with 7 repeats.  Here is my analysis: mkanalysis -s vz -a 
rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48 -paradigm 
rtopy.par.
The data doesn't look right.  I assume that the analysis does require the 
stimuli presentation as a full circle, which means that the last 15 TR blank 
was accounted as the stimuli presentation time. If I am correct,  is there 
simple way to take care of it in mkanalysis-sess? Second, the ring and wedge 
were presented in different frequency. It seems that the anslysis-sess does not 
take this into account in the current configration. Is there a way to specify 
this? 
Thanks very much for the help. 
Xiaomin 
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[Freesurfer] a retinotopy question

[Xiaomin Yue]

Hi All,

During the experiment, a wedge was presented clockwise, starting from the low 
vertical meridian, and a ring was presented from center to peripheral.  The 
analysis done successfully with fs5.3 generated values of polar angle and 
eccentricity for each voxel.  For example, the voxel A has polar: 1.79, and 
eccen: 4.8.  From those values, can I determine where in the visual field the 
voxel A represent?  If so, how?

Thanks,
Xiaomin
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[Freesurfer] B1 correction

[Xiaomin Yue]

Hi,
B1 field correction was collected during the scan.  My question is how it can 
be used in the surface reconstruction?
Thanks,
Xiaomin Yue   ___
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[Freesurfer] fsfast question

[Xiaomin Yue]

Hi,   
The analysis necessary to my study is to run some analysis on the raw time 
course data.  Before working on the raw time course data, it is necessary to 
remove linear drifting, mean, and head motion.  Can I just specify those 
parameters without having conditions in the steps of generating design matrix?  
If so, what command should be used?
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Re: [Freesurfer] B1 correction

[Xiaomin Yue]

Hi Bruce,
Thanks for your response.  It is B0 normalization scan.  What it does is to get 
an homogeneity image, which could be used to normalize the MRRAGE image by 
dividing it.  Is there an build in function in freesurfer to do this operation?
Thanks,Xiaomin 

Date: Mon, 24 Mar 2014 12:42:52 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
can you be more specific? What kind of B1 field map did you collect? Do 
you mean B1 transmit or receive?
 
cheers
Bruce
On Mon, 24 Mar 2014, Xiaomin Yue wrote:
 
> Hi,
> 
> B1 field correction was collected during the scan.  My question is how it can 
> be used in the surface reconstruction?
> 
> Thanks,
> 
> Xiaomin Yue
> 
>

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Re: [Freesurfer] B1 correction

[Xiaomin Yue]

thanks.
Xiaomin Yue

Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.
 
I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.
 
cheers Bruce
 
 
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
 
> Hi Bruce,
> Thanks for your response.  It is B0 normalization scan.  What it does is to
> get an homogeneity image, which could be used to normalize the MRRAGE image
> by dividing it.  Is there an build in function in freesurfer to do this
> operation?
> 
> Thanks,
> Xiaomin 
> 
> Date: Mon, 24 Mar 2014 12:42:52 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] B1 correction
> 
> Hi Xiaomin
> 
> can you be more specific? What kind of B1 field map did you collect? Do 
> you mean B1 transmit or receive?
> 
> cheers
> Bruce
> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
> 
> > Hi,
> > 
> > B1 field correction was collected during the scan.  My question is how it 
> can be used in the surface reconstruction?
> > 
> > Thanks,
> > 
> > Xiaomin Yue
> > 
> >
> 
> ___ Freesurfer mailing list
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> 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
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> and properly dispose of the e-mail.
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Re: [Freesurfer] fsfast question

[Xiaomin Yue]

I like to regress out the linear drift, mean, and head motion generated by the 
motion correction step of fsfast from the raw time course only.  Is it possible 
using fsfast?
Xiaomin

> Date: Wed, 26 Mar 2014 11:28:57 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fsfast question
> 
> 
> Sorry, I don't follow what you are asking. FSFAST does not do any drift 
> removal from the raw data, all of that is in the design matrix
> doug
> 
> On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> > Hi,
> >
> > The analysis necessary to my study is to run some analysis on the raw 
> > time course data.  Before working on the raw time course data, it is 
> > necessary to remove linear drifting, mean, and head motion.  Can I 
> > just specify those parameters without having conditions in the steps 
> > of generating design matrix?  If so, what command should be used?
> >
> > Thanks,
> > Xiaomin Yue
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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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.
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Re: [Freesurfer] B1 correction

[Xiaomin Yue]

Hi Bruce,
You are correct that it is B1.  How could I incorporate this data into the 
reconstruction stream?
Thanks,Xiaomin

From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] B1 correction
Date: Wed, 26 Mar 2014 13:54:37 -0400




thanks.
Xiaomin Yue

Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.
 
I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.
 
cheers Bruce
 
 
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
 
> Hi Bruce,
> Thanks for your response.  It is B0 normalization scan.  What it does is to
> get an homogeneity image, which could be used to normalize the MRRAGE image
> by dividing it.  Is there an build in function in freesurfer to do this
> operation?
> 
> Thanks,
> Xiaomin 
> 
> Date: Mon, 24 Mar 2014 12:42:52 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] B1 correction
> 
> Hi Xiaomin
> 
> can you be more specific? What kind of B1 field map did you collect? Do 
> you mean B1 transmit or receive?
> 
> cheers
> Bruce
> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
> 
> > Hi,
> > 
> > B1 field correction was collected during the scan.  My question is how it 
> can be used in the surface reconstruction?
> > 
> > Thanks,
> > 
> > Xiaomin Yue
> > 
> >
> 
> ___ Freesurfer mailing list
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> 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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Re: [Freesurfer] fsfast question

[Xiaomin Yue]

Thanks very much,  i will try it.
Xiaomin
From: cschwie...@mail.rockefeller.edu
Date: Wed, 26 Mar 2014 14:56:26 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question

you could try to run mkanalysis-sess with -notask and your nuisance regressors 
specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to 
save the residuals. 
maybe that solves your problem? 


caspar


2014-03-26 14:38 GMT-04:00 Douglas N Greve :


No, sorry

On 03/26/2014 01:54 PM, Xiaomin Yue wrote:

> I like to regress out the linear drift, mean, and head motion

> generated by the motion correction step of fsfast from the raw time

> course only.  Is it possible using fsfast?

>

> Xiaomin

>

> > Date: Wed, 26 Mar 2014 11:28:57 -0400

> > From: gr...@nmr.mgh.harvard.edu

> > To: freesurfer@nmr.mgh.harvard.edu

> > Subject: Re: [Freesurfer] fsfast question

> >

> >

> > Sorry, I don't follow what you are asking. FSFAST does not do any drift

> > removal from the raw data, all of that is in the design matrix

> > doug

> >

> > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:

> > > Hi,

> > >

> > > The analysis necessary to my study is to run some analysis on the raw

> > > time course data. Before working on the raw time course data, it is

> > > necessary to remove linear drifting, mean, and head motion. Can I

> > > just specify those parameters without having conditions in the steps

> > > of generating design matrix? If so, what command should be used?

> > >

> > > Thanks,

> > > Xiaomin Yue

> > >

> > >

> > > ___

> > > Freesurfer mailing list

> > > Freesurfer@nmr.mgh.harvard.edu

> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

> >

> > --

> > Douglas N. Greve, Ph.D.

> > MGH-NMR Center

> > gr...@nmr.mgh.harvard.edu

> > Phone Number: 617-724-2358

> > Fax: 617-726-7422

> >

> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html

> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

> >

> > ___

> > 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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> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--

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MGH-NMR Center

gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422



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[Freesurfer] recon error

[Xiaomin Yue]

Hi, 
I got this error while running recon:  'imgreg_4dfp 
/opt/freesurfer-530/average/711-2C_as_mni_average_305 
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none 
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: 
mpr2mni305 execution aborted
Xiaomin
From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] fsfast question
Date: Wed, 26 Mar 2014 17:03:48 -0400





Thanks very much,  i will try it.
Xiaomin
From: cschwie...@mail.rockefeller.edu
Date: Wed, 26 Mar 2014 14:56:26 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question

you could try to run mkanalysis-sess with -notask and your nuisance regressors 
specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to 
save the residuals. 
maybe that solves your problem? 


caspar


2014-03-26 14:38 GMT-04:00 Douglas N Greve :


No, sorry

On 03/26/2014 01:54 PM, Xiaomin Yue wrote:

> I like to regress out the linear drift, mean, and head motion

> generated by the motion correction step of fsfast from the raw time

> course only.  Is it possible using fsfast?

>

> Xiaomin

>

> > Date: Wed, 26 Mar 2014 11:28:57 -0400

> > From: gr...@nmr.mgh.harvard.edu

> > To: freesurfer@nmr.mgh.harvard.edu

> > Subject: Re: [Freesurfer] fsfast question

> >

> >

> > Sorry, I don't follow what you are asking. FSFAST does not do any drift

> > removal from the raw data, all of that is in the design matrix

> > doug

> >

> > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:

> > > Hi,

> > >

> > > The analysis necessary to my study is to run some analysis on the raw

> > > time course data. Before working on the raw time course data, it is

> > > necessary to remove linear drifting, mean, and head motion. Can I

> > > just specify those parameters without having conditions in the steps

> > > of generating design matrix? If so, what command should be used?

> > >

> > > Thanks,

> > > Xiaomin Yue

> > >

> > >

> > > ___

> > > Freesurfer mailing list

> > > Freesurfer@nmr.mgh.harvard.edu

> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

> >

> > --

> > Douglas N. Greve, Ph.D.

> > MGH-NMR Center

> > gr...@nmr.mgh.harvard.edu

> > Phone Number: 617-724-2358

> > Fax: 617-726-7422

> >

> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html

> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

> >

> > ___

> > 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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> Freesurfer@nmr.mgh.harvard.edu

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gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422



Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

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[Freesurfer] recon error

[Xiaomin Yue]

Hi, 
I got this error while running recon-all :  'imgreg_4dfp 
/opt/freesurfer-530/average/711-2C_as_mni_average_305 
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none 
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: 
mpr2mni305 execution aborted
Any idea what could be the cause?
Thanks,Xiaomin  Yue

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[Freesurfer] recon all with 7T data

[Xiaomin Yue]

I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with 
error:  imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none 
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254.  This seems 
happened for many others.  However, the reconstruction worked fine as using 
data collected from 3T, which means the freesurfer was installed correct, and 
environment settings are correct as well.  Also, the reconstruction on the 7T 
data can go through using additional  parameter: -use-mritotal.  My question is 
how the -use-mritotal parameter would affect final surface?
Thanks for providing your input on this.
Xiaomin Yue
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Re: [Freesurfer] recon all with 7T data

[Xiaomin Yue]

Hi Joe,
Thanks for your response.  For the future reference, it also needs the 
parameter -notal-check, otherwise it will fail again.  Although the 
reconstruction was completed surprisingly without error, a significant amount 
of cortex in the top of the brain was cut off in the brain.mgz file.  It needs 
to be rerun after correcting that error(s).
Xiaomin 

> Date: Tue, 1 Apr 2014 19:52:53 -0400
> From: j...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon all with 7T data
> 
> 
> hi Xiaomin,
> 
> 7T data can sometimes cause Talairach failures with the standard
> registration tools due to the strong bias fields. the Talairach
> transformation is used for identifying seed points, and the -use-mritotal
> flag just specifies that the MINC software will be used for the
> Talairach'ing.
> 
> see this page for more info:
>   http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29
> 
> 
> -jon
> 
> 
> 
> 
> 
> 
> 
> On Fri, 28 Mar 2014, Xiaomin Yue wrote:
> 
> >
> > I tried to do surfer reconstruction (version 5.3) collected in SIEMENS
> > 7T, with error:  imgreg_4dfp
> > /opt/freesurfer-530/average/711-2C_as_mni_average_305
> > /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11
> > none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254.
> > This seems happened for many others.  However, the reconstruction worked
> > fine as using data collected from 3T, which means the freesurfer was
> > installed correct, and environment settings are correct as well.  Also,
> > the reconstruction on the 7T data can go through using additional
> > parameter: -use-mritotal.  My question is how the -use-mritotal
> > parameter would affect final surface?
> > Thanks for providing your input on this.
> > Xiaomin Yue
> >
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> 
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Re: [Freesurfer] recon all with 7T data

[Xiaomin Yue]

Hi Falk,
Thanks for this valuable information.  For sure, I will try it out, and let you 
know how it goes. 
Xiaomin

From: falk.lu...@gmx.net
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 3 Apr 2014 00:32:23 +
Subject: Re: [Freesurfer] recon all with 7T data







Hi Xiaomin,
you could also try to follow the first few steps of the HiresRecon 
(http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The parameters of the 
inhomogeneity correction are optimized for 7T data which should help in 
reducing errors due to strong bias fields.
Best,Falk
Von: Xiaomin Yue
Gesendet: ‎Mittwoch‎, ‎2‎. ‎April‎ ‎2014 ‎15‎:‎23
An: Freesurfer support list
Hi Joe,
Thanks for your response.  For the future reference, it also needs the 
parameter -notal-check, otherwise it will fail again.  Although the 
reconstruction was completed surprisingly without error, a significant amount 
of cortex in the top of the brain was cut off in the brain.mgz file.  It needs 
to be rerun after correcting that error(s).
Xiaomin 

> Date: Tue, 1 Apr 2014 19:52:53 -0400
> From: j...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon all with 7T data
> 
> 
> hi Xiaomin,
> 
> 7T data can sometimes cause Talairach failures with the standard
> registration tools due to the strong bias fields. the Talairach
> transformation is used for identifying seed points, and the -use-mritotal
> flag just specifies that the MINC software will be used for the
> Talairach'ing.
> 
> see this page for more info:
>   http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29
> 
> 
> -jon
> 
> 
> 
> 
> 
> 
> 
> On Fri, 28 Mar 2014, Xiaomin Yue wrote:
> 
> >
> > I tried to do surfer reconstruction (version 5.3) collected in SIEMENS
> > 7T, with error:  imgreg_4dfp
> > /opt/freesurfer-530/average/711-2C_as_mni_average_305
> > /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11
> > none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254.
> > This seems happened for many others.  However, the reconstruction worked
> > fine as using data collected from 3T, which means the freesurfer was
> > installed correct, and environment settings are correct as well.  Also,
> > the reconstruction on the 7T data can go through using additional
> > parameter: -use-mritotal.  My question is how the -use-mritotal
> > parameter would affect final surface?
> > Thanks for providing your input on this.
> > Xiaomin Yue
> >
> ___
> 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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[Freesurfer] freeview and ?h.cortex.patch.flat

[Xiaomin Yue]

Hi,
Can the developmental freeview display ?h.cortex.patch.flat?  I can't find 
answers in the mail list.  If not, is there any way to convert the patch.flat 
to a format freeview can display?
Thanks,Xiaomin___
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Re: [Freesurfer] freeview and ?h.cortex.patch.flat

[Xiaomin Yue]

Thanks

Xiaomin




On Tue, Oct 6, 2015 at 11:35 AM -0700, "Lee Tirrell" 
 wrote:
Hi Xiaomin,

At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview.  You
can load it using tksurfer by loading your subject's inflated surface, then
going to File -> Patch -> LoadPatch and choosing the correct patch.flat file.
These instructions are detailed here:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening

Best,
Lee

On Thu, 1 Oct 2015, Xiaomin Yue wrote:

> Hi,
> Can the developmental freeview display ?h.cortex.patch.flat?  I can't find 
> answers in the mail list.  If not, is there any way to convert the patch.flat 
> to a format freeview can display?
>
> Thanks,
> Xiaomin
>
>
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Re: [Freesurfer] mri_surf2vol {Disarmed}

[Xiaomin Yue]

The voxel size is 1.5mm.  Some of voxels in the gray matter are not included in 
the mask as well.  Why?
Xiaomin




On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" 
 wrote:





That point is fairly close to the pial surface. What is your voxel size?
It will include any voxel even if only a corner of it has some surface
in it.

On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
> here it is.  thanks,
>
>
>
> > To: freesurfer@nmr.mgh.harvard.edu
> > From: gr...@nmr.mgh.harvard.edu
> > Date: Fri, 15 Jan 2016 12:00:02 -0500
> > Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
> >
> > it is hard to tell from that view. Can you click on a point that
> appears
> > to be outside the brain so we can see what it looks like around that
> > point in all three views?
> >
> > On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
> > > Hi All,
> > >
> > > In fs5.3, I tried to generate a volume mask from the pial surface
> > > using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg
> > > $subjsess/bold/001/register.dof6.dat --template
> > > $subjsess/bold/001/template.nii --surf pial --o
> > > $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully.
> > > I doubled check the registration between the EPI and high resolution
> > > T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898.
> > > however, when I overlaid the mask on the T1.mgz, it is clear that
> > > some voxels outside brain are in the mask, and some voxels in the
> gray
> > > matter are not in the mask (see attached figure). Did I use the
> > > function incorrectly?
> > >
> > > Thanks very much for your help.
> > >
> > > Xiaomin
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_surf2vol {Disarmed}

[Xiaomin Yue]

Maybe, I misunderstand it.  Is the pial surface same as gray matter?  If not,  
how could I create a gray matter mask?
Thanks,

Xiaomin




On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" 
 wrote:





I think you could easily hit all those voxels with a 1.5mm voxel size.
Not sure what you are asking about in terms of gray matter.

On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
> The voxel size is 1.5mm.  Some of voxels in the gray matter are not
> included in the mask as well.  Why?
>
> Xiaomin
>
>
>
>
> On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> That point is fairly close to the pial surface. What is your voxel size?
> It will include any voxel even if only a corner of it has some surface
> in it.
>
> On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
> > here it is.  thanks,
> >
> >
> >
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > From: gr...@nmr.mgh.harvard.edu
> > > Date: Fri, 15 Jan 2016 12:00:02 -0500
> > > Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
> > >
> > > it is hard to tell from that view. Can you click on a point that
> > appears
> > > to be outside the brain so we can see what it looks like around that
> > > point in all three views?
> > >
> > > On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
> > > > Hi All,
> > > >
> > > > In fs5.3, I tried to generate a volume mask from the pial surface
> > > > using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg
> > > > $subjsess/bold/001/register.dof6.dat --template
> > > > $subjsess/bold/001/template.nii --surf pial --o
> > > > $subjsess/bold/001/lh.pialmask.vol.nii. The command run
> successfully.
> > > > I doubled check the registration between the EPI and high resolution
> > > > T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898.
> > > > however, when I overlaid the mask on the T1.mgz, it is clear that
> > > > some voxels outside brain are in the mask, and some voxels in the
> > gray
> > > > matter are not in the mask (see attached figure). Did I use the
> > > > function incorrectly?
> > > >
> > > > Thanks very much for your help.
> > > >
> > > > Xiaomin
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > ___
> > > 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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___

Re: [Freesurfer] mri_surf2vol {Disarmed}

[Xiaomin Yue]

Thanks.

Xiaomin




On Fri, Jan 15, 2016 at 11:41 AM -0800, "Douglas N Greve" 
 wrote:





or you can add --fillribbon to your surf2vol command (but the label2vol
method is probably better)

On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
> Maybe, I misunderstand it.  Is the pial surface same as gray matter?
>  If not,  how could I create a gray matter mask?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve"
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I think you could easily hit all those voxels with a 1.5mm voxel size.
> Not sure what you are asking about in terms of gray matter.
>
> On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
> > The voxel size is 1.5mm.  Some of voxels in the gray matter are not
> > included in the mask as well.  Why?
> >
> > Xiaomin
> >
> >
> >
> >
> > On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve"
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > That point is fairly close to the pial surface. What is your voxel size?
> > It will include any voxel even if only a corner of it has some surface
> > in it.
> >
> > On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
> > > here it is.  thanks,
> > >
> > >
> > >
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > From: gr...@nmr.mgh.harvard.edu
> > > > Date: Fri, 15 Jan 2016 12:00:02 -0500
> > > > Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
> > > >
> > > > it is hard to tell from that view. Can you click on a point that
> > > appears
> > > > to be outside the brain so we can see what it looks like around that
> > > > point in all three views?
> > > >
> > > > On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
> > > > > Hi All,
> > > > >
> > > > > In fs5.3, I tried to generate a volume mask from the pial surface
> > > > > using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg
> > > > > $subjsess/bold/001/register.dof6.dat --template
> > > > > $subjsess/bold/001/template.nii --surf pial --o
> > > > > $subjsess/bold/001/lh.pialmask.vol.nii. The command run
> > successfully.
> > > > > I doubled check the registration between the EPI and high
> resolution
> > > > > T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898.
> > > > > however, when I overlaid the mask on the T1.mgz, it is clear that
> > > > > some voxels outside brain are in the mask, and some voxels in the
> > > gray
> > > > > matter are not in the mask (see attached figure). Did I use the
> > > > > function incorrectly?
> > > > >
> > > > > Thanks very much for your help.
> > > > >
> > > > > Xiaomin
> > > > >
> > > > >
> > > > > ___
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > > gr...@nmr.mgh.harvard.edu
> > > > Phone Number: 617-724-2358
> > > > Fax: 617-726-7422
> > > >
> > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > >
> > > > ___
> > > > 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
> > &g

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

Thanks for your response.  I do have contrast at the temporal lobe.   I can 
upload the images to your file drop site if you want.

Xiaomin




On Fri, Apr 15, 2016 at 9:08 AM -0700, "Bruce Fischl" 
 wrote:





Hi Xiaomin

it's really hard to say without seeing more detail in your images. Do you
have contrast in the temporal lobe? Frequently it goes away at 7T due to
dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
things!) expert.

cheers
Bruce


  On Fri, 15 Apr 2016, Xiaomin Yue wrote:

> Hi Bruce,
> I have done the recon-all (fs5.3) with the data collected from a 7T scanner
> using MP2Rage.  The recon went well without problem.  But the the temporal
> reconstruction looks clearly not correct (see attached).  I tried to push
> the pial surface outside by editing the white matter evidenced in the
> attached figures, but has no effect to genera correct pial surface.  I do
> realize that the contrast is low in the anterior temporal lobes.  However, I
> am wondering if there are expert parameters I can use to push the pial
> surface into the right place.  If that isn't a option, can I use some other
> images collected during the MP2rage scan to help the segmentation in the
> anterior temporal lobe?  Those extract scans are: inv1_nd, inv1_phs_nd, ,
> t1, inv2_nd, invs_phas_nd,
>
> thanks very much.
>
> Xiaomin
>
>
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Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

Hi Jon Polimeni,
Do you have any suggestions on the following questions?  
Thanks,Xiaomin

Date: Fri, 15 Apr 2016 12:07:48 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] temporal lobe pial surface problem

Hi Xiaomin
 
it's really hard to say without seeing more detail in your images. Do you 
have contrast in the temporal lobe? Frequently it goes away at 7T due to 
dielectric effects. I'll cc Jon Polimeni who is our 7T (among other 
things!) expert.
 
cheers
Bruce
 
 
  On Fri, 15 Apr 2016, Xiaomin Yue wrote:
 
> Hi Bruce,
> I have done the recon-all (fs5.3) with the data collected from a 7T scanner
> using MP2Rage.  The recon went well without problem.  But the the temporal
> reconstruction looks clearly not correct (see attached).  I tried to push
> the pial surface outside by editing the white matter evidenced in the
> attached figures, but has no effect to genera correct pial surface.  I do
> realize that the contrast is low in the anterior temporal lobes.  However, I
> am wondering if there are expert parameters I can use to push the pial
> surface into the right place.  If that isn't a option, can I use some other
> images collected during the MP2rage scan to help the segmentation in the
> anterior temporal lobe?  Those extract scans are: inv1_nd, inv1_phs_nd, ,
> t1, inv2_nd, invs_phas_nd,  
> 
> thanks very much.
> 
> Xiaomin
> 
>

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Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

Hi Bruce,
the data was uploaded to the ftp site.  The file name is xyueSubj.mgz.
thanks,Xiaomin 

From: fis...@nmr.mgh.harvard.edu
Date: Mon, 18 Apr 2016 22:58:30 -0400
To: freesurfer@nmr.mgh.harvard.edu
CC: macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem

It's tough to make out much from the snapshots, if you upload the entire 
subject dir to our ftp site I'll take a lookCheersBruce
On Apr 18, 2016, at 7:13 PM, Xiaomin Yue  wrote:




Hi Jon,
Thanks for your answers.   There is gray-white contrast in the temporal lobe, 
but same as you said that the gray-csf is low.  Attached is a screenshot.  
let's me know if you need more information. 
Xiaomin
> Date: Mon, 18 Apr 2016 17:43:47 -0400
> From: j...@nmr.mgh.harvard.edu
> To: yu...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
> 
> 
> hi Xiaomin,
> 
> it is tough to say what might be causing the problem since a lot can go
> wrong in the anterior temporal lobes at 7T. you say that your contrast is
> low there? it is possible to have OK gray-white contrast but low overall
> signal levels (so poor gray-CSF contrast) due to dielectric effects as
> bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> region. also some adiabatic inversion pulses break down around the
> temporal poles due to the B0 inhomogeneity around the ear canals. if you
> could send a screenshot we'd have a better chance at diagnosing the
> problem.
> 
> 
> -jon
> 
> 
> 
> 
> On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> 
> > Hi Jon Polimeni,
> > Do you have any suggestions on the following questions?
> > Thanks,Xiaomin
> >
> > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > Hi Xiaomin
> >
> > it's really hard to say without seeing more detail in your images. Do you
> > have contrast in the temporal lobe? Frequently it goes away at 7T due to
> > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > things!) expert.
> >
> > cheers
> > Bruce
> >
> >
> >   On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> >
> > > Hi Bruce,
> > > I have done the recon-all (fs5.3) with the data collected from a 7T 
> > > scanner
> > > using MP2Rage.  The recon went well without problem.  But the the temporal
> > > reconstruction looks clearly not correct (see attached).  I tried to push
> > > the pial surface outside by editing the white matter evidenced in the
> > > attached figures, but has no effect to genera correct pial surface.  I do
> > > realize that the contrast is low in the anterior temporal lobes.  
> > > However, I
> > > am wondering if there are expert parameters I can use to push the pial
> > > surface into the right place.  If that isn't a option, can I use some 
> > > other
> > > images collected during the MP2rage scan to help the segmentation in the
> > > anterior temporal lobe?  Those extract scans are: inv1_nd, inv1_phs_nd, ,
> > > t1, inv2_nd, invs_phas_nd,
> > >
> > > thanks very much.
> > >
> > > Xiaomin
> > >
> > >
> >
> > ___
> > 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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The in

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

The white matter in the anterior temporal lobe is around 70, the gray matter is 
about 30.  The number is read from brain.finalsurfs.mgz.
Xiaomin

> Date: Tue, 19 Apr 2016 09:29:50 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> CC: macar...@libero.it; yu...@hotmail.com
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
> 
> yes, you can do that for both mris_make_surfaces and mri_segment, but 
> that will only help if you've removed the majority of the bias field. Is 
> anterior temporal white matter near 110? If so, what is the gray matter 
> at?
> On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
> 
> > Hi Xiaomin,
> > currently I don't have access to my notes, however, if I remember correctly,
> > you can specify thresholds in mris_make_surfaces for consideration in the
> > surface placement. This obviously works well only if the contrast between
> > WM/GM/CSF is high enough.
> > 
> > If you are interested and nobody jumps in giving you the according flags,
> > let me know.
> > 
> > Best,
> > Falk
> > 
> > ____________
> > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > [yu...@hotmail.com]
> > Gesendet: Dienstag, 19. April 2016 01:13
> > An: Freesurfer support list
> > Cc: macar...@libero.it
> > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> > 
> > Hi Jon,
> > Thanks for your answers.   There is gray-white contrast in the temporal
> > lobe, but same as you said that the gray-csf is low.  Attached is a
> > screenshot.  let's me know if you need more information. 
> > 
> > Xiaomin
> > 
> > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > From: j...@nmr.mgh.harvard.edu
> > > To: yu...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > >
> > > hi Xiaomin,
> > >
> > > it is tough to say what might be causing the problem since a lot can go
> > > wrong in the anterior temporal lobes at 7T. you say that your contrast is
> > > low there? it is possible to have OK gray-white contrast but low overall
> > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > region. also some adiabatic inversion pulses break down around the
> > > temporal poles due to the B0 inhomogeneity around the ear canals. if you
> > > could send a screenshot we'd have a better chance at diagnosing the
> > > problem.
> > >
> > >
> > > -jon
> > >
> > >
> > >
> > >
> > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > >
> > > > Hi Jon Polimeni,
> > > > Do you have any suggestions on the following questions?
> > > > Thanks,Xiaomin
> > > >
> > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > > Hi Xiaomin
> > > >
> > > > it's really hard to say without seeing more detail in your images. Do
> > you
> > > > have contrast in the temporal lobe? Frequently it goes away at 7T due to
> > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > things!) expert.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Bruce,
> > > > > I have done the recon-all (fs5.3) with the data collected from a 7T
> > scanner
> > > > > using MP2Rage. The recon went well without problem. But the the
> > temporal
> > > > > reconstruction looks clearly not correct (see attached). I tried to
> > push
> > > > > the pial surface outside by editing the white matter evidenced in the
> > > > > attached figures, but has no effect to genera correct pial surface. I
> > do
> > > > > realize that the contrast is low in the anterior temporal lobes.
> > However, I
> > > > > am wondering if there are exp

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

OK.  I will do it.  
Xiaomin

Date: Tue, 19 Apr 2016 10:56:15 -0400
From: fis...@nmr.mgh.harvard.edu
To: yu...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem

then you need to put some control points in the white matter. 70 is way 
too low
On Tue, 19 Apr 2016, Xiaomin Yue wrote:
 
> The white matter in the anterior temporal lobe is around 70, the gray matter
> is about 30.  The number is read from brain.finalsurfs.mgz.
> Xiaomin
> 
> > Date: Tue, 19 Apr 2016 09:29:50 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macar...@libero.it; yu...@hotmail.com
> > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > yes, you can do that for both mris_make_surfaces and mri_segment, but
> > that will only help if you've removed the majority of the bias field. Is
> > anterior temporal white matter near 110? If so, what is the gray matter
> > at?
> > On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
> >
> > > Hi Xiaomin,
> > > currently I don't have access to my notes, however, if I remember
> correctly,
> > > you can specify thresholds in mris_make_surfaces for consideration in
> the
> > > surface placement. This obviously works well only if the contrast
> between
> > > WM/GM/CSF is high enough.
> > >
> > > If you are interested and nobody jumps in giving you the according
> flags,
> > > let me know.
> > >
> > > Best,
> > > Falk
> > >
> > >___
> _
> > > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > > [yu...@hotmail.com]
> > > Gesendet: Dienstag, 19. April 2016 01:13
> > > An: Freesurfer support list
> > > Cc: macar...@libero.it
> > > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > > Hi Jon,
> > > Thanks for your answers.   There is gray-white contrast in the temporal
> > > lobe, but same as you said that the gray-csf is low.  Attached is a
> > > screenshot.  let's me know if you need more information. 
> > >
> > > Xiaomin
> > >
> > > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > > From: j...@nmr.mgh.harvard.edu
> > > > To: yu...@hotmail.com
> > > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > >
> > > > hi Xiaomin,
> > > >
> > > > it is tough to say what might be causing the problem since a lot can
> go
> > > > wrong in the anterior temporal lobes at 7T. you say that your contrast
> is
> > > > low there? it is possible to have OK gray-white contrast but low
> overall
> > > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > > region. also some adiabatic inversion pulses break down around the
> > > > temporal poles due to the B0 inhomogeneity around the ear canals. if
> you
> > > > could send a screenshot we'd have a better chance at diagnosing the
> > > > problem.
> > > >
> > > >
> > > > -jon
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Jon Polimeni,
> > > > > Do you have any suggestions on the following questions?
> > > > > Thanks,Xiaomin
> > > > >
> > > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > > From: fis...@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > > >
> > > > > Hi Xiaomin
> > > > >
> > > > > it's really hard to say without seeing more detail in your images.
> Do
> > > you
> > > > > have contrast in the temporal lobe? Frequently it goes away at 7T
> due to
> > > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > > things!) expert.
> > > > >
> > > > > cheers
> > >

[Freesurfer] Basename error

[Xiaomin Yue]

Hi all,
I am analyzing functional data using fsfast 5.3 with the error: Error using==> 
basename.  It seems that the same problem was reported before in the mail list 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html),
 but I can't find answer in the discussion thread in the above link.
Any suggestions?  Thanks,
Xiaomin Yue   ___
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Basename error

[Xiaomin Yue]

Hi Doug
Thanks for you response.  The command line is: selxavg3-sess -s subject_0101 -d 
. -analysis DoD_looming_lh.
I checked the basename function in the matlab installed in my computer, which 
is 2010b.  It seems that the basename in the 2010b matlab only accepts one 
parameter.  I tried two ways to avoid the problem.  First, I replaced the 
matlab's basename function with my own basename function.  Second, I removed 
the motion regressor from the analysis.info.  The two method indeed avoided the 
basename function error, but new errors were created as the following:
Error using ==> fmri_hemodynToo many input argument.
Error in ==> flac_ev2irf at 74xirf = fmri_hemodync(tirf, delay, tau, alpha);
Error in ==> flac_desmat at 66[xirf tirf] = flac_ev2irf(ev, TER, flac, 
RefEventDur);
Error in ==> flac_customize at 356flacnew = flac_desmat(flacnew);
Error in ==> fast_selxavg3 at 65flac0=flac_customize(flac0);

I suspected that  the errors was caused by matlab?  if so, what version is 
required to run 5.3 version correctly?

Thanks for your help!
Xiaomin
Date: Thu, 19 Jun 2014 20:41:28 +0200
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Basename error


  

  
  


what is your command line and terminal output







On 6/19/14 4:36 PM, Xiaomin Yue wrote:



  
  Hi all,



I am analyzing functional data using fsfast 5.3 with the
  error: Error using==> basename.  It seems that the same
  problem was reported before in the mail list 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html),
 but I can't find answer in the discussion thread in the above
link.


  
Any suggestions?  Thanks,
    

  
Xiaomin Yue
  
  
  

  
  

  ___
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Basename error

[Xiaomin Yue]

Hi Doug,
Thanks very much for the information.  I will try it.
XIaomin
> Date: Mon, 23 Jun 2014 09:19:20 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Basename error
> 
> If it is not using the basename.m in freesurfer it may fail. Try putting 
> $FREESURFER_HOME/fsfast/toolbox first in your matlab path
> 
> 
> On 06/22/2014 02:52 PM, Xiaomin Yue wrote:
> > Hi Doug
> >
> > Thanks for you response.  The command line is: selxavg3-sess -s 
> > subject_0101 -d . -analysis DoD_looming_lh.
> >
> > I checked the basename function in the matlab installed in my 
> > computer, which is 2010b.  It seems that the basename in the 2010b 
> > matlab only accepts one parameter.  I tried two ways to avoid the 
> > problem.  First, I replaced the matlab's basename function with my own 
> > basename function.  Second, I removed the motion regressor from the 
> > analysis.info.  The two method indeed avoided the basename function 
> > error, but new errors were created as the following:
> >
> > Error using ==> fmri_hemodyn
> > Too many input argument.
> >
> > Error in ==> flac_ev2irf at 74
> > xirf = fmri_hemodync(tirf, delay, tau, alpha);
> >
> > Error in ==> flac_desmat at 66
> > [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur);
> >
> > Error in ==> flac_customize at 356
> > flacnew = flac_desmat(flacnew);
> >
> > Error in ==> fast_selxavg3 at 65
> > flac0=flac_customize(flac0);
> >
> >
> > I suspected that  the errors was caused by matlab?  if so, what 
> > version is required to run 5.3 version correctly?
> >
> > Thanks for your help!
> >
> > Xiaomin
> >
> > --------
> > Date: Thu, 19 Jun 2014 20:41:28 +0200
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Basename error
> >
> >
> > what is your command line and terminal output
> >
> >
> >
> > On 6/19/14 4:36 PM, Xiaomin Yue wrote:
> >
> > Hi all,
> >
> > I am analyzing functional data using fsfast 5.3 with the error:
> > Error using==> basename.  It seems that the same problem was
> > reported before in the mail list
> > 
> > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html),
> > but I can't find answer in the discussion thread in the above link.
> >
> > Any suggestions?  Thanks,
> >
> > Xiaomin Yue
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  <mailto: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 
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> > 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
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
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[Freesurfer] wm.mgz

[Xiaomin Yue]

Hi,  

My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz.   I 
re-run the anlysis using recon-all -s cologna -autorecon2-wm.  From some 
reason, the analysis regenerated wm.mgz from brain.mgz, which of course 
replaced my edited wm.mgz.   Did I do some wrong here?
Thanks,Xiaomin___
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Re: [Freesurfer] wm.mgz

[Xiaomin Yue]

Hi Bruce,


Thanks for your response.  the editing was done in freeview. I saved the edited 
version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz.  is that the 
problem?  Is it necessary to save the edited wm.mgz as wm.mgz in freeview?  I 
hope it is clear what I did. 






Thanks,

Xiaomin 





From: Bruce Fischl
Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM
To: Freesurfer support list





Hi Xiaomin

how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) 
and you reran recon-all it should have preserved your edits, even though it 
regenerated the file. Have you checked?

Bruce


On Fri, 25 Jul 2014, Xiaomin Yue wrote:

> Hi,  
> 
> My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz.   I 
> re-run the anlysis using
> recon-all -s cologna -autorecon2-wm.  From some reason, the analysis 
> regenerated wm.mgz from brain.mgz,
> which of course replaced my edited wm.mgz.   Did I do some wrong here?
> 
> Thanks,
> Xiaomin
> 
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Re: [Freesurfer] wm.mgz

[Xiaomin Yue]

It is 5.3.  The voxels erased  was set as 0.  Is that the problem? If so,  I 
can try to replace 0 with 1.

Xiaomin

From: Bruce Fischl<mailto:fis...@nmr.mgh.harvard.edu>
Sent: ‎7/‎25/‎2014 9:22 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz

What version? Check the voxels you erased and see if they were set to 1 instead 
of 0

> On Jul 25, 2014, at 8:39 PM, Xiaomin Yue  wrote:
>
> Hi Bruce,
>
> Thanks for your response.  the editing was done in freeview. I saved the 
> edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz.  is 
> that the problem?  Is it necessary to save the edited wm.mgz as wm.mgz in 
> freeview?  I hope it is clear what I did.
>
> Thanks,
> Xiaomin
>
> From: Bruce Fischl
> Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM
> To: Freesurfer support list
>
> Hi Xiaomin
>
> how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview)
> and you reran recon-all it should have preserved your edits, even though it
> regenerated the file. Have you checked?
>
> Bruce
>
>
> On Fri, 25 Jul 2014, Xiaomin Yue wrote:
>
> > Hi,
> >
> > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz.   I 
> > re-run the anlysis using
> > recon-all -s cologna -autorecon2-wm.  From some reason, the analysis 
> > regenerated wm.mgz from brain.mgz,
> > which of course replaced my edited wm.mgz.   Did I do some wrong here?
> >
> > Thanks,
> > Xiaomin
> >
> >
> ___
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Re: [Freesurfer] wm.mgz

[Xiaomin Yue]

Thanks.  I will replace 0 with 1.

Xiaomin

From: Bruce Fischl<mailto:fis...@nmr.mgh.harvard.edu>
Sent: ‎7/‎25/‎2014 9:43 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz

Yes, they won't be preserved unless they are 1

> On Jul 25, 2014, at 9:33 PM, Xiaomin Yue  wrote:
>
> It is 5.3.  The voxels erased  was set as 0.  Is that the problem? If so,  I 
> can try to replace 0 with 1.
>
> Xiaomin
> From: Bruce Fischl
> Sent: ‎7/‎25/‎2014 9:22 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] wm.mgz
>
> What version? Check the voxels you erased and see if they were set to 1 
> instead of 0
>
> On Jul 25, 2014, at 8:39 PM, Xiaomin Yue  wrote:
>
>> Hi Bruce,
>>
>> Thanks for your response.  the editing was done in freeview. I saved the 
>> edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz.  is 
>> that the problem?  Is it necessary to save the edited wm.mgz as wm.mgz in 
>> freeview?  I hope it is clear what I did.
>>
>> Thanks,
>> Xiaomin
>>
>> From: Bruce Fischl
>> Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM
>> To: Freesurfer support list
>>
>> Hi Xiaomin
>>
>> how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview)
>> and you reran recon-all it should have preserved your edits, even though it
>> regenerated the file. Have you checked?
>>
>> Bruce
>>
>>
>> On Fri, 25 Jul 2014, Xiaomin Yue wrote:
>>
>> > Hi,
>> >
>> > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz.   I 
>> > re-run the anlysis using
>> > recon-all -s cologna -autorecon2-wm.  From some reason, the analysis 
>> > regenerated wm.mgz from brain.mgz,
>> > which of course replaced my edited wm.mgz.   Did I do some wrong here?
>> >
>> > Thanks,
>> > Xiaomin
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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Re: [Freesurfer] missing anterior temporal lobe

[Xiaomin Yue]

Hi,
I had successfully reconstructed a primate brain using fs5.3.  But one part of 
left anterior temporal lobe was not correct, even with the accurate wm.mgz.   
See attached image for what I mean.  Are there parameters to be used to correct 
this problem?
Thanks,Xiaomin  




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Re: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

[Xiaomin Yue]

The title has been FedEx for overnight.  Please let me know after getting it.

Xiaomin

From: Thomas, Adam (NIH/NIMH) [E]
Sent: ‎7/‎30/‎2014 6:36 AM
To: freesurfer@nmr.mgh.harvard.edu; FSL 
- FMRIB's Software Library; 
s...@jiscmail.ac.uk; 
annou...@fmrib.ox.ac.uk
Subject: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

Posted on behalf of Dr. Judy Rapoport:

Department of Health and Human Services (DHHS)
National Institutes of Health (NIH)
National Institute of Mental Health (NIMH)
Division of Intramural Research Programs (DIRP)
Section on Childhood Neuropsychiatric Disorders (SCND)
Child Psychiatry Branch (CPB)

Staff Scientist position available


The Child Psychiatry Branch, in Bethesda, Maryland, is recruiting
applicants for a Staff Scientist position.  As a Staff Scientist, the
primary duties will include conducting statistical analyses on clinical,
neurobiological and treatment studies carried out in the Branch. This
includes but is not limited to tasks such as maintaining the appropriate
data sets, clearly conveying statistical results and methods both orally
and in writing, reviewing and writing statistical content for manuscripts
prior to submission, and working closely with and providing statistical
support for all Branch members.  The Staff Scientist position entails 25%
time allotted to pursuing individual research interests.


The Child Psychiatry Branch is a highly productive and collaborative group
with a rich, multimodal dataset that seeks to understand
neuro-developmental disorders, with a focus on childhood-onset
schizophrenia.  There is a strong scientific and statistical computing
core facility in existence, which can benefit this work.  For more
information about the Child Psychiatry Branch, please utilize the
following link:
http://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/chp/in
dex.shtml


Interested candidates should have a Ph.D., M.D. or equivalent doctoral
degree and five years post-doctoral experience.  Applicants should have a
strong background in statistics as well as interests and experience in
neuroimaging and behavioral research.  The recruit should be adept at
writing his/her own code to clean, organize, analyze, and visualize data.
In addition some highly desirable skills include: experience analyzing
structural MRI, functional MRI and/or MEG data; knowledge of cognitive
neuroscience or clinical psychology; a solid foundation in multivariate
statistics and longitudinal data analysis; proficiency in statistical
programs such as R and MATLAB and visualization methods.


SALARY RANGE:  Salary is commensurate with experience and accomplishments.

BENEFITS: The federal government offers a comprehensive benefits package
including vacation, sick leave, holidays, life insurance, health benefits,
and participation in the Federal Employees Retirement System.  For more
information go to new employee benefits at the NIH
(http://hr.od.nih.gov/Benefits/permanentemployee.htm) and other employee
benefits information (http://tiny.cc/saVcr).


Interested applicants should send their CV and cover letter to:

Dr. Judith Rapoport, NIMH, 10 Center Drive, Bldg. 10, Rm. 3N202 (MSC-1600),
Bethesda, MD  20892 USA, or by email: rapop...@mail.nih.gov

SUBMISSION DEADLINE:  September 1, 2014

NIH and DHHS are Equal Opportunity Employers.

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[Freesurfer] volume to surface registration problem

[Xiaomin Yue]

Hi,
When I used preproc-sess processing my data, the registration output is off a 
great of deal.  The functional data was collected using 7T, and the surface was 
reconstructed successfully from 3T data and was checked visually multiple 
times.   I am using fs5.3 installed on a linux system.   Attached is the 
registration log file.  
Any suggestions will be appreciated.  
Xiaomin Yue   Logfile for bbregister
Thu Oct 16 10:54:36 EDT 2014

setenv SUBJECTS_DIR /misc/data41/yuex/human_anat
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
/opt/freesurfer-530/bin/bbregister --s field --init-fsl --6 --bold --mov 
bold/template.nii --reg bold/register.dof6.dat --init-reg-out 
bold/init.register.dof6.dat

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer-530
mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii
mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from bold/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999653, -0.00336006, -0.0261388)
j_ras = (-2.83047e-08, -0.991839, 0.127499)
k_ras = (-0.0263539, 0.127455, 0.991494)
writing to bold/tmp.bbregister.16782/template.nii...
fslregister --s field --mov bold/tmp.bbregister.16782/template.nii --reg 
bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov 
--tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz

Log file is bold/tmp.bbregister.16782/reg.init.dat.fslregister.log

Thu Oct 16 10:54:37 EDT 2014
--s field --mov bold/tmp.bbregister.16782/template.nii --reg 
bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov 
--tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
konis
Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz 
bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii
mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz 
bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /misc/data41/yuex/human_anat/field/mri/brainmask.mgz...
TR=6.88, TE=2.72, TI=725.00, flip angle=10.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii...
--
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_convert bold/tmp.bbregister.16782/template.nii 
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --frame 0
mri_convert bold/tmp.bbregister.16782/template.nii 
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from bold/tmp.bbregister.16782/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999653, -0.00336006, -0.0261388)
j_ras = (-2.83047e-08, -0.991839, 0.127499)
k_ras = (-0.0263539, 0.127455, 0.991494)
keeping frame 0
writing to bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii...
Mov determinant is 2.94386
Swapping dims for pos det
WARNING:: Flipping Left/Right orientation (as det < 0)
tkregister_tcl /opt/freesurfer-530/tktools/tkregister2.tcl
target  volume bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
movable volume bold/tmp.bbregister.16782/template.nii
reg file   bold/tmp.bbregister.16782/fslregister/swapreg.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target 
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable bold/tmp.bbregister.16782/template.nii
Tmov: 
-1.408   0.000   0.000   100.000;
 0.000   0.000   1.484  -30.422;
 0.000  -1.408   0.000   100.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
 Input registration matrix (computed) 
 1.000   0.003   0.026   1.408;
-0.026   0.127   0.991   0.000;
 0.000   0.992  -0.127  -0.000;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.003   0.026

Re: [Freesurfer] volume to surface registration problem

[Xiaomin Yue]

Hi Doug,
Thanks for the promptly response.   I do have spm8 and spm12b installed.  Which 
version should I use?  Also, how to change the spm as the inital registration 
method in the preproc-sess?  
Xiaomin

> Date: Thu, 16 Oct 2014 12:00:04 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] volume to surface registration problem
> 
> 
> The problem is probabably that the fsl flirt registration failed and 
> that caused bbr to fail. If you have spm and matlab installed, running 
> it with
> 
> cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
> bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg 
> bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat
> 
> 
> 
> 
> On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
> > Hi,
> >
> > When I used preproc-sess processing my data, the registration output 
> > is off a great of deal.  The functional data was collected using 7T, 
> > and the surface was reconstructed successfully from 3T data and was 
> > checked visually multiple times.   I am using fs5.3 installed on a 
> > linux system. Attached is the registration log file.
> >
> > Any suggestions will be appreciated.
> >
> > Xiaomin Yue
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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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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Re: [Freesurfer] volume to surface registration problem

[Xiaomin Yue]

Is it right that the prep roc-sess includes the following steps: 1) 
mktemplate-sess; 2) mkbrainmask-sess; 3)register-sess; 4) mc-sess; 5) 
rawfunc2surf-sess.  So, I need to rerun step3, 4, and 5 manually, is that 
right? 
Thanks,Xiaomin

> Date: Thu, 16 Oct 2014 12:12:23 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] volume to surface registration problem
> 
> 
> I have not tested it with spm12, so use spm8. There is not currently a 
> way to run the spm init from preproc-sess, so you'll have to run it from 
> register-sess.
> 
> On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
> > Hi Doug,
> >
> > Thanks for the promptly response.   I do have spm8 and spm12b 
> > installed.  Which version should I use?  Also, how to change the spm 
> > as the inital registration method in the preproc-sess?
> >
> > Xiaomin
> >
> > > Date: Thu, 16 Oct 2014 12:00:04 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] volume to surface registration problem
> > >
> > >
> > > The problem is probabably that the fsl flirt registration failed and
> > > that caused bbr to fail. If you have spm and matlab installed, running
> > > it with
> > >
> > > cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
> > > bbregister --s field --init-spm --6 --bold --mov bold/template.nii 
> > --reg bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat
> > >
> > >
> > >
> > >
> > > On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
> > > > Hi,
> > > >
> > > > When I used preproc-sess processing my data, the registration output
> > > > is off a great of deal. The functional data was collected using 7T,
> > > > and the surface was reconstructed successfully from 3T data and was
> > > > checked visually multiple times. I am using fs5.3 installed on a
> > > > linux system. Attached is the registration log file.
> > > >
> > > > Any suggestions will be appreciated.
> > > >
> > > > Xiaomin Yue
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > ___
> > > 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
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] thickness from pial and white

[Xiaomin Yue]

Hi All,

 

Cortical surface reconstructed using caret from a high resolution
MRI data (0.25 mm) has been converted to freesurfer format, and viewed
correctly using freeview.  My questions
are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and
?h.white; 2) wm.mgz file using ?h.pial and ?h.white

 

Thanks very much for your inputs.
Xiaomin

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Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Hi Bruce,

Thanks for your response.  What's the inputs to the mris_thickness?  I need the 
wm.mgz to generate the ratio of gray vs. white matter.  

Xiaomin

Date: Tue, 9 Dec 2014 09:55:21 -0500
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white

the thickness you can generate using mris_thikness. Why do you want to 
generate a wm.mgz? I guess you could from the wmparc
 
On Mon, 8 Dec 2014, 
Xiaomin Yue wrote:
 
> 
> Hi All,
> 
>  
> 
> Cortical surface reconstructed using caret from a high resolution MRI data
> (0.25 mm) has been converted to freesurfer format, and viewed correctly
> using freeview.  My questions are whether it is possible to generate 1) a
> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial and
> ?h.white
> 
>  
> 
> Thanks very much for your inputs.
> 
> 
> Xiaomin
> 
> 
>

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Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

What I mean by inputs is the default files the mris_thickness will be looking 
for to run correctly 

Xiaomin 


> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
> 
> Hi Bruce,
> 
> Thanks for your response.  What's the inputs to the mris_thickness?  I need 
> the wm.mgz to generate the ratio of gray vs. white matter.  
> 
> Xiaomin
> 
> Date: Tue, 9 Dec 2014 09:55:21 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] thickness from pial and white
> 
> the thickness you can generate using mris_thikness. Why do you want to 
> generate a wm.mgz? I guess you could from the wmparc
>  
> On Mon, 8 Dec 2014, 
> Xiaomin Yue wrote:
>  
> > 
> > Hi All,
> > 
> >  
> > 
> > Cortical surface reconstructed using caret from a high resolution MRI data
> > (0.25 mm) has been converted to freesurfer format, and viewed correctly
> > using freeview.  My questions are whether it is possible to generate 1) a
> > ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial and
> > ?h.white
> > 
> >  
> > 
> > Thanks very much for your inputs.
> > 
> > 
> > Xiaomin
> > 
> > 
> >
> 
> ___ Freesurfer mailing list 
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> 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 
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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
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Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Thanks very much.  Does this create curvature file?  Again, is it possible to 
generate wm.mgz from those files?

Thanks,
Xiaomin 


> On Dec 9, 2014, at 4:19 PM, Bruce Fischl  wrote:
> 
> I think just the ?h.white and ?h.pial
> 
> cheers
> Bruce
>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>> 
>> What I mean by inputs is the default files the mris_thickness will be
>> looking for to run correctly 
>> Xiaomin 
>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
>> 
>>  Hi Bruce,
>> 
>>  Thanks for your response.  What's the inputs to the
>>  mris_thickness?  I need the wm.mgz to generate the ratio of gray
>>  vs. white matter. 
>> 
>>  Xiaomin
>> 
>>  Date: Tue, 9 Dec 2014 09:55:21 -0500
>>  From: fis...@nmr.mgh.harvard.edu
>>  To: freesurfer@nmr.mgh.harvard.edu
>>  Subject: Re: [Freesurfer] thickness from pial and white
>> the thickness you can generate using mris_thikness. Why do you want to 
>> generate a wm.mgz? I guess you could from the wmparc
>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>> > > Hi All,
>> > >  
>> > > Cortical surface reconstructed using caret from a high resolution MRI 
>> > > data
>> > (0.25 mm) has been converted to freesurfer format, and viewed correctly
>> > using freeview.  My questions are whether it is possible to generate 1) a
>> > ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a
>> nd
>> > ?h.white
>> > >  
>> > > Thanks very much for your inputs.
>> > > > Xiaomin
>> > > >
>> 
>>  ___ 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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>>  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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> 
> 
> 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
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Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Thanks.  I will try mris_fill.






Xiaomin 





From: Bruce Fischl
Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM
To: Freesurfer support list





it creates a file in curvature format, yes. Did you try mris_fill for the 
wm.mgz? It won't be exactly the same as the one we would generate. You 
could use mris_fill to generate the interior of the ?h.white surface, 
then use the aseg to remove non-wm voxels I guess
On Tue, 9 Dec 2014, 
Xiaomin Yue wrote:

> Thanks very much.  Does this create curvature file?  Again, is it possible to 
> generate wm.mgz from those files?
>
> Thanks,
> Xiaomin
>
>
>> On Dec 9, 2014, at 4:19 PM, Bruce Fischl  wrote:
>>
>> I think just the ?h.white and ?h.pial
>>
>> cheers
>> Bruce
>>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>>>
>>> What I mean by inputs is the default files the mris_thickness will be
>>> looking for to run correctly
>>> Xiaomin
>>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
>>>
>>>  Hi Bruce,
>>>
>>>  Thanks for your response.  What's the inputs to the
>>>  mris_thickness?  I need the wm.mgz to generate the ratio of gray
>>>  vs. white matter.
>>>
>>>  Xiaomin
>>>
>>>  Date: Tue, 9 Dec 2014 09:55:21 -0500
>>>  From: fis...@nmr.mgh.harvard.edu
>>>  To: freesurfer@nmr.mgh.harvard.edu
>>>  Subject: Re: [Freesurfer] thickness from pial and white
>>> the thickness you can generate using mris_thikness. Why do you want to 
>>> generate a wm.mgz? I guess you could from the wmparc
>>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>>>>> Hi All,
>>>>>
>>>>> Cortical surface reconstructed using caret from a high resolution MRI data
>>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly
>>>> using freeview.  My questions are whether it is possible to generate 1) a
>>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a
>>> nd
>>>> ?h.white
>>>>>
>>>>> Thanks very much for your inputs.
>>>>>> Xiaomin
>>>>>>
>>>
>>>  ___ 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
>>>
>>>  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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>>
>> 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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>
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Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Hi Bruce,
the mris_thickness was looking for ?h.gray file to run correctly.  But no such 
file exists.  The freesurfer used is 5.3.  Any ideas?  The command line is: 
mris_thickness test_DB48 lh lh.thicknessThe error: reading gray matter surface 
/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray 
MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open 
file.
Thanks,Xiaomin

From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white
Date: Wed, 10 Dec 2014 02:47:02 +







Thanks.  I will try mris_fill.

Xiaomin 
From: Bruce Fischl
Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM
To: Freesurfer support list

it creates a file in curvature format, yes. Did you try mris_fill for the 

wm.mgz? It won't be exactly the same as the one we would generate. You 

could use mris_fill to generate the interior of the ?h.white surface, 

then use the aseg to remove non-wm voxels I guess

On Tue, 9 Dec 2014, 

Xiaomin Yue wrote:



> Thanks very much.  Does this create curvature file?  Again, is it possible to 
> generate wm.mgz from those files?

>

> Thanks,

> Xiaomin

>

>

>> On Dec 9, 2014, at 4:19 PM, Bruce Fischl  wrote:

>>

>> I think just the ?h.white and ?h.pial

>>

>> cheers

>> Bruce

>>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:

>>>

>>> What I mean by inputs is the default files the mris_thickness will be

>>> looking for to run correctly

>>> Xiaomin

>>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:

>>>

>>>  Hi Bruce,

>>>

>>>  Thanks for your response.  What's the inputs to the

>>>  mris_thickness?  I need the wm.mgz to generate the ratio of gray

>>>  vs. white matter.

>>>

>>>  Xiaomin

>>>

>>>  Date: Tue, 9 Dec 2014 09:55:21 -0500

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

>>>  To: freesurfer@nmr.mgh.harvard.edu

>>>  Subject: Re: [Freesurfer] thickness from pial and white

>>> the thickness you can generate using mris_thikness. Why do you want to 
>>> generate a wm.mgz? I guess you could from the wmparc

>>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:

>>>>> Hi All,

>>>>>

>>>>> Cortical surface reconstructed using caret from a high resolution MRI data

>>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly

>>>> using freeview.  My questions are whether it is possible to generate 1) a

>>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a

>>> nd

>>>> ?h.white

>>>>>

>>>>> Thanks very much for your inputs.

>>>>>> Xiaomin

>>>>>>

>>>

>>>  ___ 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

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>>>  contact the sender and properly dispose of the e-mail.

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>>>

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>>>  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

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>>>  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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>>

>>

>> The information in this e-mail is intended only for the person to who

Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Yes, lh.pial exists

Xiaomin 

> On Dec 10, 2014, at 10:33 AM, Bruce Fischl  wrote:
> 
> it only looks for that if it can't find lh.pial. Does that exist?
> 
>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>> 
>> Hi Bruce,
>> the mris_thickness was looking for ?h.gray file to run correctly.  But no
>> such file exists.  The freesurfer used is 5.3.  Any ideas?  
>> The command line is: mris_thickness test_DB48 lh lh.thickness
>> The error: reading gray matter surface
>> /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
>>
>>  MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not
>> open file.
>> Thanks,
>> Xiaomin
>> 
>> From: yu...@hotmail.com
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] thickness from pial and white
>> Date: Wed, 10 Dec 2014 02:47:02 +
>> Thanks.  I will try mris_fill.
>> Xiaomin
>> From: Bruce Fischl
>> Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM
>> To: Freesurfer support list
>> it creates a file in curvature format, yes. Did you try mris_fill for the
>> wm.mgz? It won't be exactly the same as the one we would generate. You
>> could use mris_fill to generate the interior of the ?h.white surface,
>> then use the aseg to remove non-wm voxels I guess
>> On Tue, 9 Dec 2014,
>> Xiaomin Yue wrote:
>> > Thanks very much.  Does this create curvature file?  Again, is it possible
>> to generate wm.mgz from those files?
>> >
>> > Thanks,
>> > Xiaomin
>> >
>> >
>> >> On Dec 9, 2014, at 4:19 PM, Bruce Fischl 
>> wrote:
>> >>
>> >> I think just the ?h.white and ?h.pial
>> >>
>> >> cheers
>> >> Bruce
>> >>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>> >>>
>> >>> What I mean by inputs is the default files the mris_thickness will be
>> >>> looking for to run correctly
>> >>> Xiaomin
>> >>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
>> >>>
>> >>>  Hi Bruce,
>> >>>
>> >>>  Thanks for your response.  What's the inputs to the
>> >>>  mris_thickness?  I need the wm.mgz to generate the ratio of gray
>> >>>  vs. white matter.
>> >>>
>> >>>  Xiaomin
>> >>>
>> >>>  Date: Tue, 9 Dec 2014 09:55:21 -0500
>> >>>  From: fis...@nmr.mgh.harvard.edu
>> >>>  To: freesurfer@nmr.mgh.harvard.edu
>> >>>  Subject: Re: [Freesurfer] thickness from pial and white
>> >>> the thickness you can generate using mris_thikness. Why do you want to
>> generate a wm.mgz? I guess you could from the wmparc
>> >>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>> >>>>> Hi All,
>> >>>>>
>> >>>>> Cortical surface reconstructed using caret from a high resolution MRI
>> data
>> >>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly
>> >>>> using freeview.  My questions are whether it is possible to generate 1)
>> a
>> >>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using
>> ?h.pial a
>> >>> nd
>> >>>> ?h.white
>> >>>>>
>> >>>>> Thanks very much for your inputs.
>> >>>>>> Xiaomin
>> >>>>>>
>> >>>
>> >>>  ___ 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@n

Re: [Freesurfer] thickness from pial and white

[Xiaomin Yue]

Yes, lh.pial exists

Xiaomin 

> On Dec 10, 2014, at 10:33 AM, Bruce Fischl  wrote:
> 
> it only looks for that if it can't find lh.pial. Does that exist?
> 
>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>> 
>> Hi Bruce,
>> the mris_thickness was looking for ?h.gray file to run correctly.  But no
>> such file exists.  The freesurfer used is 5.3.  Any ideas?  
>> The command line is: mris_thickness test_DB48 lh lh.thickness
>> The error: reading gray matter surface
>> /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
>> 
>> MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not
>> open file.
>> Thanks,
>> Xiaomin
>> 
>> From: yu...@hotmail.com
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] thickness from pial and white
>> Date: Wed, 10 Dec 2014 02:47:02 +
>> Thanks.  I will try mris_fill.
>> Xiaomin
>> From: Bruce Fischl
>> Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM
>> To: Freesurfer support list
>> it creates a file in curvature format, yes. Did you try mris_fill for the
>> wm.mgz? It won't be exactly the same as the one we would generate. You
>> could use mris_fill to generate the interior of the ?h.white surface,
>> then use the aseg to remove non-wm voxels I guess
>> On Tue, 9 Dec 2014,
>> Xiaomin Yue wrote:
>>> Thanks very much.  Does this create curvature file?  Again, is it possible
>> to generate wm.mgz from those files?
>>> 
>>> Thanks,
>>> Xiaomin
>>> 
>>> 
>>>> On Dec 9, 2014, at 4:19 PM, Bruce Fischl 
>> wrote:
>>>> 
>>>> I think just the ?h.white and ?h.pial
>>>> 
>>>> cheers
>>>> Bruce
>>>>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>>>>> 
>>>>> What I mean by inputs is the default files the mris_thickness will be
>>>>> looking for to run correctly
>>>>> Xiaomin
>>>>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
>>>>> 
>>>>> Hi Bruce,
>>>>> 
>>>>> Thanks for your response.  What's the inputs to the
>>>>> mris_thickness?  I need the wm.mgz to generate the ratio of gray
>>>>> vs. white matter.
>>>>> 
>>>>> Xiaomin
>>>>> 
>>>>> Date: Tue, 9 Dec 2014 09:55:21 -0500
>>>>> From: fis...@nmr.mgh.harvard.edu
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] thickness from pial and white
>>>>> the thickness you can generate using mris_thikness. Why do you want to
>> generate a wm.mgz? I guess you could from the wmparc
>>>>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>>>>>>> Hi All,
>>>>>>> 
>>>>>>> Cortical surface reconstructed using caret from a high resolution MRI
>> data
>>>>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly
>>>>>> using freeview.  My questions are whether it is possible to generate 1)
>> a
>>>>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using
>> ?h.pial a
>>>>> nd
>>>>>> ?h.white
>>>>>>> 
>>>>>>> Thanks very much for your inputs.
>>>>>>>> Xiaomin
>>>>> 
>>>>> ___ 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] thickness from pial and white

[Xiaomin Yue]

The problem was solved.  I typed the wrong name.  
mris_fill had generated wm.mgz correctly, with the problem that a significant 
portion of white matter was cutted off.  The problem I believe is that the 
resolution or the matrix size of wm.mgz is limited to 256 X 256 X 256, but the 
high resolution data has dimension larger than that.  Is it possible to have a 
wm.mgz larger than 256^3?  Or some kind of trick to make it happen?

Thanks,Xiaomin  
Date: Wed, 10 Dec 2014 11:37:29 -0500
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness from pial and white

what version of FS do you have? You can try runing it with -pial pial but 
I wouldn't think that is needed. Is the lh.pial in 
/misc/data41/yuex/recon_test/test_DB48/surf/
 
and is it readable?
 
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
 
> Yes, lh.pial exists
>
> Xiaomin
>
>> On Dec 10, 2014, at 10:33 AM, Bruce Fischl  
>> wrote:
>>
>> it only looks for that if it can't find lh.pial. Does that exist?
>>
>>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>>>
>>> Hi Bruce,
>>> the mris_thickness was looking for ?h.gray file to run correctly.  But no
>>> such file exists.  The freesurfer used is 5.3.  Any ideas?
>>> The command line is: mris_thickness test_DB48 lh lh.thickness
>>> The error: reading gray matter surface
>>> /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
>>>
>>>  MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not
>>> open file.
>>> Thanks,
>>> Xiaomin
>>> 
>>> From: yu...@hotmail.com
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] thickness from pial and white
>>> Date: Wed, 10 Dec 2014 02:47:02 +
>>> Thanks.  I will try mris_fill.
>>> Xiaomin
>>> From: Bruce Fischl
>>> Sent: Tuesday, December 9, 2014 4:31 PM
>>> To: Freesurfer support list
>>> it creates a file in curvature format, yes. Did you try mris_fill for the
>>> wm.mgz? It won't be exactly the same as the one we would generate. You
>>> could use mris_fill to generate the interior of the ?h.white surface,
>>> then use the aseg to remove non-wm voxels I guess
>>> On Tue, 9 Dec 2014,
>>> Xiaomin Yue wrote:
>>>> Thanks very much.  Does this create curvature file?  Again, is it possible
>>> to generate wm.mgz from those files?
>>>>
>>>> Thanks,
>>>> Xiaomin
>>>>
>>>>
>>>>> On Dec 9, 2014, at 4:19 PM, Bruce Fischl 
>>> wrote:
>>>>>
>>>>> I think just the ?h.white and ?h.pial
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>>> On Tue, 9 Dec 2014, Xiaomin Yue wrote:
>>>>>>
>>>>>> What I mean by inputs is the default files the mris_thickness will be
>>>>>> looking for to run correctly
>>>>>> Xiaomin
>>>>>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue  wrote:
>>>>>>
>>>>>>  Hi Bruce,
>>>>>>
>>>>>>  Thanks for your response.  What's the inputs to the
>>>>>>  mris_thickness?  I need the wm.mgz to generate the ratio of gray
>>>>>>  vs. white matter.
>>>>>>
>>>>>>  Xiaomin
>>>>>>
>>>>>>  Date: Tue, 9 Dec 2014 09:55:21 -0500
>>>>>>  From: fis...@nmr.mgh.harvard.edu
>>>>>>  To: freesurfer@nmr.mgh.harvard.edu
>>>>>>  Subject: Re: [Freesurfer] thickness from pial and white
>>>>>> the thickness you can generate using mris_thikness. Why do you want to
>>> generate a wm.mgz? I guess you could from the wmparc
>>>>>> On Mon, 8 Dec 2014, Xiaomin Yue wrote:
>>>>>>>> Hi All,
>>>>>>>>
>>>>>>>> Cortical surface reconstructed using caret from a high resolution MRI
>>> data
>>>>>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly
>>>>>>> using freeview.  My questions are whether it is possible to generate 1)
>>> a
>>>>>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using
>>> ?h.pial a
>>>>>> nd
>>>>>>> ?h.white
>>>>>>>>
>>>>>>>> Thanks very much for your inp

[Freesurfer] freeview 3.0

[Xiaomin Yue]

External Email - Use Caution

Dear all,

The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, 
pial, white) in a solid color.  The Freeview is currently running under WSL and 
was running without a problem until I updated libXm4.  Is there a particular 
library file associated with libXm4  the Freeview needs to run without this 
problem?

Thanks
Xiaomin
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Re: [Freesurfer] freeview 3.0

[Xiaomin Yue]

External Email - Use Caution

Thanks for your response.  Why does freeview 2 work?

Thanks,
Xiaomin

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: Thursday, July 9, 2020 10:20 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: yu...@hotmail.com<mailto:yu...@hotmail.com>
Subject: Re: [Freesurfer] freeview 3.0


External Email - Use Caution
I don’t see freeview directly linking against libXm.so from Motif, though it 
does link against X windows libraries like libXmu.so and libX11..so.  You can 
see this with the “ldd” command  (some examples in screenshot below).   I don't 
think the RPM installer for freesurfer installs any Motif libraries.  I don't 
have any Motif libraries installed on my CentOS 7.7 image running under WSL 
that runs freeview/freesurfer.

Now it could be you installed some packages on your system that installed Motif 
and/or also maybe changed the X windows distribution libraries (as used by 
freeview).

- R.



On Jul 9, 2020, at 12:54, Xiaomin Yue  wrote:

External Email - Use Caution

Hi,

Here is the command I used in the freeview 3.0: freeview – f 
$SUBJECTS_DIR/LOO/surf/lh.inflated.lh.inflated was created using FS7.1.  
The freeview display is attached in this email.  The inflated brain is 
displayed correctly when I run the same command in freeview 2.0. (see attached).

Thanks,
Xiaomin

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: Thursday, July 9, 2020 1:56 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: yu...@hotmail.com<mailto:yu...@hotmail.com>
Subject: Re: [Freesurfer] freeview 3.0

External Email - Use Caution
Hello Xiaomin,

It might help for you to send along an example freeview command and file that 
demonstrates this issue in the WSL environment.

- R.


On Jul 8, 2020, at 12:08, Xiaomin Yue 
mailto:yu...@hotmail.com>> wrote:

External Email - Use Caution

Dear all,

The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, 
pial, white) in a solid color.  The Freeview is currently running under WSL and 
was running without a problem until I updated libXm4.  Is there a particular 
library file associated with libXm4  the Freeview needs to run without this 
problem?

Thanks
Xiaomin
___
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Re: [Freesurfer] freeview 3.0

[Xiaomin Yue]

External Email - Use Caution

Hi Ruopeng,

Thanks for taking time to answer my question.  I wish I can revert back to the 
early version of libraries Freeview uses.  Is there a way to figure out version 
number of libraries asccoated with  Freeview?  If not, I has to stick with 
freeview 2.


Thanks,
Xiaomin

From: Wang, Ruopeng<mailto:rwa...@mgh.harvard.edu>
Sent: Friday, July 10, 2020 9:08 AM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview 3.0

Hi Xiaomin,

Freeview 2 was built against much older Qt and VTK libraries. But unfortunately 
we still do not know why the new version has problem with libXm4. Is there any 
way you can revert back to your previous libXm? From the screenshot you sent it 
appears to be some kind of rendering artifact, which could result from a lot of 
factors, such as incompatible libraries or graphics card driver.

Ruopeng

On Jul 9, 2020, at 10:38 PM, Xiaomin Yue 
mailto:yu...@hotmail.com>> wrote:

External Email - Use Caution

Thanks for your response.  Why does freeview 2 work?

Thanks,
Xiaomin

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: Thursday, July 9, 2020 10:20 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: yu...@hotmail.com<mailto:yu...@hotmail.com>
Subject: Re: [Freesurfer] freeview 3.0

External Email - Use Caution
I don’t see freeview directly linking against libXm.so from Motif, though it 
does link against X windows libraries like libXmu.so and libX11..so.  You can 
see this with the “ldd” command  (some examples in screenshot below).   I don't 
think the RPM installer for freesurfer installs any Motif libraries.  I don't 
have any Motif libraries installed on my CentOS 7.7 image running under WSL 
that runs freeview/freesurfer.

Now it could be you installed some packages on your system that installed Motif 
and/or also maybe changed the X windows distribution libraries (as used by 
freeview).

- R.



On Jul 9, 2020, at 12:54, Xiaomin Yue 
mailto:yu...@hotmail.com>> wrote:

External Email - Use Caution

Hi,

Here is the command I used in the freeview 3.0: freeview – f 
$SUBJECTS_DIR/LOO/surf/lh.inflated.lh.inflated was created using FS7.1.  
The freeview display is attached in this email.  The inflated brain is 
displayed correctly when I run the same command in freeview 2.0. (see attached).

Thanks,
Xiaomin

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: Thursday, July 9, 2020 1:56 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: yu...@hotmail.com<mailto:yu...@hotmail.com>
Subject: Re: [Freesurfer] freeview 3.0

External Email - Use Caution
Hello Xiaomin,

It might help for you to send along an example freeview command and file that 
demonstrates this issue in the WSL environment.

- R.


On Jul 8, 2020, at 12:08, Xiaomin Yue 
mailto:yu...@hotmail.com>> wrote:

External Email - Use Caution

Dear all,

The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, 
pial, white) in a solid color.  The Freeview is currently running under WSL and 
was running without a problem until I updated libXm4.  Is there a particular 
library file associated with libXm4  the Freeview needs to run without this 
problem?

Thanks
Xiaomin
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[Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (core 
dumped) mri_fieldsign --fs 
$line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar 
$line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz 
$line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s 
$subjname --hemi $hemi --sphere
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Re: [Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

Hi All,

Just in case the below poster was missed.

Thanks,
Xiaomin

From: Xiaomin Yue<mailto:yu...@hotmail.com>
Sent: Saturday, July 11, 2020 1:43 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_fieldsign error


External Email - Use Caution
Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (core 
dumped) mri_fieldsign --fs 
$line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar 
$line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz 
$line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s 
$subjname --hemi $hemi --sphere

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Re: [Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

Hi Doug,

The file LOO.tar.gz has been uploaded to transfer/incoming directory on the ftp 
server.  Please let me know what else you need to solve this problem.


Thanks,
Xiaomin

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, July 15, 2020 11:15 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error

I don't know what is going wrong here. One simple thing to check is to make 
sure that all the input files have the same number of vertices as the surface. 
If that is the case, then upload the subject and input files using the 
instructions below

>From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 7/15/2020 11:07 AM, Xiaomin Yue wrote:

External Email - Use Caution
Hi All,

Just in case the below poster was missed.

Thanks,
Xiaomin

From: Xiaomin Yue<mailto:yu...@hotmail.com>
Sent: Saturday, July 11, 2020 1:43 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_fieldsign error


External Email - Use Caution
Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (core 
dumped) mri_fieldsign --fs 
$line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar 
$line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz 
$line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s 
$subjname --hemi $hemi --sphere

Re: [Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

Yes.  I will try it on a real Linux box and let you know.


Thanks,
Xiaomin

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 17, 2020 5:32 PM
To: Xiaomin Yue<mailto:yu...@hotmail.com>; Freesurfer support 
list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it has something 
to do with WSL. Do you have a real linux box you can try it on?
On 7/17/2020 5:24 PM, Xiaomin Yue wrote:

External Email - Use Caution
HI Doug,

Sorry for the slow response.  I got the same “segmentation fault (core dumped)” 
error when running the left hemi. I tested it multiple times.   Does this 
function create a detailed log I can send to you?

Thanks,
Xiaomin

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 17, 2020 1:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You sent me left hemi 
data, so I ran the command below

mri_fieldsign --fs fieldsign.71.nii.gz --polar LOO.wedge.polar.lh.real.nii.gz 
LOO.wedge.polar.lh.imag.nii.gz --eccen LOO.ring.eccen.lh.real.nii.gz 
LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere

But I also noticed that the command that you gave below is for the right hemi. 
Do you know if the left hemi works?



On 7/11/2020 1:43 PM, Xiaomin Yue wrote:

External Email - Use Caution
Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (core 
dumped) mri_fieldsign --fs 
$line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar 
$line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz 
$line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz 
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s 
$

Re: [Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel  fedora’ with the 
same “segmentation fault (core dumped)” error.

Thanks,
Xiaomin

From: Xiaomin Yue<mailto:yu...@hotmail.com>
Sent: Friday, July 17, 2020 6:07 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error


External Email - Use Caution

Yes.  I will try it on a real Linux box and let you know.


Thanks,
Xiaomin

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 17, 2020 5:32 PM
To: Xiaomin Yue<mailto:yu...@hotmail.com>; Freesurfer support 
list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it has something 
to do with WSL. Do you have a real linux box you can try it on?
On 7/17/2020 5:24 PM, Xiaomin Yue wrote:

External Email - Use Caution
HI Doug,

Sorry for the slow response.  I got the same “segmentation fault (core dumped)” 
error when running the left hemi. I tested it multiple times.   Does this 
function create a detailed log I can send to you?

Thanks,
Xiaomin

From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, July 17, 2020 1:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You sent me left hemi 
data, so I ran the command below

mri_fieldsign --fs fieldsign.71.nii.gz --polar LOO.wedge.polar.lh.real.nii.gz 
LOO.wedge.polar.lh.imag.nii.gz --eccen LOO.ring.eccen.lh.real.nii.gz 
LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere

But I also noticed that the command that you gave below is for the right hemi. 
Do you know if the left hemi works?


On 7/11/2020 1:43 PM, Xiaomin Yue wrote:

External Email - Use Caution
Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (co