Re: [Freesurfer] Convert mgz to nii

[Bruce Fischl]

Hi Jessica

in general if you specify .nii or .nii.gz as the extension of any output 
file we will write it in nifti format. This makes using mri_convert easy:


mri_convert any_volume.mgz any_volume.nii.gz

should work fine
cheers
Bruce


On 
Sun, 31 May 2020, Hua, Jessica wrote:




External Email - Use Caution

Hi FreeSurfer experts,

Also in case the code is different, how would I convert my T1.mgz  file to a
.nii file to be used in DTI analyses?

Thanks!

Jessica


---

Jessica Hua, M.A. Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology 
University of Missouri

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Re: [Freesurfer] Convert mgz to nii

[Bruce Fischl]

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

should do the trick

cheers
Bruce

On Sun, 31 May 2020, Hua, Jessica wrote:



External Email - Use Caution

Hi FreeSurfer experts,

I would like to convert my .mgz parcellation file to a .nii file to be used
in DTI analyses.  How would I convert my participant's aparc+aseg.mgz file
to a .nii file?

Best,

Jessica

---

Jessica Hua, M.A. Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology 
University of Missouri

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Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

Hi Prad

that is a hard question to answer. brain.mgz has been more aggressively 
bias corrected than norm and will have removed most of the variability in 
the wm. If gm is all you care about you could use it, but if you also 
care about wm you might use the norm (or even the nu)


cheers
Bruce
On Fri, 29 May 2020, 
Pradyumna Bharadwaj wrote:




External Email - Use Caution

Thanks for clarifying that! Just one more question: For either pctsurfcon or
mri_cnr, is brain.mgz the more appropriate volume to extract the g-w
contrasts or g-w or g-csf CNR values from cortical parcels? (compared to
norm.mgz)

Thanks,
Prad

On Fri, May 29, 2020 at 9:32 AM Bruce Fischl 
wrote:
  External Email

  Hi Prad

  for mri_cnr, yes, it samples inwards and outwards 1mm along the
  surface
  normal. And I think pctsurfcon is the tool I meant, but
  hopefully David
  and/or Doug can confirm
  cheers
  Bruce
  On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl, 
  > It looks like pctsurfcon was the tool you were referring to.
  Is this the
  > right one?
  >
  > Also, would brain.mgz be the appropriate volume to use to
  extract the G-W
  > contrast ratios for the cortical parcels?
  >
  > Finally, for mri_cnr according to this post, the CNR values
  are computed
  > using the voxels at the interface of the white and 
pialsurface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg3882
  9.html)
  >
  > Are these voxels offset from the white and pial surfaces by a
  specific
  > default distance?
  >
  > Thanks,
  > Prad
  >
  > On Thu, May 28, 2020 at 10:47 AM Pradyumna Bharadwaj
  >  wrote:
  >       Is it the pctsurfcon tool? (
  >       https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon)
  >
  > On Thu, May 28, 2020 at 10:12 AM Bruce Fischl
  >  wrote:
  >       External Email
  >
  >       David and Doug: can you point Prad in the right
  direction
  >       for looking at
  >       gray and white signal changes and ratios?
  >       On Thu, 28 May 2020, Pradyumna
  >       Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi Dr. Fischl,
  >       > Thank you for suggesting that. 
  >       > Would it be possible to share a link to a page with
  >       information about this
  >       > stream or to a patch?
  >       >
  >       > Thanks,
  >       > Prad
  >       >
  >       > On Thu, May 28, 2020 at 9:46 AM Bruce Fischl
  >       
  >       > wrote:
  >       >       External Email
  >       >
  >       >       I see. I think Doug has a more modern stream for
  >       this that David
  >       >       Salat
  >       >       has also used a lot
  >       >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hi Dr. Fischl,
  >       >       > Thanks for confirming that!
  >       >       > We were broadly interested in testing whether
  >       age-related
  >       >       differences in
  >       >       > cortical measures were impacted by the CNR in
  >       each ROI.
  >       >       >
  >       >       > Best,
  >       >       > Prad
  >       >       >
  >       >       > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
  >       >       
  >       >       > wrote:
  >       >       >       External Email
  >       >       >
  >       >       >       Hi Prad
  >       >       >
  >       >       >       what is your goal? What you describe
  below
  >       should work
  >       >       >
  >       >       >       cheers
  >       >       >       Bruce
  >       >       >       On Thu, 28 May 2020,
  >       >       >       Pradyumna Bharadwaj wrote:
  >       >       >
  >       >       >       >
  >       >       >       > External Email - Use
  >       Caution
  >       >       >       >
  >       >       >       > Hi Dr. Fischl,
  >       >      

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

Hi Prad

for mri_cnr, yes, it samples inwards and outwards 1mm along the surface 
normal. And I think pctsurfcon is the tool I meant, but hopefully David 
and/or Doug can confirm

cheers
Bruce
On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:



External Email - Use Caution

Hi Dr. Fischl, 
It looks like pctsurfcon was the tool you were referring to. Is this the
right one?

Also, would brain.mgz be the appropriate volume to use to extract the G-W
contrast ratios for the cortical parcels?

Finally, for mri_cnr according to this post, the CNR values are computed
using the voxels at the interface of the white and pial 
surface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38829.html)

Are these voxels offset from the white and pial surfaces by a specific
default distance?

Thanks,
Prad

On Thu, May 28, 2020 at 10:47 AM Pradyumna Bharadwaj
 wrote:
  Is it the pctsurfcon tool? (
  https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon)

On Thu, May 28, 2020 at 10:12 AM Bruce Fischl
 wrote:
  External Email

  David and Doug: can you point Prad in the right direction
  for looking at
  gray and white signal changes and ratios?
  On Thu, 28 May 2020, Pradyumna
  Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl,
  > Thank you for suggesting that. 
  > Would it be possible to share a link to a page with
  information about this
  > stream or to a patch?
  >
  > Thanks,
  > Prad
  >
  > On Thu, May 28, 2020 at 9:46 AM Bruce Fischl
  
  > wrote:
  >       External Email
  >
  >       I see. I think Doug has a more modern stream for
  this that David
  >       Salat
  >       has also used a lot
  >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi Dr. Fischl,
  >       > Thanks for confirming that!
  >       > We were broadly interested in testing whether
  age-related
  >       differences in
  >       > cortical measures were impacted by the CNR in
  each ROI.
  >       >
  >       > Best,
  >       > Prad
  >       >
  >       > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
  >       
  >       > wrote:
  >       >       External Email
  >       >
  >       >       Hi Prad
  >       >
  >       >       what is your goal? What you describe below
  should work
  >       >
  >       >       cheers
  >       >       Bruce
  >       >       On Thu, 28 May 2020,
  >       >       Pradyumna Bharadwaj wrote:
  >       >
  >       >       >
  >       >       > External Email - Use
  Caution
  >       >       >
  >       >       > Hi Dr. Fischl,
  >       >       > Thank you for clarifying that!
  >       >       >
  >       >       > As a follow up question, I just wanted
  to double check
  >       that
  >       >       the method
  >       >       > outlined in this post is still a valid
  approach to
  >       obtaining
  >       >       the CNR values
  >       >       > for each of the ROIs 
intheDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.ha
  rva
  >       rd.edu/msg62066.
  >       >       html)
  >       >       > .
  >       >       >
  >       >       > Briefly, you recommended converting the
  aparc
  >       annotation to
  >       >       labels in the
  >       >       > atlas, and applying mri_cnr to each
  label.
  >       >       >
  >       >       > Best,
  >       >       > Prad
  >       >       >
  >       >       > On Thu, May 28, 2020 at 9:14 AM Bruce
  Fischl
  >       >       
  >       >       > wrote:
  >       >       >       External Email
  >       >       >
  >       >       >       Hi Prad
  >       >       >
  >       >       >       if you use the cortex.label is
  will avoid using
  >       the
  >       >       non-cortical
  >       >       >       regions in
  >       >       >       the surface, like the midline, so
  should be a
  >       more
  >       >       accurate
  >       >       >       measure
  >       >       >

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

Hi Marina

can you upload this subject? I'm not sure what is going on. Or send us the 
recon-all.log?


The vertex error means that the surfaces don't match. This usually means 
that you recreated some but not all of the surfaces for one of the hemis


cheers
Bruce




On Thu, 28 May 2020, Marina Fernández wrote:



External Email - Use Caution

Hi Bruce,

The talairach transform is reasonable and the aseg segment the cc correctly.

I run with freesurfer dev version the same command (recon all -autorecon-2wm
-subjid post_006) and now I have more information about what could be the
problem. The output of the terminal (that you can see below) says that there
is a vertex in the curv file of each hemisphere that has one vertex number
that it  is not expected. When I open the curv file in tksurfer there is a 0
in these positions.

Maybe this output can be useful to help me solve the problem. 
What do you think I should do? Thanks in advance! 


mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10
rh.inflated

setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11]
total integrated curvature = 0.637*4pi (8.002) --> 0 handles
ICI = 1.5, FI = 8.0, variation=142.940
106 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at
99.90% level
curvature mean = 0.000, std = 0.001
125 vertices thresholded to be in [-0.16 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std =
0.023
done.
@#@FSTIME  2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P
99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76
@#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77

#-
#@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats
-F smoothwm post_006 lh curv sulc

             Toggling save flag on curvature files                       [
ok ]
                 Outputting results using filestem   [
../stats/lh.curv.stats ]
             Toggling save flag on curvature files                       [
ok ]
                                   Setting surface     [
post_006/lh.smoothwm ]
                                Reading surface...                       [
ok ]
                                   Setting texture                     [
curv ]
                                Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/lh.curv

***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.

You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.

Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*

      Calculating Discrete Principal Curvatures...
      Determining geometric order for vno faces... [] [
ok ]
                      Determining KH curvatures... [] [
ok ]
                    Determining k1k2 curvatures... [] [
ok ]
                                   deltaViolations                      [
208 ]

WARN:    S lookup   min:                          -0.238596
WARN:    S explicit min:                          0.00 vertex = 1525
@#@FSTIME  2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U
2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77
@#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77

#-
#@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats
-F smoothwm post_006 rh curv sulc

             Toggling save flag on curvature files                       [
ok ]
                 Outputting results using filestem   [
../stats/rh.curv.stats ]
             Toggling save flag on curvature files                       [
ok ]
                                   Setting surface     [
post_006/rh.smoothwm ]
                                Reading surface...                       [
ok ]
                                   Setting texture                     [
curv ]
                                Reading texture...error: No such file or
directory
error: MRISreadNewCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/post_006/surf/rh.curv

***WARNING!***
Some error has occurred while reading 'rh.curv'.
This might be due a vertex

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

David and Doug: can you point Prad in the right direction for looking at 
gray and white signal changes and ratios?
On Thu, 28 May 2020, Pradyumna 
Bharadwaj wrote:




External Email - Use Caution

Hi Dr. Fischl,
Thank you for suggesting that. 
Would it be possible to share a link to a page with information about this
stream or to a patch?

Thanks,
Prad

On Thu, May 28, 2020 at 9:46 AM Bruce Fischl 
wrote:
  External Email

  I see. I think Doug has a more modern stream for this that David
  Salat
  has also used a lot
  On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl,
  > Thanks for confirming that!
  > We were broadly interested in testing whether age-related
  differences in
  > cortical measures were impacted by the CNR in each ROI.
  >
  > Best,
  > Prad
  >
  > On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
  
  > wrote:
  >       External Email
  >
  >       Hi Prad
  >
  >       what is your goal? What you describe below should work
  >
  >       cheers
  >       Bruce
  >       On Thu, 28 May 2020,
  >       Pradyumna Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi Dr. Fischl,
  >       > Thank you for clarifying that!
  >       >
  >       > As a follow up question, I just wanted to double check
  that
  >       the method
  >       > outlined in this post is still a valid approach to
  obtaining
  >       the CNR values
  >       > for each of the ROIs in 
theDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harva
  rd.edu/msg62066.
  >       html)
  >       > .
  >       >
  >       > Briefly, you recommended converting the aparc
  annotation to
  >       labels in the
  >       > atlas, and applying mri_cnr to each label.
  >       >
  >       > Best,
  >       > Prad
  >       >
  >       > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
  >       
  >       > wrote:
  >       >       External Email
  >       >
  >       >       Hi Prad
  >       >
  >       >       if you use the cortex.label is will avoid using
  the
  >       non-cortical
  >       >       regions in
  >       >       the surface, like the midline, so should be a
  more
  >       accurate
  >       >       measure
  >       >
  >       >       cheers
  >       >       Bruce
  >       >
  >       >
  >       >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hi,
  >       >       >
  >       >       > I had a question about the -label flag in
  mri_cnr.
  >       >       >
  >       >       > 1) When you do not use the -label option and
  just use
  >       the
  >       >       following command:
  >       >       >  mri_cnr $FREESURFER_HOME/subjects/bert/surf 
   
  >       >       $FREESURFER_HOME/subjects/be
  >       >       > rt/mri/norm.mgz
  >       >       >
  >       >       > The output is as follows
  >       >       >
  >       >       >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
  >       55.3+-16.6
  >       >       gray/white CNR = 1.
  >       >       > 983, gray/csf CNR = 0.907
  >       >       >
  >       >       >  lh CNR = 1.445
  >       >       >
  >       >       > white = 96.4+-6.0, gray = 76.0+-13.3, csf =
  55.6+-16.2
  >       >       gray/white CNR = 1.95
  >       >       > 2, gray/csf CNR = 0.943
  >       >       >
  >       >       > rh CNR = 1.448
  >       >       >
  >       >       >  total CNR = 1.446
  >       >       >
  >       >       >
  >       >       > 2) When you add  -label
  >       >     
   $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >       >       > 
  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label
  >       to the
  >       >       first comm

Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

I see. I think Doug has a more modern stream for this that David Salat 
has also used a lot

On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:



External Email - Use Caution

Hi Dr. Fischl,
Thanks for confirming that!
We were broadly interested in testing whether age-related differences in
cortical measures were impacted by the CNR in each ROI.

Best,
Prad

On Thu, May 28, 2020 at 9:33 AM Bruce Fischl 
wrote:
  External Email

  Hi Prad

  what is your goal? What you describe below should work

  cheers
  Bruce
  On Thu, 28 May 2020,
  Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi Dr. Fischl,
  > Thank you for clarifying that!
  >
  > As a follow up question, I just wanted to double check that
  the method
  > outlined in this post is still a valid approach to obtaining
  the CNR values
  > for each of the ROIs in the 
Desikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.
  html)
  > .
  >
  > Briefly, you recommended converting the aparc annotation to
  labels in the
  > atlas, and applying mri_cnr to each label.
  >
  > Best,
  > Prad
  >
  > On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
  
  > wrote:
  >       External Email
  >
  >       Hi Prad
  >
  >       if you use the cortex.label is will avoid using the
  non-cortical
  >       regions in
  >       the surface, like the midline, so should be a more
  accurate
  >       measure
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi,
  >       >
  >       > I had a question about the -label flag in mri_cnr.
  >       >
  >       > 1) When you do not use the -label option and just use
  the
  >       following command:
  >       >  mri_cnr $FREESURFER_HOME/subjects/bert/surf   
  >       $FREESURFER_HOME/subjects/be
  >       > rt/mri/norm.mgz
  >       >
  >       > The output is as follows
  >       >
  >       >   white = 96.6+-6.0, gray = 75.7+-13.5, csf =
  55.3+-16.6
  >       gray/white CNR = 1.
  >       > 983, gray/csf CNR = 0.907
  >       >
  >       >  lh CNR = 1.445
  >       >
  >       > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
  >       gray/white CNR = 1.95
  >       > 2, gray/csf CNR = 0.943
  >       >
  >       > rh CNR = 1.448
  >       >
  >       >  total CNR = 1.446
  >       >
  >       >
  >       > 2) When you add  -label
  >       $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >       >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label
  to the
  >       first command,
  >       > you get different (lower) cnr values.
  >       >
  >       > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
  >       gray/white CNR = 1.38
  >       > 9, gray/csf CNR = 0.644
  >       >
  >       > lh CNR = 1.016
  >       >
  >       > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
  >       gray/white CNR = 1.35
  >       > 3, gray/csf CNR = 0.652
  >       >
  >       > rh CNR = 1.002
  >       >
  >       > total CNR = 1.009
  >       >
  >       > How is the lh.cortex and rh.cortex label changing the
  CNR
  >       computation?
  >       >
  >       > Any inputs or thoughts on this matter are greatly
  appreciated!
  >       >
  >       > Thanks,
  >       > Prad
  >       >
  >       >___
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  >     
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  >
  >
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Re: [Freesurfer] [EXT]Re: mri_cnr label flag

[Bruce Fischl]

Hi Prad

what is your goal? What you describe below should work

cheers
Bruce
On Thu, 28 May 2020, 
Pradyumna Bharadwaj wrote:




External Email - Use Caution

Hi Dr. Fischl,
Thank you for clarifying that!

As a follow up question, I just wanted to double check that the method
outlined in this post is still a valid approach to obtaining the CNR values
for each of the ROIs in the Desikan-Killiany 
atlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html)
.

Briefly, you recommended converting the aparc annotation to labels in the
atlas, and applying mri_cnr to each label.

Best,
Prad

On Thu, May 28, 2020 at 9:14 AM Bruce Fischl 
wrote:
  External Email

  Hi Prad

  if you use the cortex.label is will avoid using the non-cortical
  regions in
  the surface, like the midline, so should be a more accurate
  measure

  cheers
  Bruce


  On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:

  >
  > External Email - Use Caution
  >
  > Hi,
  >
  > I had a question about the -label flag in mri_cnr.
  >
  > 1) When you do not use the -label option and just use the
  following command:
  >  mri_cnr $FREESURFER_HOME/subjects/bert/surf   
  $FREESURFER_HOME/subjects/be
  > rt/mri/norm.mgz
  >
  > The output is as follows
  >
  >   white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6
  gray/white CNR = 1.
  > 983, gray/csf CNR = 0.907
  >
  >  lh CNR = 1.445
  >
  > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2
  gray/white CNR = 1.95
  > 2, gray/csf CNR = 0.943
  >
  > rh CNR = 1.448
  >
  >  total CNR = 1.446
  >
  >
  > 2) When you add  -label
  $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
  >  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the
  first command,
  > you get different (lower) cnr values.
  >
  > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5
  gray/white CNR = 1.38
  > 9, gray/csf CNR = 0.644
  >
  > lh CNR = 1.016
  >
  > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3
  gray/white CNR = 1.35
  > 3, gray/csf CNR = 0.652
  >
  > rh CNR = 1.002
  >
  > total CNR = 1.009
  >
  > How is the lh.cortex and rh.cortex label changing the CNR
  computation?
  >
  > Any inputs or thoughts on this matter are greatly appreciated!
  >
  > Thanks,
  > Prad
  >
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Re: [Freesurfer] mri_cnr label flag

[Bruce Fischl]

Hi Prad

if you use the cortex.label is will avoid using the non-cortical regions in 
the surface, like the midline, so should be a more accurate measure


cheers
Bruce


On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:



External Email - Use Caution

Hi,

I had a question about the -label flag in mri_cnr.

1) When you do not use the -label option and just use the following command:
 mri_cnr $FREESURFER_HOME/subjects/bert/surf    $FREESURFER_HOME/subjects/be
rt/mri/norm.mgz

The output is as follows

  white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.
983, gray/csf CNR = 0.907 


 lh CNR = 1.445

white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.95
2, gray/csf CNR = 0.943 


rh CNR = 1.448

 total CNR = 1.446


2) When you add  -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
 $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command, 
you get different (lower) cnr values.


white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.38
9, gray/csf CNR = 0.644 


lh CNR = 1.016

white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.35
3, gray/csf CNR = 0.652 


rh CNR = 1.002

total CNR = 1.009

How is the lh.cortex and rh.cortex label changing the CNR computation?

Any inputs or thoughts on this matter are greatly appreciated!

Thanks,
Prad

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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

have you also looked at the talairach transform to make sure it is 
reasonable? And does the aseg segment the cc properly? That is, does it 
label it as wm as it crosses from one hemi to the other?
On Thu, 28 May 
2020, Marina Fernández wrote:




External Email - Use Caution

Hi Bruce,
Yes, everything seems normal in the input files of mri_fill. We review it
slice by slice in freeview.

Do you know what could have happened?

Best regards,
Marina



---
---


  Hi Marina

 
  have you looked at the inputs to mri_fill? Does the
  aseg.auto_noCCseg.mgz and the wm.mgz look ok?
  Bruce

  On Wed, 27 May 2020, Marina Fernández wrote:
  External Email - Use Caution Dear Freesurfer
  experts, When I run "recon-all -autorecon2-wm -subjid post_006"
  I get the following
  error: ... #
  #@# Fill Tue May 26 16:13:33 CEST 2020
  /usr/local/freesurfer/subjects/post_006/mri  mri_fill -a
  ../scripts/ponscc.cut.log -xform transforms/talairach.lta
  -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging
  cutting plane coordinates to ../scripts/ponscc.cut.log...
  INFO: Using transforms/talairach.lta and its offset for
  Talairach volume ...
  using segmentation aseg.auto_noCCseg.mgz...
  reading input volume...done.
  searching for cutting planes...voxel to talairach voxel
  transform
   1.03994   0.01456   0.07738  -16.87541;
  -0.02607   1.18971   0.24142  -16.40842;
  -0.06544  -0.23822   1.03825   18.09422;
   0.0   0.0   0.0   1.0;
  reading colortable from MGH file...
  colortable with 14176 entries read (originally
  /usr/local/freesurfer/FreeSurferColorLUT.txt)
  voxel to talairach voxel transform
   1.03994   0.01456   0.07738  -16.87541;
  -0.02607   1.18971   0.24142  -16.40842;
  -0.06544  -0.23822   1.03825   18.09422;
   0.0   0.0   0.0   1.0;
  reading segmented volume aseg.auto_noCCseg.mgz...
  mri_fill: could not find any points where lh and rh wm  are nbrs
  No such file or directory
  Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May
  30 11:18:27
  UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006
  exited with ERRORS at Tue May 26 16:13:41 CEST 2020 To report a
  problem, see
  http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have
  seen in other questions that this error may be due to the CC and
  the
  aseg files, and it is interesting because when I load
  aseg.auto.mgz or
  aseg.auto_noCCseg.mgz files in Freeview, the following message
  in Freeview
  terminal is shown in red:
  "colortable with 14176 entries read (originally
  /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think
  they should be
  1475 entries. I'm using freesurfer v6.0. Could you help me to
  solve this problem?
  Thank you in advance! Marina.


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Re: [Freesurfer] mris_register using manual label(s) as guides

[Bruce Fischl]

Hi Danny

yes, you can specify up to 100 labels. Make sure that the label name is 
exactly as it appears in the parcellation though


cheers
Bruce
On Wed, 27 May 2020, Danny 
Kim wrote:




External Email - Use Caution

Hi FreeSurfer experts,


I'm currently working on a brain with a bit of atypical morphology and was
wanting to parcellate through the DKT labels, but by using manually drawn
labels as guides. The intent here is to fix specific labels to be where they
are on the surface by drawing them manually and then automatically classify
other labels around them (e.g. fix precentral and superiortemporal using
manual labels).


However, it seems like during the mris_register step, I'm able to use one of
my manual label to guide the registration to the sphere, but not more than
one.


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs
precentral -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg
(WORKS, after mris_ca_label, precentral is where the manual label was.
Superior temporal label is not where the manual label is)


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs
precentral -L label/manual_superiortemporal.label DKTatlas40.gcs
superiortemporal -curv sphere folding.atlas.acfb40.noaparc.tif
surf/sphere.reg (Runs but output looks exactly the same as before, i.e.
superiortemporal label is not where the manual label was specified)


Is there a trick to specifying multiple manual labels in guiding
mris_register?
I am not sure if the -L flag can be specified multiple times and there's no
information on that on the mris_register manual.

I'm using the following FreeSurfer on my MAC:
freesurfer-i386-apple-darwin11.4.2-stable6-20170119

Thanks for your time in this experts!

Danny Kim





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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

Hi Marina

have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz 
and the wm.mgz look ok?

Bruce


On Wed, 27 May 2020, Marina 
Fernández wrote:




External Email - Use Caution

Dear Freesurfer experts,

When I run "recon-all -autorecon2-wm -subjid post_006" I get the following
error:

...

#
#@# Fill Tue May 26 16:13:33 CEST 2020
/usr/local/freesurfer/subjects/post_006/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading colortable from MGH file...
colortable with 14176 entries read (originally
/usr/local/freesurfer/FreeSurferColorLUT.txt)
voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading segmented volume aseg.auto_noCCseg.mgz...
mri_fill: could not find any points where lh and rh wm  are nbrs
No such file or directory
Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




I have seen in other questions that this error may be due to the CC and the
aseg files, and it is interesting because when I load aseg.auto.mgz or
aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
terminal is shown in red:
"colortable with 14176 entries read (originally
/usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
1475 entries.

I'm using freesurfer v6.0.

Could you help me to solve this problem?
Thank you in advance!

Marina.

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Re: [Freesurfer] mris_register intermediate results display

[Bruce Fischl]

Hi Chris

if you specify -w  on the command line it will write out a surface 
every n iterations of the minimization (-n 1 will write out every step). 
You can then write a script to turn those into tiffs with freeview


cheers
Bruce
On Thu, 
21 May 2020, Chris Adamson wrote:




External Email - Use Caution

Freesurfer devs,

 

Apologies if this has already been asked. I’m looking for a way that I can
look at the progress of mris_register to investigate the accuracy of
registration. Given that the registration is done on the 2D
parameterisations of the curvature maps, how can I take a spherical surface
and write out a tif file with the curvature maps of the surface that I’m
registering and the target surface. I presume I need to use mrisp_write but
it is unclear how I choose the curvature map to write in the image.

 

Thanks in advance,

 

Chris.

 

Dr Chris Adamson

Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)

Software Engineer, Cardiovascular Research (0.7 EFT)

 

Murdoch Childrens Research Institute

The Royal Children’s Hospital

Flemington Road, Parkville, VIC 3052 Australia

E chris.adam...@mcri.edu.au 

www.mcri.edu.au

 



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Re: [Freesurfer] FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"

[Bruce Fischl]

Sure, send us a .nii volume that fails and we will take a look
Bruce

> On May 19, 2020, at 11:38 PM, Safi Ullah .  wrote:
> 
> 
> External Email - Use Caution
> 
> Thank You Sir, 
> 
> Below is the header info of the volume, I read in Matlab. 
> "   srcbext: ''
> analyzehdr: []
>   bhdr: []
>vol: [256×146×256 double]
>   niftihdr: [1×1 struct]
>  fspec: 'D:\FS_Shared\New 
> folder\PPMI_3000_MR_sag_3D_FSPGR_BRAVO_straight__br_raw_20110322143431148_70_S102119_I224562.nii'
>pwd: 'D:\Safi\Parkinson'
> flip_angle: 0
> tr: 0
> te: 0
> ti: 0
>   vox2ras0: [4×4 double]
>volsize: [256 146 256]
> height: 256
>  width: 146
>  depth: 256
>nframes: 1
>vox2ras: [4×4 double]
>nvoxels: 9568256
>  xsize: 1.2000
>  ysize: 1.
>  zsize: 1.
>x_r: 0.9992
>x_a: 0.0283
>x_s: 0.0298
>y_r: -0.0204
>y_a: 0.9709
>y_s: -0.2386
>z_r: -0.0357
>z_a: 0.2378
>z_s: 0.9707
>c_r: 2.1796
>c_a: 7.4944
>c_s: -8.3277
>   vox2ras1: [4×4 double]
>Mdc: [3×3 double]
> volres: [1. 1.2000 1.]
> tkrvox2ras: [4×4 double]"
> 
> 
> So, the raw image size is 256x146x256
> and voxal size is 1x1.2x1 mm
> i downloaded as T1 (ticked button) from PPMI, and also visually looks ok 
> 
> Regards, 
> 
> Safi
> 
>> On Wed, May 20, 2020 at 11:27 AM Douglas N. Greve  
>> wrote:
>> Have you looked at the images? Are they T1-weighted? What is their 
>> resolution?
>> 
>> On 5/19/2020 5:20 PM, Safi Ullah . wrote:
>>> External Email - Use Caution
>>> 
>>> Thank you Sir,
>>> I downloaded the volumes from PPMI, it is .nii,  it is whole brain. Can I 
>>> send you one sample volume? 
>>> 
>>> On Wed, May 20, 2020, 12:33 AM Douglas N. Greve  
>>> wrote:
 It looks like mri_ca_register failed to create the m3z. If this is failing 
 on 13 subjects, then there is something systematically wrong. What kind of 
 input do you have? Eg, MPRAGE? What is the resolution? Is it whole brain? 
 
> On 5/19/2020 11:17 AM, Safi Ullah . wrote:
> External Email - Use Caution
> 
> Dear Freesurfer, 
> 
> Using Freesurfer version 7.1, I was running recon-all on 13 subjects, 
> using the command below
> ls *.nii | parallel -jobs 8 recon-all -s {.} -I {} -all –qcache
> (also checked with this one find . -name '*.nii' | parallel -j 8 
> recon-all -s {.} -i {} -all -qcache)
> but each time i face the same error as attached with the mail. 
> I checked the transformation folder, but the said file, talairach.m3z, is 
> not there. 
> the error is not same for all cases, some cases showed a different 
> errors, stating "IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF 
> ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH:" as attached file 
> recon-all(2nd type).log
> 
> Regards
> 
> 
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Re: [Freesurfer] vol2subfield single time course from multiple regions

[Bruce Fischl]

--replaceonly   \
--replaceonly   \
.
.
.

On Mon, 18 May 2020, std...@virgilio.it wrote:



External Email - Use Caution

As reported in previous mails I have do it but with some problems.

Moreover, how can I do with multiple arguments (more than 2)?

  Il 17 maggio 2020 alle 21.30 Bruce Fischl <
  fis...@nmr.mgh.harvard.edu> ha scritto:


Hi Stefano

--replaceonly takes two arguments - the label you want to replace and
the
one you want to replace it with

cheers
Bruce


On Sun, 17 May 2020, std...@virgilio.it wrote:

  External Email - Use Caution

just a kind reminder

many thanks

  Il 15 maggio 2020 alle 1.05 std...@virgilio.it ha scritto:

  mri_binarize --i
  $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
--replaceonly 8204 --replaceonly 8205 --replaceonly 8206
--replaceonly 8217 --replaceonly 8218 --o
$SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8205 unknown


mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
--replaceonly 8204 --replaceonly 8205 --replaceonly 8217
--replaceonly
8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8217 unknown
Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"
< dgr...@mgh.harvard.edu> ha scritto:

  Just add more --replaceonly args

  On 5/14/2020 10:38 AM, std...@virgilio.it wrote:

  External Email - Use Caution

  Moreover, how can I merge, with mri_binarize, more
thalamic regions?

  e.g. 8204 8205 8206 8217 8218

  Il 13 maggio 2020 alle 23.03 "Douglas N.
Greve" < dgr...@mgh.harvard.edu> ha
scritto:

  It problably means that seg 8130 does
not exist in the input mgz. Can you
confirm that it does?

  On 5/13/2020 12:51 PM,
std...@virgilio.it wrote:

  External Email - Use
Caution

  indeed. I would like to merge two
regions and extract the fMRI time serie.
if no difference is there, somewhat is
wrong. the L-VP file contains the same
information of ThalamicNuclei.v10.T1.

  thanks

  Il 13 maggio 2020 alle 17.02
"Douglas N. Greve"
< dgr...@mgh.harvard.edu> ha
scritto:

  That means there is no
difference

  On 5/13/2020 10:47 AM,
std...@virgilio.it wrote:

  External Email - Use
Caution

  is the command line ok?

  by running

  mri_binarize --i
ThalamicNuclei.v10.T1.mgz
--replace-only 8130 8133 --o
L-VP.mgz

  mri_diff --po
mri/ThalamicNuclei.v10.T1.mgz
L-VP.mgz  

  I obtain
diffcount 0

  Il 12 maggio 2020 alle
0.53
std...@virgilio.it ha
scritto:

  by running
mri_diff --po
mri/ThalamicNuclei.v10.T1.mgz
L-VP.mgz  
I obtain
diffcount 0

  Il 11 maggio
2020 alle 19.18
"Douglas N.
Greve"
< dgr...@mgh.harvard.edu>
ha scritto:

  Try running this
to see if there
is a difference
mri_diff --po
ThalamicNuclei.v10.T1.mgz
Left-Ventroposterior.mgz
Sometimes it is
not easy to see
a difference
that is just a
few voxels

  On 5/11/2020
3:02 AM,
std...@virgilio.it
wrote:

  External
Email -
Use
Caution

  By
visualizing
the output
by
freeview,
I found
that it
was the
same
of ThalamicNuclei.v10.T1.mgz.

  Thanks

  Il
11
maggio
2020
alle
2.19
Bruce
Fischl
<
fis...@nmr.mgh.harvard.edu>
ha
scritto:


Hi Stefano

can you
elaborate?
Why do you
suspect
there is
an error?

cheers
Bruce
On Mon, 11
May
2020,
std...@virgilio.it
wrote:

  External
Email
-
Use
Caution

Please,
could
you
check
the
command
line.
I
suspect
that
an
error
is
there.
Thanks.
Stefano

mri_binarize
--i
ThalamicNuclei.v10.T1.mgz
--replace-only
8130

8133
--o
Left-Ventroposterior.mgz

  Il
30
aprile
2020
alle
18.51
"Douglas
N.
Greve"
<
dgr...@mgh.harvard.edu>
ha
scritto:

  You
can
use
mri_binarize
--i
ThalamicNuclei.v10.T1.mgz
--replace-only
segid
segidreplace
...
--o
newseg.mgz
to
create
a
new
segmentation
with
merged
segments,
then
using
vol2subfield
with
the
newseg
seg
as
--sf

  On
4/29/2020
7:57
PM,
std...@virgilio.it
wrote:

  External
Email
-
Use
Caution

  Hi
list,

  vol2subfield
--i
fmcpr.nii.gz
--reg
register.dof6.lta
--sf
ThalamicNuclei.v10.T1.mgz
--stats
stats.dat
--avgwf
avgwf.dat
--avgwfvol
avgwfvol.mgz
--o
f2subf.nii.gz

  extracts
the
time
course
from
each
thalamic
subregions.

  If
I
would
like
to
merge
multiple
regions
(e.g. --id
8115
--id
8116)
and
extract
a
single
time
course
from
them,
which
is
the
way?

  Thanks

  Stefano



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Re: [Freesurfer] rh postcentral gyrus segmentation error

[Bruce Fischl]

Hi Ken

have you identified why it is missing cortex? Is the wm dark-ish (<<110) 
there? Did the skull stripping remove something? Was the wm.mgz/?h.orig 
correct?


cheers
Bruce

On Mon, 18 May 2020, 
KennethSPrice wrote:




External Email - Use Caution

Hello Freesurfer Experts!

I am looking for some guidance on improving the pial surface estimation at
the right post-central gyrus. Looking at the aparc+aseg file, it is clear
that the pial surface estimation missed some cortex. I have already
experimented with different -wthresh values. 

Thanks,
Ken


Sent with ProtonMail Secure Email.


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Re: [Freesurfer] vol2subfield single time course from multiple regions

[Bruce Fischl]

Hi Stefano

--replaceonly takes two arguments - the label you want to replace and the 
one you want to replace it with


cheers
Bruce


On Sun, 17 May 2020, std...@virgilio.it wrote:



External Email - Use Caution

just a kind reminder

many thanks


  Il 15 maggio 2020 alle 1.05 std...@virgilio.it ha scritto:

  mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
  --replaceonly 8204 --replaceonly 8205 --replaceonly 8206
  --replaceonly 8217 --replaceonly 8218 --o
  $SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8205 unknown


mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
--replaceonly 8204 --replaceonly 8205 --replaceonly 8217 --replaceonly
8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8217 unknown
  Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"
   ha scritto:

  Just add more --replaceonly args

  On 5/14/2020 10:38 AM, std...@virgilio.it wrote:

  External Email - Use Caution

  Moreover, how can I merge, with mri_binarize, more
  thalamic regions?

  e.g. 8204 8205 8206 8217 8218


Il 13 maggio 2020 alle 23.03 "Douglas N.
Greve"  ha
scritto:

It problably means that seg 8130 does
not exist in the input mgz. Can you
confirm that it does?

On 5/13/2020 12:51 PM,
std...@virgilio.it wrote:

  External Email - Use
  Caution

  indeed. I would like to merge two
  regions and extract the fMRI time serie.
  if no difference is there, somewhat is
  wrong. the L-VP file contains the same
  information of ThalamicNuclei.v10.T1.

  thanks


Il 13 maggio 2020 alle 17.02
"Douglas N. Greve"
 ha
scritto:

That means there is no
difference

On 5/13/2020 10:47 AM,
std...@virgilio.it wrote:

  External Email - Use
  Caution

  is the command line ok?

  by running

  mri_binarize --i
  ThalamicNuclei.v10.T1.mgz
  --replace-only 8130 8133 --o
  L-VP.mgz

  mri_diff --po
  mri/ThalamicNuclei.v10.T1.mgz
  L-VP.mgz  

  I obtain
diffcount 0


  Il 12 maggio 2020 alle
  0.53
  std...@virgilio.it ha
  scritto:

  by running
mri_diff --po
mri/ThalamicNuclei.v10.T1.mgz
L-VP.mgz  
I obtain
diffcount 0


  Il 11 maggio
  2020 alle 19.18
  "Douglas N.
  Greve"
  
  ha scritto:

  Try running this
  to see if there
  is a difference
  mri_diff --po
  ThalamicNuclei.v10.T1.mgz
  Left-Ventroposterior.mgz
  Sometimes it is
  not easy to see
  a difference
  that is just a
  few voxels

  On 5/11/2020
  3:02 AM,
  std...@virgilio.it
  wrote:

  External
  Email -
  Use
  Caution

  By
  visualizing
  the output
  by
  freeview,
  I found
  that it
  was the
  same
  of ThalamicNuclei.v10.T1.mgz.

  Thanks

Il
11
maggio
2020
    alle
    2.19
Bruce
Fischl
<
fis...@nmr.mgh.harvard.edu>
ha
scritto:


Hi Stefano

can you
elaborate?
Why do you
suspect
there is
an error?

cheers
Bruce
On Mon, 11
May
2020,
std...@virgilio.it
wrote:

  External
  Email
  -
  Use
  Caution

Please,
could
you
check
the
command
line.
I
suspect
that
an
error
is
there.
Thanks.
Stefano

mri_binarize
--i
ThalamicNuclei.v10.T1.mgz
--replace-only
8130
 
8133
--o
Left-Ventroposterior.mgz

  Il
  30
  aprile
  2020
  alle
  18.51
  "Douglas
  N.
  Greve"
<
dgr...@mgh.harvard.edu>
ha
scritto:

  You
  can
  use
  mri_binarize
  --i
  ThalamicNuclei.v10.T1.mgz
--replace-only
segid
segidreplace
...
--o
newseg.mgz
to
create
a
new
segmentation
with
merged
segments,
then
using
vol2subfield
with
the
newseg
seg
as
--sf

  On
  4/29/2020
  7:57
  PM,
  std...@virgilio.it
  wrote:

  External
  Email
  -
  Use
  Caution

  Hi
  list,

  vol2subfield
  --i
  fmcpr.nii.gz
  --reg
  register.dof6.lta
  --sf
ThalamicNuclei.v10.T1.mgz
--stats
stats.dat
--avgwf
avgwf.dat
--avgwfvol
avgwfvol.mgz
--o
f2subf.nii.gz

  extracts
  the
  time
  course
  from
  each
  thalamic
  subregions.

  If
  I
  would
  like
  to
  merge
  multiple
  regions
  (e.g. --id
  8115
--id
8116)
and
extract
a
single
time
course
from
them,
which
is
the
way?

  Thanks

  Stefano



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list
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Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

oh, then check out the bbregister help and see if you can get it working
On 
Sun, 17 May 2020, Amar Shukla wrote:




External Email - Use Caution

yes 

On Sun, May 17, 2020 at 8:54 PM Bruce Fischl 
wrote:
  sorry, I'm not sure I understand. bbregister will let you
  register a T2
  to the T1 of the same subject, is that what you want?

  cheers
  Bruce
  On Sun, 17 May 2020,
  Amar Shukla wrote:

  >
  > External Email - Use Caution
  >
  > Dear Sir,
  > thank you, Sir, for your valuable advice,
  >
  > Can I register all the t2 types file with a Structural
  template,
  > cross-registration we can do or not?
  >
  >
  >
  > On Mon, May 11, 2020 at 11:04 PM Douglas N. Greve
  
  > wrote:
  >       It is probably more up-to-date to run
  >       bbregister --help
  >
  >       On 5/9/2020 1:10 PM, Bruce Fischl wrote:
  >       https://surfer.nmr.mgh.harvard.edu/fswiki/bbregister
  >       On Sat, 9 May 2020, Amar Shukla wrote:
  >
  >
  >             External Email - Use Caution
  >
  >             Dear Sir,
  >             Thank you for valuable information, do we have
  >             any link or resource to get
  >             through this tool.
  >
  >             regards
  >             Amar Shukla
  >
  >             On Sat, May 9, 2020 at 10:31 PM Bruce Fischl
  >             
  >             wrote:
  >               Hi Amar
  >
  >               no restriction - all of those should be
  >             registerable using
  >               Doug's
  >               excellent bbregister tool
  >
  >               cheers
  >               Bruce
  >               On Sat, 9 May 2020, Amar Shukla wrote:
  >
  >               >
  >               > External Email - Use
  >             Caution
  >               >
  >               > Dear SirDo we have restriction in the
  >             registration with a
  >               different format
  >               > of data like DTI, sMRI, PET and many
  >             more or we can go for
  >               registration in
  >               > any combination in FREE Surfer.
  >               >
  >               > regards
  >               > Amar Shukla
  >               >
  >               > On Mon, Apr 13, 2020 at 8:14 PM Amar
  >             Shukla
  >                wrote:
  >               >       Thank you so much sir
  >               >
  >               > On Mon, 13 Apr 2020, 19:56 Bruce
  >             Fischl,
  >               
  >               > wrote:
  >               >       yes, that should be doable if
  >             you process in the order I
  >               >       suggested below
  >               >       cheers
  >               >       Bruce
  >               >       On
  >               >       Mon, 13 Apr 2020, Amar Shukla
  >             wrote:
  >               >
  >               >       >
  >               >       > External Email - Use
  >             Caution
  >               >       >
  >               >       > Dear Sir,
  >               >       >
  >               >       > Thank you for your precious
  >             reply  
  >               >       >
  >               >       > Actually i am working on to
  >             the study of Disease which
  >               >       have the effect on
  >               >       > the brain.
  >               >       >
  >               >       > 1) First i am using t1 image
  >             for analysis of the same
  >               >       subject of that
  >               >       > disease.
  >               >       >
  >               >       > 2) I am using Diffussion image
  >             for the analysis  for
  >               the
  >               >       same subject.
  >               >       >
  >               >       > So can i make any relation
  >             be

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

sorry, I'm not sure I understand. bbregister will let you register a T2 
to the T1 of the same subject, is that what you want?


cheers
Bruce
On Sun, 17 May 2020, 
Amar Shukla wrote:




External Email - Use Caution

Dear Sir,
thank you, Sir, for your valuable advice,

Can I register all the t2 types file with a Structural template,
cross-registration we can do or not?



On Mon, May 11, 2020 at 11:04 PM Douglas N. Greve 
wrote:
  It is probably more up-to-date to run
  bbregister --help

  On 5/9/2020 1:10 PM, Bruce Fischl wrote:
  https://surfer.nmr.mgh.harvard.edu/fswiki/bbregister
  On Sat, 9 May 2020, Amar Shukla wrote:


External Email - Use Caution

Dear Sir,
Thank you for valuable information, do we have
any link or resource to get
through this tool.

regards
Amar Shukla

On Sat, May 9, 2020 at 10:31 PM Bruce Fischl

wrote:
  Hi Amar

  no restriction - all of those should be
registerable using
  Doug's
  excellent bbregister tool

  cheers
  Bruce
  On Sat, 9 May 2020, Amar Shukla wrote:

  >
  > External Email - Use
Caution
  >
  > Dear SirDo we have restriction in the
registration with a
  different format
  > of data like DTI, sMRI, PET and many
more or we can go for
  registration in
  > any combination in FREE Surfer.
  >
  > regards
  > Amar Shukla
  >
  > On Mon, Apr 13, 2020 at 8:14 PM Amar
Shukla
   wrote:
  >       Thank you so much sir
  >
      > On Mon, 13 Apr 2020, 19:56 Bruce
Fischl,
  
  > wrote:
  >       yes, that should be doable if
you process in the order I
  >       suggested below
  >       cheers
  >       Bruce
  >       On
  >       Mon, 13 Apr 2020, Amar Shukla
wrote:
  >
  >       >
  >       > External Email - Use
Caution
  >       >
  >       > Dear Sir,
  >       >
  >       > Thank you for your precious
reply  
  >       >
  >       > Actually i am working on to
the study of Disease which
  >       have the effect on
  >       > the brain.
  >       >
  >       > 1) First i am using t1 image
for analysis of the same
  >       subject of that
  >       > disease.
  >       >
  >       > 2) I am using Diffussion image
for the analysis  for
  the
  >       same subject.
  >       >
  >       > So can i make any relation
between trac based analysis
  >       of diffusion image
  >       > and Volumetric analysis of T1
weighted image of same
  >       subject.
  >       >
      >       > regards
  >       > Amar Shukla
  >       >
  >       >
  >       > On Mon, 13 Apr 2020, 19:09
Bruce Fischl,
  >       
wrote:
  >       >       Hi Amar
  >       >
  >       >       I'm not quite sure I
understand your question,
  but
  >       in FS you
  >       >       would use
  >       >       the T1 as input to
recon-all, then the outputs
  of
  >       that and the
  >       >       diffusion
  >       >       data would let you run
tracula
  >       >
  >       >       cheers
  >       >       Bruce
  >       >       On Mon, 13 Apr 2020,
Amar Shukla wrote:
  >       >
  &g

Re: [Freesurfer] why fsaverage fold is a "link folder"

[Bruce Fischl]

because it is a folder we distribute that doesn't change for each study. 
You can certainly remove the link and cp -r it in from our distribution 
if you prefer.


cheers
Bruce
On Sun, 17 May 2020, ZhangBo wrote:



External Email - Use Caution

Hi teams, 
For recon-all in parallel, why fsaverage fold is a "link folder"?
I run recon-all in one computer (Ubuntu), and copy the result to another
computer for analysis. And error happened when I need to use data in
fsaverage folder.

Thanks
Bo


 


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Re: [Freesurfer] command not found: tksurfer

[Bruce Fischl]

Hi Bo

tkmedit and tksurfer have been deprecated for years. Try using freeview 
instead.


cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:



External Email - Use Caution

Hi teams, 
After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing
guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer.
It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh:
command not found: tksurfer", "zsh: command not found: tkmedit". Could you
please give some advice about how to solve this? Thanks.

Bo


 


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Re: [Freesurfer] Which subject does recon-all register surfaces to?

[Bruce Fischl]

Hi Ian

we don't register to an individual subject - we register to a 
probabilistic atlas compiled from many subjects. The fsaverage subjects 
were also generated from that data so they are in register, but the actual 
atlas is a .tif file that you can find as the target of mris_register in 
your recon-all.log file


cheers
Bruce


On Wed, 13 May 
2020, Ian wrote:




External Email - Use Caution

Hi guys.

After recon-all, the /surf/?h.sphere.reg file implies a registration has
been performed to an "average" subject on a sphere.  Can you please tell me
which subject this is?  Is it SUBJECTS_DIR/fsaverage?  If so, what is
SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to?  If not, where can I
find the subject that recon-all registers to?

Thanks,

Ian

--

Ian Hardingham



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Re: [Freesurfer] vol2subfield single time course from multiple regions

[Bruce Fischl]

Hi Stefano

can you elaborate? Why do you suspect there is an error?

cheers
Bruce
On Mon, 11 May 
2020, std...@virgilio.it wrote:




External Email - Use Caution

Please, could you check the command line.
I suspect that an error is there.
Thanks.
Stefano

mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130   8133 --o
Left-Ventroposterior.mgz


  Il 30 aprile 2020 alle 18.51 "Douglas N. Greve"
   ha scritto:

  You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz
  --replace-only segid segidreplace ... --o newseg.mgz
  to create a new segmentation with merged segments, then using
  vol2subfield with the newseg seg as --sf

  On 4/29/2020 7:57 PM, std...@virgilio.it wrote:

  External Email - Use Caution

  Hi list,

  vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf
  ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf
  avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz

  extracts the time course from each thalamic subregions.

  If I would like to merge multiple regions (e.g. --id 8115
  --id 8116) and extract a single time course from them,
  which is the way?

  Thanks


  Stefano



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Re: [Freesurfer] mris_fix_topology command does not finish

[Bruce Fischl]

no, I wouldn't think so. YOu can try mris_topo_fixer instead if you want, 
but really you need to diagnose what the cause of your problem is


On Sun, 10 May 2020, Billah, Tashrif wrote:


Hi Bruce,

Thanks for your prompt reply. I shall look at them as you noted. In the
meantime, putting in some more logs from the perpetuating defect correction
by mris_fix_topology:

13381 modVnum: vno:23308 has 6673 immediate neighbours
mrisurf_topology.cpp:370
13382 vno:23308 now has 6673 immediate neighbours  mrisurf_topology.cpp:400
13383 modVnum: vno:23308 has 6674 immediate neighbours
mrisurf_topology.cpp:370
13384 vno:23308 now has 6674 immediate neighbours  mrisurf_topology.cpp:400
13385 modVnum: vno:23308 has 6675 immediate neighbours
mrisurf_topology.cpp:370
13386 vno:23308 now has 6675 immediate neighbours  mrisurf_topology.cpp:400
13387 modVnum: vno:23308 has 6676 immediate neighbours
mrisurf_topology.cpp:370
13388 vno:23308 now has 6676 immediate neighbours  mrisurf_topology.cpp:400
13389 modVnum: vno:23308 has 6677 immediate neighbours
mrisurf_topology.cpp:370
13390 vno:23308 now has 6677 immediate neighbours  mrisurf_topology.cpp:400
13391 modVnum: vno:23308 has 6678 immediate neighbours
mrisurf_topology.cpp:370
13392 vno:23308 now has 6678 immediate neighbours  mrisurf_topology.cpp:400


However, will it help to play with the following args of mris_fix_topology?

        -niters N
                stop genetic algorithm after N iterations

        -seed N
                set random number generator to seed N

        -s N
                smooth corrected surface by N iterations

Cheers,
Tashrif


From: Billah, Tashrif 
Sent: Sunday, May 10, 2020 3:05 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: mris_fix_topology command does not finish  
Running the commands separately, I see the following log for some of the
defects. Is the weblink my cue?

CORRECTING DEFECT 0 (vertices=4912, convex hull=886, v0=0)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from
wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, 
seehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free
view

-Tashrif
.


From: Billah, Tashrif
Sent: Sunday, May 10, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Bouix, Sylvain,Ph.D. ; Knyazhanskaya, Evdokiya

Subject: mris_fix_topology command does not finish  
Hi there,

The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2`
does not finish for some of our data:

#@# Fix Topology lh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
lh

#@# Fix Topology rh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
rh

Waiting for PID 57296 of (57296 57299) to complete...
Waiting for PID 57299 of (57296 57299) to complete...

We kept them running for about 48 hours in multiple attempts, yet no luck.
Moreover, mris_fix_topology​ is a binary file so I am unable to debug
through.

Any suggestion on where to look at?

Best,
Tashrif


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Re: [Freesurfer] mris_fix_topology command does not finish

[Bruce Fischl]

what does the aseg look like? Why isn't the cerebllum being removed? Dura 
is harder (unless you have a T2 or FLAIR)
On Sun, 10 May 2020, Billah, 
Tashrif wrote:



Running the commands separately, I see the following log for some of the
defects. Is the weblink my cue?

CORRECTING DEFECT 0 (vertices=4912, convex hull=886, v0=0)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from
wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, 
seehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free
view

-Tashrif
.


From: Billah, Tashrif
Sent: Sunday, May 10, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Bouix, Sylvain,Ph.D. ; Knyazhanskaya, Evdokiya

Subject: mris_fix_topology command does not finish  
Hi there,

The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2`
does not finish for some of our data:

#@# Fix Topology lh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
lh

#@# Fix Topology rh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
rh

Waiting for PID 57296 of (57296 57299) to complete...
Waiting for PID 57299 of (57296 57299) to complete...

We kept them running for about 48 hours in multiple attempts, yet no luck.
Moreover, mris_fix_topology​ is a binary file so I am unable to debug
through.

Any suggestion on where to look at?

Best,
Tashrif


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Re: [Freesurfer] mris_fix_topology command does not finish

[Bruce Fischl]

Hi Tashrif

it is most likely not a bug in mris_fix_topology, but rather a defect 
that is too large to accurately correct. The topology correction 
complexity is quadratic in the side of the largest defects, so small ones 
are fast and big ones are super slow. In most cases the really big ones are 
caused by other things going wrong that the topology fixer wouldn't have 
corrected in any case (e.g. skull being attached to brain, hemispheres 
incorrectly connected, etc). You should check the ?h.inflated.nofix and 
?h.orig.nofix surfaces to see what is going on


cheers
Bruce


On Sun, 10 May 2020, 
Billah, Tashrif wrote:



Hi there,

The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2`
does not finish for some of our data:

#@# Fix Topology lh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
lh

#@# Fix Topology rh Sat May  9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
rh

Waiting for PID 57296 of (57296 57299) to complete...
Waiting for PID 57299 of (57296 57299) to complete...

We kept them running for about 48 hours in multiple attempts, yet no luck.
Moreover, mris_fix_topology​ is a binary file so I am unable to debug
through.

Any suggestion on where to look at?

Best,
Tashrif


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Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

https://surfer.nmr.mgh.harvard.edu/fswiki/bbregister
On Sat, 9 May 2020, 
Amar Shukla wrote:




External Email - Use Caution

Dear Sir,
Thank you for valuable information, do we have any link or resource to get
through this tool.

regards
Amar Shukla

On Sat, May 9, 2020 at 10:31 PM Bruce Fischl 
wrote:
  Hi Amar

  no restriction - all of those should be registerable using
  Doug's
  excellent bbregister tool

  cheers
  Bruce
  On Sat, 9 May 2020, Amar Shukla wrote:

  >
  > External Email - Use Caution
  >
  > Dear SirDo we have restriction in the registration with a
  different format
  > of data like DTI, sMRI, PET and many more or we can go for
  registration in
  > any combination in FREE Surfer.
  >
  > regards
  > Amar Shukla
  >
  > On Mon, Apr 13, 2020 at 8:14 PM Amar Shukla
   wrote:
  >       Thank you so much sir
  >
      > On Mon, 13 Apr 2020, 19:56 Bruce Fischl,
  
  > wrote:
  >       yes, that should be doable if you process in the order I
  >       suggested below
  >       cheers
  >       Bruce
  >       On
  >       Mon, 13 Apr 2020, Amar Shukla wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Dear Sir,
  >       >
  >       > Thank you for your precious reply  
  >       >
  >       > Actually i am working on to the study of Disease which
  >       have the effect on
  >       > the brain.
  >       >
  >       > 1) First i am using t1 image for analysis of the same
  >       subject of that
  >       > disease.
  >       >
  >       > 2) I am using Diffussion image for the analysis  for
  the
  >       same subject.
  >       >
  >       > So can i make any relation between trac based analysis
  >       of diffusion image
  >       > and Volumetric analysis of T1 weighted image of same
  >       subject.
  >       >
  >       > regards
  >       > Amar Shukla
  >       >
  >       >
  >       > On Mon, 13 Apr 2020, 19:09 Bruce Fischl,
  >        wrote:
  >       >       Hi Amar
  >       >
  >       >       I'm not quite sure I understand your question,
  but
  >       in FS you
  >       >       would use
  >       >       the T1 as input to recon-all, then the outputs
  of
  >       that and the
  >       >       diffusion
  >       >       data would let you run tracula
  >       >
  >       >       cheers
  >       >       Bruce
  >       >       On Mon, 13 Apr 2020, Amar Shukla wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hello Freesurfer,
  >       >       >
  >       >       > Can we go through the volumetric  [surface
  area
  >       and many more
  >       >       ] through DTI
  >       >       > images and  T1 or t2 weighted images of the
  same
  >       subject. Can
  >       >       we provide
  >       >       > common study and can we develop any analysis
  on
  >       these studies.
  >       >       > My research is focused on these direction o or
  >       any kind of
  >       >       corelation
  >       >       > through different Images .
  >       >       > basis of diffusion images and  T1 or t2
  weighted
  >       images,
  >       >       >
  >       >       > so please give suggestions and comment on
  these.
  >       >       >
  >       >       >
  >       >       >
  >       >       > --
  >       >       > With Regards,
  >       >       > Amar Shukla
  >       >       >
  >       >       >
  >       >       >___
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  >       >     
  >     
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >       >
  >       >
  >       >___
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  >       Freesurfer@nmr.mgh.harvard.edu
  >  

Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

Hi Amar

no restriction - all of those should be registerable using Doug's 
excellent bbregister tool


cheers
Bruce
On Sat, 9 May 2020, Amar Shukla wrote:



External Email - Use Caution

Dear SirDo we have restriction in the registration with a different format
of data like DTI, sMRI, PET and many more or we can go for registration in
any combination in FREE Surfer.

regards
Amar Shukla

On Mon, Apr 13, 2020 at 8:14 PM Amar Shukla  wrote:
  Thank you so much sir

On Mon, 13 Apr 2020, 19:56 Bruce Fischl, 
wrote:
  yes, that should be doable if you process in the order I
  suggested below
  cheers
  Bruce
  On
  Mon, 13 Apr 2020, Amar Shukla wrote:

  >
  > External Email - Use Caution
  >
  > Dear Sir,
  >
  > Thank you for your precious reply  
  >
  > Actually i am working on to the study of Disease which
  have the effect on
  > the brain.
  >
  > 1) First i am using t1 image for analysis of the same
  subject of that
  > disease.
  >
  > 2) I am using Diffussion image for the analysis  for the
  same subject.
  >
  > So can i make any relation between trac based analysis
  of diffusion image
  > and Volumetric analysis of T1 weighted image of same
  subject.
  >
  > regards
  > Amar Shukla
  >
  >
  > On Mon, 13 Apr 2020, 19:09 Bruce Fischl,
   wrote:
  >       Hi Amar
  >
  >       I'm not quite sure I understand your question, but
  in FS you
  >       would use
  >       the T1 as input to recon-all, then the outputs of
  that and the
  >       diffusion
  >       data would let you run tracula
  >
  >       cheers
  >       Bruce
  >       On Mon, 13 Apr 2020, Amar Shukla wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hello Freesurfer,
  >       >
  >       > Can we go through the volumetric  [surface area
  and many more
  >       ] through DTI
  >       > images and  T1 or t2 weighted images of the same
  subject. Can
  >       we provide
  >       > common study and can we develop any analysis on
  these studies.
  >       > My research is focused on these direction o or
  any kind of
  >       corelation
  >       > through different Images .
  >       > basis of diffusion images and  T1 or t2 weighted
  images,
  >       >
  >       > so please give suggestions and comment on these.
  >       >
  >       >
  >       >
  >       > --
  >       > With Regards,
  >       > Amar Shukla
  >       >
  >       >
  >       >___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >     
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  >
  >
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--
With Regards,
Amar Shukla
Assistant Professor, 
M tech AI ANN(2014-2016),
Centre Of Information Technology,
UPES 
Contact :+91 897 977 8016

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Re: [Freesurfer] recon-all-rms error < 2.00

[Bruce Fischl]

it looks to me like recon-all finished without a problem. Have you looked 
at the outputs? Is there another reason you think there is an issue? There 
are lots of internal "error" metrics we use to optimize things that are not 
errors in the programatic sense - they  are functionals we are 
minimizing/maximizing


cheers
Bruce


On Thu, 7 May 2020, jiahui wrote:



External Email - Use Caution

Hello FreeSurfer Developers,
I run the recon-all -all command:

this true error?how to resolve this problem?
 ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0

250/300: dt: 0.9000, rms radial error=134. 022, avgs=0

255/300: dt: 0.9000, rms radial error=133.265, avgs=0

260/300: dt: 0.9000, rMS radial error=132.513, avgs=0

265/300: dt: 0.9000, rms radial error=131. 766,

avgs=0

270/300: dt: 0.9000, rmS radial error=131. 022 ,

avgs=0

275/300: dt: 0.9000, rMS radial error=130 .283, avgs=o

280/300: dt: 0.9000, rMS radial error=129.548, avgs0

285/300: dt: 0.9000, rmS radial error=128.817 , avgs=0

290/300: dt: 0.9000, rms radial error=128 .090, avgs=0

295/300: dt: 0.9000, rMS radial error=127 .367 , avgs=0

300/300: dt: 0.9000, rMs radial error=126.648, avgs=0

final distance error %24.71

pass 1: epoch 1 of 3 starting distance error %19.14

pass 1: epoch 2 of 3 starting distance error %19.08

starting distance error X19.04

final distance error %19.04

pass 1: epoch 1 of 3 starting distance error %19.50

pass 1: epoch 2 of 3 starting distance error %19.45

starting distance error %19. 41

final distance error %19.43

recon-all -s 100034 finished without error at 2020# 05A 05E

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2be
b96c



 



 



 



 



 



 



 



 


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Re: [Freesurfer] recon-all-rms error < 2.00

[Bruce Fischl]

can you send us the recon-all.log file (as a text file)?
On Thu, 7 May 2020, 
jiahui wrote:




External Email - Use Caution

Hello FreeSurfer Developers,
I run the recon-all -all command:

this true error?how to resolve this problem?
 ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0

250/300: dt: 0.9000, rms radial error=134. 022, avgs=0

255/300: dt: 0.9000, rms radial error=133.265, avgs=0

260/300: dt: 0.9000, rMS radial error=132.513, avgs=0

265/300: dt: 0.9000, rms radial error=131. 766,

avgs=0

270/300: dt: 0.9000, rmS radial error=131. 022 ,

avgs=0

275/300: dt: 0.9000, rMS radial error=130 .283, avgs=o

280/300: dt: 0.9000, rMS radial error=129.548, avgs0

285/300: dt: 0.9000, rmS radial error=128.817 , avgs=0

290/300: dt: 0.9000, rms radial error=128 .090, avgs=0

295/300: dt: 0.9000, rMS radial error=127 .367 , avgs=0

300/300: dt: 0.9000, rMs radial error=126.648, avgs=0

final distance error %24.71

pass 1: epoch 1 of 3 starting distance error %19.14

pass 1: epoch 2 of 3 starting distance error %19.08

starting distance error X19.04

final distance error %19.04

pass 1: epoch 1 of 3 starting distance error %19.50

pass 1: epoch 2 of 3 starting distance error %19.45

starting distance error %19. 41

final distance error %19.43

recon-all -s 100034 finished without error at 2020# 05A 05E

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2be
b96c



 



 



 



 



 



 



 


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Re: [Freesurfer] T1 recon -all error "XL defect detected"

[Bruce Fischl]

ok, now I'm confused. Did recon-all finish or is it still running? What 
does the end of the recon-all.log file say?


Note that the spatial location of the inflated surfaces relative to the 
volumes doesn't mean anything


cheers
Bruce



On Wed, 6 May 2020, Zeng, Qi 
wrote:




External Email - Use Caution

Hi Bruce, 

After examining the sagittal view of the parietal lobe, it is fine including
the area. 
However, after examining the outputs in surf/, I noticed that after it
generated lh.defects, it stopped processing lh.smoothwm and never got a
chance to generate rh.defects. Compared to normal subjects that successfully
finished, there is a clear mismatch between the inflated.nofix and the
brainmask & wm.mgz. Attached below. 

Can you help confirm the fact of mismatch and let me know if there is any
way to fix this?

Thank you so much !
Best, 
Qi 

On Wed, May 6, 2020 at 10:12 AM Bruce Fischl 
wrote:
  Hi Qi

  it is not obvious from that one image that something is wrong
  there. What
  does a saggital view look like with the cursor on that region?
  Also, can
  you send an image of the rh.inflated.nofix in 3D mode? Sometime
  XL
  defects are fixable automatically, which may be the case for
  your
  subjects with very large ventricles, but sometimes not

  cheers
  Bruce
  On Tue, 5 May 2020,
  Zeng, Qi wrote:

  >
  > External Email - Use Caution
  >
  > Hi Douglas, 
  >
  > Compared to the ones without error, the subject surface misses
  including
  > left parietal lobe. Is that correct? Attached the comparison. 
  >
  > Thank you so much!
  > Best, 
  > Qi 
  >
  > On Tue, May 5, 2020 at 1:58 PM Douglas N. Greve
  
  > wrote:
  >       You should load that volume along with the orig.nofix
  hemisphere
  >       that is giving you problems and look for a large area
  that
  >       should not be within the surface
  >
  >       On 5/5/2020 1:23 PM, Zeng, Qi wrote:
  >
  >       External Email - Use Caution
  >
  >       Hi Douglas, 
  >
  > The cerebrum is removed and with no skull attached. 
  > However, compared to others that run normally,  it may have
  > problems with white matter segmentation and missing brainstem
  > (no clear). Attached the comparison below. Can you help figure
  > it out?
  >
  >
  >
  > Thank you so much!
  > Best, 
  > Qi 
  >
  > On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve
  >  wrote:
  >       You should look at the wm.mgz to see where the
  >       defect is. Probably cerebellum is still attached or
  >       maybe a big piece of skull.
  >
  >       On 5/4/2020 11:19 PM, Zeng, Qi wrote:
  >
  >       External Email - Use Caution
  >
  >       Hi, 
  >
  > I've conducted longitudinal T1 recon-all. One
  > subject's last-scan ran into error in the first
  > independent recon all step: " recon-all -s SUBJ1
  > -SUBJ1.nii -all'. 
  > Error: "CORRECTING DEFECT 0 (vertices=14101, convex
  > hull=2297, v0=1419) XL defect detected...". Log file
  > attached below. 
  >
  > I've increased the memory usage limit as some
  > suggestions did, but no help. Also T1.nii looks
  > fine, same parameter setting as first scan, also
  > attached below. Subject first scan and all the other
  > subjects were finished without errors. Can you help
  > figure out what has caused it?
  >
  > Thank you so much!
  > Best, 
  > Qi 
  >
  > --
  >
  > Ph.D. candidate 
  > Icahn School of Medicine at Mount Sinai
  >
  >
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  > Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

sorry, I'm going to defer to Doug on surf2surf
On Wed, 6 May 2020, Ian 
Hardingham wrote:




External Email - Use Caution

Thanks Bruce.

So a reminder I'm calling:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz --trgsurfval
{output_dir}/registered_lh.white

I'm assuming that means the "input surface" is
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white, and here's the
mris_info for that, but bear in mind that I don't know for sure from that
line that that's what is being used.

SURFACE INFO 
type    : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 163842
num faces   : 327680
num strips  : 0
surface area: 65417
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470
group avg surface area: 82220
ctr : (-31.9282, -18.8144, 16.3699)
vertex locs : surfaceRAS
talairch.xfm:
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
surfaceRAS to talaraiched surfaceRAS:
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
talairached surfaceRAS to surfaceRAS:
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
Volume Geometry (vg)
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 0.,  0.,  0.)
file    : ../mri/orig.mgz
Volume Geometry vox2ras
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
Volume Geometry vox2ras-tkr
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mris_info
creationtime 2020/05/06-14:31:38-GMT
sysname  Linux
hostname ryzen-cumnor
machine  x86_64
surfacefile /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
hemicode    0
talairach_flag  0
rescale 0.00
nvertices   163842
nfaces  327680
total_area  65416.984375
group_avg_surf_area  82219.960938
group_avg_vtxarea_loaded 1
avgvtxarea  0.399269
avgvtxdist  0.721953
stdvtxdist  0.195470
vtx0xyz   -36.806278 -18.292723 64.461525

On 06/05/2020 15:23, Bruce Fischl wrote:
  hmm, that is not an icosahedral surface, which should have 160K
  vertices. Can you check your input surface? You'll also need to
  fix your freeview problem, but someone else will have to help
  you with that
  On Wed, 6 May 2020, Ian Hardingham wrote:


External Email - Use Caution

FSLInfo attached, thanks Bruce.

When trying to run freeview I get "freeview.bin:
error while loading shared
libraries: libpng12.so.0: cannot open shared object
file: No such file or
directory" - do I need to add
/usr/local/freesurfer/lib/* to path or
something along those lines?

SURFACE INFO

type    :
MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 102020
num faces   : 204036
num strips  : 0
surface area: 65520.5
AvgVtxArea   0.642232
AvgVtxDist   0.940503
StdVtxDist   0.417776
ctr : (-31.9056, -18.8197, 16.3545)
vertex locs : surfaceRAS
Volume Geometry (vg)
volume geometry:
extent  : (176, 224, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-0.9990, -0.0436,  0.)
y_(ras) : (-0.0436,  0.9990,  0.)
z_(ras) : ( 0.,  0.,  1.)
c_(ras) : (-0.5431,  8.9290, -17.0723)
file    : /media/ian/bronson/subject/T1_nifti.nii.gz
Volume Geometry vox2ras
-0.99905  -0.04362   0.0   92.25847;
-0.04362   0.99905   0.0  -99.12585;
 0.0   0.0   1.0  -145.07230;
 0.0   0.0   0.0   1.0;
Volume Geometry vox2ras-tkr
-1.0   0.0   0.0   88.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   112.0;
 0.0   0.0   0.0   1.0;
cmd[0]: mris_remove_intersection ../surf/lh.orig
../surf/lh.orig
ProgramVersion: $Name: st

Re: [Freesurfer] recon-all-rms error < 2.00

[Bruce Fischl]

please don't send text files as images! We can't search them, etc...

The final distance error sis not a problem. Does recon-all stop? Please 
send the recon-all.log as a text file


cheers
Bruce
On Tue, 
5 May 2020, jiahui wrote:




External Email - Use Caution

Hello FreeSurfer Developers,
I'm attempting to compute  gray matter volume, but for some of my subjects I
 get the following error when I run the recon-all -all command:
 ERROR: inflating to sphere (rms error < 2.00)  final distance error(this is
 true error?) 
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2be

b96c
2) Platform: ubuntu 16.04.6 LTS 
3) recon-all.log  and  figure1.png: see attached



 



 



 



 


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

hmm, that is not an icosahedral surface, which should have 160K vertices. 
Can you check your input surface? You'll also need to fix your freeview 
problem, but someone else will have to help you with that
On Wed, 6 May 
2020, Ian Hardingham wrote:




External Email - Use Caution

FSLInfo attached, thanks Bruce.

When trying to run freeview I get "freeview.bin: error while loading shared
libraries: libpng12.so.0: cannot open shared object file: No such file or
directory" - do I need to add /usr/local/freesurfer/lib/* to path or
something along those lines?

SURFACE INFO 
type    : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 102020
num faces   : 204036
num strips  : 0
surface area: 65520.5
AvgVtxArea   0.642232
AvgVtxDist   0.940503
StdVtxDist   0.417776
ctr : (-31.9056, -18.8197, 16.3545)
vertex locs : surfaceRAS
Volume Geometry (vg)
volume geometry:
extent  : (176, 224, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-0.9990, -0.0436,  0.)
y_(ras) : (-0.0436,  0.9990,  0.)
z_(ras) : ( 0.,  0.,  1.)
c_(ras) : (-0.5431,  8.9290, -17.0723)
file    : /media/ian/bronson/subject/T1_nifti.nii.gz
Volume Geometry vox2ras
-0.99905  -0.04362   0.0   92.25847;
-0.04362   0.99905   0.0  -99.12585;
 0.0   0.0   1.0  -145.07230;
 0.0   0.0   0.0   1.0;
Volume Geometry vox2ras-tkr
-1.0   0.0   0.0   88.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   112.0;
 0.0   0.0   0.0   1.0;
cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
ProgramVersion: $Name: stable5 $  TimeStamp: 2016/05/26-23:14:53-GMT 
BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mris_remove_intersection.c,v
1.6 2011/03/02 00:04:32 nicks Exp $  User: fsuser  Machine:
xubuntu-VirtualBox  Platform: Linux  PlatformVersion: 3.2.0-23-generic 
CompilerName: GCC  CompilerVersion: 30400 
cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $  TimeStamp:
2016/05/26-23:14:56-GMT  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id:
mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User:
fsuser  Machine: xubuntu-VirtualBox  Platform: Linux  PlatformVersion:
3.2.0-23-generic  CompilerName: GCC  CompilerVersion: 30400 
cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
ProgramVersion: $Name: stable5 $  TimeStamp: 2016/05/26-23:18:33-GMT 
BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mris_smooth.c,v 1.28
2011/03/02 00:04:34 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox 
Platform: Linux  PlatformVersion: 3.2.0-23-generic  CompilerName: GCC 
CompilerVersion: 30400 
cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion:
$Name: stable5 $  TimeStamp: 2016/05/26-23:18:36-GMT  BuildTimeStamp: May 13
2013 18:53:32  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp
$  User: fsuser  Machine: xubuntu-VirtualBox  Platform: Linux 
PlatformVersion: 3.2.0-23-generic  CompilerName: GCC  CompilerVersion:
30400 
cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
ProgramVersion: $Name: stable5 $  TimeStamp: 2016/05/26-23:20:12-GMT 
BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id: mris_sphere.c,v 1.57
2011/03/02 00:04:34 nicks Exp $  User: fsuser  Machine: xubuntu-VirtualBox 
Platform: Linux  PlatformVersion: 3.2.0-23-generic  CompilerName: GCC 
CompilerVersion: 30400 
cmd[5]: mris_register -curv ../surf/lh.sphere
/usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif
../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $  TimeStamp:
2016/05/27-00:03:14-GMT  BuildTimeStamp: May 13 2013 18:53:32  CVS: $Id:
mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: fsuser 
Machine: xubuntu-VirtualBox  Platform: Linux  PlatformVersion:
3.2.0-23-generic  CompilerName: GCC  CompilerVersion: 30400 
mris_info
creationtime 2020/05/06-14:18:48-GMT
sysname  Linux
hostname ryzen-cumnor
machine  x86_64
surfacefile /home/ian/cdm_registered_test/registered_lh.white
hemicode    1
talairach_flag  0
rescale 0.00
nvertices   102020
nfaces  204036
total_area  65520.492188
group_avg_vtxarea_loaded 0
avgvtxarea  0.642232
avgvtxdist  0.940503
stdvtxdist  0.417776
vtx0xyz   -8.576451 -101.319672 3.333434

On 06/05/2020 15:00, Bruce Fischl wrote:
  can you run mris_info on the output surfcae? And maybe send a
  freeview snapshot of it (in 3d rendering mode)

  On Wed, 6 May 2020, Ian wrote:

   External Email - Use Caution
Thanks Tim and Doug.

I have the files generating and loading properly
now, but I'm not convinced it's giving the output
I'm looking for.

I am trying to convert the "fsaverage" subject's
surface coordinates 

Re: [Freesurfer] T1 recon -all error "XL defect detected"

[Bruce Fischl]

Hi Qi

it is not obvious from that one image that something is wrong there. What 
does a saggital view look like with the cursor on that region? Also, can 
you send an image of the rh.inflated.nofix in 3D mode? Sometime XL 
defects are fixable automatically, which may be the case for your 
subjects with very large ventricles, but sometimes not


cheers
Bruce
On Tue, 5 May 2020, 
Zeng, Qi wrote:




External Email - Use Caution

Hi Douglas, 

Compared to the ones without error, the subject surface misses including
left parietal lobe. Is that correct? Attached the comparison. 

Thank you so much!
Best, 
Qi 

On Tue, May 5, 2020 at 1:58 PM Douglas N. Greve 
wrote:
  You should load that volume along with the orig.nofix hemisphere
  that is giving you problems and look for a large area that
  should not be within the surface

  On 5/5/2020 1:23 PM, Zeng, Qi wrote:

  External Email - Use Caution

  Hi Douglas, 

The cerebrum is removed and with no skull attached. 
However, compared to others that run normally,  it may have
problems with white matter segmentation and missing brainstem
(no clear). Attached the comparison below. Can you help figure
it out?



Thank you so much!
Best, 
Qi 

On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve
 wrote:
  You should look at the wm.mgz to see where the
  defect is. Probably cerebellum is still attached or
  maybe a big piece of skull.

  On 5/4/2020 11:19 PM, Zeng, Qi wrote:

  External Email - Use Caution

  Hi, 

I've conducted longitudinal T1 recon-all. One
subject's last-scan ran into error in the first
independent recon all step: " recon-all -s SUBJ1
-SUBJ1.nii -all'. 
Error: "CORRECTING DEFECT 0 (vertices=14101, convex
hull=2297, v0=1419) XL defect detected...". Log file
attached below. 

I've increased the memory usage limit as some
suggestions did, but no help. Also T1.nii looks
fine, same parameter setting as first scan, also
attached below. Subject first scan and all the other
subjects were finished without errors. Can you help
figure out what has caused it?

Thank you so much!
Best, 
Qi 

--

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Icahn School of Medicine at Mount Sinai


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Icahn School of Medicine at Mount Sinai


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Icahn School of Medicine at Mount Sinai


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

can you run mris_info on the output surfcae? And maybe send a freeview 
snapshot of it (in 3d rendering mode)


On Wed, 6 May 2020, Ian wrote:

   External Email - Use Caution 


Thanks Tim and Doug.

I have the files generating and loading properly now, but I'm not convinced 
it's giving the output I'm looking for.


I am trying to convert the "fsaverage" subject's surface coordinates to my 
own subject's surface space.


FSaverage's lh.white file is 5898808 bytes:

5898808 Apr 11  2013 /usr/local/freesurfer/subjects/fsaverage/surf/lh.white

After converting with this command:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject 
fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz --trgsurfval 
{output_dir}/registered_lh.white


My newly registered lh.white file is half the size:

3316997 May  6 10:41 /home/ian/cdm_registered_test/registered_lh.white

(and appears to have half the vertices accordingly.)

So this must be incorrect, or at least not my intended purpose.

To try and be clear, I'm looking to get the position of every vertex in 
fsaverage's surfaces "on" the surface of my subject's surfaces.  So if 
there's a vertex at the peak of a particular sulcii on fsaverage, I'm looking 
to find where the peak of that sulcii is on my subject.


Thanks,
Ian

On 06/05/2020 09:08, Tim Schäfer wrote:

  External Email - Use Caution

 Just a note: there should be no need to convert to gifti, nibabel can read
 the FreeSurer binary surface format directly with
 `nibabel.freesurfer.io.read_geometry()`.

 The docs are here:
 
https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.io.read_geometry

 Best,

 Tim


 On May 5, 2020 at 7:59 PM "Douglas N. Greve" 
 wrote:


 You should load the surfaces in FV. If it load in FV ok but nibable is
 crashing, you should contact them.

 On 5/5/2020 1:05 PM, Ian Hardingham wrote:

  External Email - Use Caution

 Thank you both.

 I've made edits and these are the current commands:

 mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
 --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
 --trgsurfval {output_dir}/registered_lh.white
 mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
 --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
 --trgsurfval {output_dir}/registered_rh.white
 mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
 --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
 --trgsurfval {output_dir}/registered_lh.pial
 mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
 --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
 --trgsurfval {output_dir}/registered_rh.pial

 These execute successfully and the file size looks about right, but
 after using mris_convert to convert to Gifti format nibabel crashes on
 trying to load them - is there anything obviously wrong in my commands?

 I'll also take a look at mris_apply_reg.

 On 05/05/2020 18:01, Douglas N. Greve wrote:

 Don't specify a --trg_type. But add --tval-xyz
 mris_apply_reg will do the same thing, but the interface might be a
 little easier

 On 5/5/2020 12:49 PM, Bruce Fischl wrote:

 no definitely not "w" format, which we don't use for anything
 anymore. YOu should use tval-xyz also I think
 On Tue, 5 May 2020, Ian Hardingham wrote:


  External Email - Use Caution

 It would appear not, as I'm getting an error on my pial output
 files but not
 my white ones.  Here are my commands:

 mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
 --trgsubject
 fs_target --trgsurfval ./registered_lh.white --trg_type w
 mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
 --trgsubject
 fs_target --trgsurfval ./registered_rh.white --trg_type w
 mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
 --trgsubject
 fs_target --trgsurfval ./registered_lh.pial --trg_type w
 mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
 --trgsubject
 fs_target --trgsurfval ./registered_rh.pial --trg_type w

 The white calls output seems to be fine, but the pial ones aren't.  I
 somewhat naively trued trg_type pial but that wasn't correct.

 On 05/05/2020 17:33, Ian Hardingham wrote:

    Thanks Bruce, extremely helpful.

    Can I just check that the "w" format is what is used by both
  the
    lh/rh.pial and the lh/rh.white files?  I only ask because my
    surf2surf command outputs the exact output filename if the end
        is ".white", but if it's ".pial" it outputs ".pial.w", which I
    find a little curious.

    Ian

    On 05/05/2020 16:34, Bruce Fischl wrote:
    yes, check out options like:
    --sval-xyz

    if you need further help though I'll have to defer to Doug
    :)
    Bruce


    On

Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

no definitely not "w" format, which we don't use for anything anymore. 
YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham 
wrote:




External Email - Use Caution

It would appear not, as I'm getting an error on my pial output files but not
my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

  Thanks Bruce, extremely helpful.

  Can I just check that the "w" format is what is used by both the
  lh/rh.pial and the lh/rh.white files?  I only ask because my
  surf2surf command outputs the exact output filename if the end
  is ".white", but if it's ".pial" it outputs ".pial.w", which I
  find a little curious.

  Ian

  On 05/05/2020 16:34, Bruce Fischl wrote:
  yes, check out options like:
  --sval-xyz

  if you need further help though I'll have to defer to Doug
  :)
  Bruce


  On Tue, 5 May 2020, Ian Hardingham wrote:


External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I
wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and
rh.white) rather than values for
something such as thickness - is there an
option for mri_surf2surf to allow
this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map
surfaces between subjects, but
  our atlas isn't really a surface. You
can use the surfaces in
  the fsaverage dir, but they are meant
for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


    External Email - Use
Caution

    Hi Freesurfers.

    I have a subject S with recon-all
having been run on
    it.

    I have the subject-specific
surface files
    /surf/lh.pial, rh.pial, lh.white,
    and rh.white.

    I would like an Atlas's lh.pial,
rh.pial, lh.white,
    and rh.white in subject
    space.

    Any helpers on how to achieve
this?

    Thanks,
    Ian

    --

    Ian Hardingham





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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

yes, check out options like:
--sval-xyz

if you need further help though I'll have to defer to Doug :)
Bruce


On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for
something such as thickness - is there an option for mri_surf2surf to allow
this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map surfaces between subjects, but
  our atlas isn't really a surface. You can use the surfaces in
  the fsaverage dir, but they are meant for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


External Email - Use Caution

Hi Freesurfers.

I have a subject S with recon-all having been run on
it.

I have the subject-specific surface files
/surf/lh.pial, rh.pial, lh.white,
and rh.white.

I would like an Atlas's lh.pial, rh.pial, lh.white,
and rh.white in subject
space.

Any helpers on how to achieve this?

Thanks,
Ian

--

Ian Hardingham





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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

Hi Ian

you can use mri_surf2surf to map surfaces between subjects, but our atlas 
isn't really a surface. You can use the surfaces in the fsaverage dir, but 
they are meant for visualization and are much smoother than individuals


cheers
Bruce


On Tue, 5 May 
2020, Ian wrote:




External Email - Use Caution

Hi Freesurfers.

I have a subject S with recon-all having been run on it.

I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white,
and rh.white.

I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject
space.

Any helpers on how to achieve this?

Thanks,
Ian

--

Ian Hardingham



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Re: [Freesurfer] Freesurfer Digest, Vol 194, Issue 45

[Bruce Fischl]

glad to hear that there are simple answers to some questions!

take care
Bruce
On Sun, 3 May 
2020, atira gan-zvi bick wrote:




External Email - Use Caution



  Hi Bruce


It worked! how simple...
Thank you so much.  

Atira

     
  --

  Message: 2
  Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT)
  From: Bruce Fischl 
  Subject: Re: [Freesurfer] exporting segmented mgz file
  To: Freesurfer support list 
  Message-ID:
         
  
  Content-Type: text/plain; charset="utf-8"

  Hi Atira

  what was your mri_convert command line? Make sure to specify no
  scaling of
  the intensity volume. Can you try adding:

  -ns 1

  to the mri_convert command line, and if that doesn't work send
  us the full
  command line and full screen output from it? This is always a
  good thing to
  do as it gives us enough information to help

  cheers
  Bruce



  On Sun, 26 Apr 2020, atira gan-zvi bick wrote:

  >
  > External Email - Use Caution
  >
  > Hi
  > I'm new to freesurfer.
  >
  > I used freesurfer to preform Thalamus segmentation, and can
  see the segmented?volume in freeview.
  > I would like to export?the segmented volume to nii to continue
  analysis in MRvista.
  > I was able to do this using?mri_convert - however the values
  in the nifti are not those on the label
  > list (as seen in ?freeview). The number of different values is
  similar but not the same, and the values
  > themselves? are totally different?(8103-8233 in freeview,
  16384 - 32767). It is possible to compare
  > regions based on visual inspection - however that is
  tedious?and might lead to mistakes.
  > How can I export the labels of each region in the segmented
  mgz?
  >
  > Any suggestions?
  > I'd appreciate?to learn fro your experience
  >
  > Thanks
  > Atira
  >
  > --
  > ?"? ? ??-??? ???
  > ? ?? 
  >  ???-???
  > ??? ??
  >
  > Atira Bick (Phd)
  > fMRI unit
  > Hadassah medical center, Hebrew University
  > Jerusalem
  >
  >

  --




--
ד"ר עתירה גן-צבי ביק
יחידת ההדמיה התפקודית
הדסה עין-כרם
האוניברסיטה העברית

Atira Bick (Phd)
fMRI unit
Hadassah medical center, Hebrew University
Jerusalem

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Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz

[Bruce Fischl]

you could I guess, but it will likely be hard, a lot of work, and not that 
repeatable


cheers
Bruce

On Sat, 2 May 2020, Zeng, Victor  (BIDMC - Keshavan - 
Psychiatry) wrote:



Hi all,

I was doing a little bit more researching. Could you just fix this sort of 
issue by editing the aparc.auto.mgz and changing the label from 
Left/Right-Cerebral-White-Matter to Left/Right-Cerebral-Cortex as necessary?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


From: Zeng,Victor  (BIDMC - Keshavan - Psychiatry)
Sent: Sunday, April 26, 2020 7:28 PM
To: Freesurfer support list
Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with 
the wm.mgz

Hi,

Thanks for the clarification. From my understanding, control points are used to 
grab regions that should be white matter, rather than remove regions that 
aren't white matter. Are there any resources on how you would use control 
points to remove intensity inhomogeneity?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Bruce Fischl 
Sent: Sunday, April 26, 2020 12:03 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the 
wm.mgz

Hi Victor

the best way to remove intensity inhomogeneities is with control points
usually. The wm.mgz gives us an initial estimate of the surface locations,
but we then deform it based on the intensities in the brain.mgz volume. So
if it looks like wm extends that far out in the brain your wm.mgz edits are
unliekly to fix things

cheers
Bruce


On Sun, 26 Apr 2020, Zeng, Victor  (BIDMC - Keshavan -
Psychiatry)
wrote:




Hi Freesurfer developers,


I have a subsample of a FS dataset that have scanner-originated 
hyperintensities in the bilateral
supramarginal/temporal lobes. I've manually removed these hyperintensities by 
editing the wm.mgz, yet FS
seems to be unable to recognize these edits when looking at the ?h.white and 
aparc+aseg.mgz. Is there a
possible way to rectify these errors?


I am using FS6 for linux


Here are some pictures:


[IMAGE]​[IMAGE]


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



This message is intended for the use of the person(s) to whom it may be 
addressed. It may contain
information that is privileged, confidential, or otherwise protected from 
disclosure under applicable
law. If you are not the intended recipient, any dissemination, distribution, 
copying, or use of this
information is prohibited. If you have received this message in error, please 
permanently delete it and
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Re: [Freesurfer] Questions about pial_lgi {Disarmed}

[Bruce Fischl]

Doug is saying that you should replace:

 --out lh.pial_lgi

with

 --out lh.pial_lgi.mgh

on your command line

cheers
Bruce
On Thu, 30 Apr 2020, 肖伏龙 wrote:



External Email - Use Caution

so how to get the pial_lgi.mgh from the pial_lgi file?



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On 04/30/2020 06:18, Douglas N. Greve wrote:
It needs to have an extension, eg, lh.pial_lgi.mgz


On 4/29/2020 9:02 AM, 肖伏龙 wrote:

  External Email - Use Caution

  hello everyone
I have a question about statistics on LGI. for the LGI
data, named as lh.pial_lgi, I used mris_preproc as
following:
mris_preproc --fsgd fsgd.fsgd --cache-in pial_lgi --target
fsaverage --hemi lh --out lh.pial_lgi
but freesurfer said 
ERROR: format for lh.pial_lgi not recognized
so is there any method to solve this problem?
Thank you



 


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Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Bruce Fischl]

Hi Marina

which surface you use depends on why you are trying to find the vertices

cheers
Bruce


On Wed, 29 Apr 2020, Marina Fernández 
wrote:




External Email - Use Caution

Hi Bruce,
Thank you very much for the information. It is very useful. I'm taking a
look at both possibilities.

Regarding the second option you gave me:

  you can just run through the list of vertices and find the one
  that is closest to your MNI coord



What file should I use to find the coordinates correspondence? Should I use
[l/r].pial? Or maybe  [l/r].orig?

Do you think it is a good idea to load that file in matlab and look for the
closest coordinates there, and see what vertex index those coordinates
correspond to?

Thank you in advance.

Best wishes,
Marina

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Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Bruce Fischl]

Hi Marina

what kind of function do you mean? There is c++ code that does this in the 
file mrishash.cpp, but it is a bit complicated (you have to build a spatial 
lookup table at a user-specified resolution, then use it in the vertex 
finding code). Alternatively if you don't have to do this a lot you can 
just run through the list of vertices and find the one that is closest to 
your MNI coord


cheers
Bruce


On Tue, 28 
Apr 2020, Marina Fernández wrote:




External Email - Use Caution

Dear Freesurfer experts,

I would like to convert the x, y, z MNI152 coordinates into the vertex index
of the fsaverage5.

I would like to do it with a function that can give me the vertex index as
output, because I would like to use this information in a matlab script that
continues with more calculations.

Is there any function that can give me the vertex index (which corresponds
to certain coordinates) as output?

Thank you very much for your attention.

Best wishes,
Marina

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Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz

[Bruce Fischl]

Hi Victor

control points are used whenever the white matter intensity is incorrect 
(>>110 or <<110). If you have regions of white matter that are too bright 
you should be able to put contgrol points in them to bring the region 
down. For example, if the gm is so bright that it looks like wm, then the 
nearby white matter should be even brighter


cheers
Bruce


On Sun, 26 Apr 2020, Zeng, Victor  (BIDMC - Keshavan - 
Psychiatry) wrote:



Hi,

Thanks for the clarification. From my understanding, control points are used to 
grab regions that should be white matter, rather than remove regions that 
aren't white matter. Are there any resources on how you would use control 
points to remove intensity inhomogeneity?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Bruce Fischl 
Sent: Sunday, April 26, 2020 12:03 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the 
wm.mgz

Hi Victor

the best way to remove intensity inhomogeneities is with control points
usually. The wm.mgz gives us an initial estimate of the surface locations,
but we then deform it based on the intensities in the brain.mgz volume. So
if it looks like wm extends that far out in the brain your wm.mgz edits are
unliekly to fix things

cheers
Bruce


On Sun, 26 Apr 2020, Zeng, Victor  (BIDMC - Keshavan -
Psychiatry)
wrote:




Hi Freesurfer developers,


I have a subsample of a FS dataset that have scanner-originated 
hyperintensities in the bilateral
supramarginal/temporal lobes. I've manually removed these hyperintensities by 
editing the wm.mgz, yet FS
seems to be unable to recognize these edits when looking at the ?h.white and 
aparc+aseg.mgz. Is there a
possible way to rectify these errors?


I am using FS6 for linux


Here are some pictures:


[IMAGE]​[IMAGE]


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



This message is intended for the use of the person(s) to whom it may be 
addressed. It may contain
information that is privileged, confidential, or otherwise protected from 
disclosure under applicable
law. If you are not the intended recipient, any dissemination, distribution, 
copying, or use of this
information is prohibited. If you have received this message in error, please 
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Re: [Freesurfer] Threshold values changed/modified before display.

[Bruce Fischl]

Hi  Devavrat

freeview definitely does not modify the values in any volumes you load 
for display.


cheers
Bruce
On Sun, 26 Apr 2020, Devavrat Vartak PhD wrote:



External Email - Use Caution

Hi freesurfer developers!,
I am using Freesurfer 6.0 and the latest (freeview  -beta) to display overlays 
on my flat surfaces.

I am a novice user of freesurfer and I am a bit confused with how the overlays 
are displayed /
thresholds calculated.

My overlay of rsquare values ranges from 0.2 to 1.0 (i.e all are positive 
values.). When the overlay is
loaded, the threshold histogram depicts values that are negative and positive 
(centered around zero).

1) Does freeview recaluate/modify the values before they are displayed?
2) Is it possible to display the values of the overlay as they are?  


Thank you. Stay healthy and safe!

Best,
Devavrat


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Re: [Freesurfer] exporting segmented mgz file

[Bruce Fischl]

Hi Atira

what was your mri_convert command line? Make sure to specify no scaling of 
the intensity volume. Can you try adding:


-ns 1

to the mri_convert command line, and if that doesn't work send us the full 
command line and full screen output from it? This is always a good thing to 
do as it gives us enough information to help


cheers
Bruce



On Sun, 26 Apr 2020, atira gan-zvi bick wrote:



External Email - Use Caution

Hi
I'm new to freesurfer.

I used freesurfer to preform Thalamus segmentation, and can see the segmented 
volume in freeview.
I would like to export the segmented volume to nii to continue analysis in 
MRvista.
I was able to do this using mri_convert - however the values in the nifti are 
not those on the label
list (as seen in  freeview). The number of different values is similar but not 
the same, and the values
themselves  are totally different (8103-8233 in freeview, 16384 - 32767). It is 
possible to compare
regions based on visual inspection - however that is tedious and might lead to 
mistakes.
How can I export the labels of each region in the segmented mgz?

Any suggestions?
I'd appreciate to learn fro your experience

Thanks
Atira

--
ד"ר עתירה גן-צבי ביק
יחידת ההדמיה התפקודית
הדסה עין-כרם
האוניברסיטה העברית

Atira Bick (Phd)
fMRI unit
Hadassah medical center, Hebrew University
Jerusalem

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Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

[Bruce Fischl]

Hi Victor

the best way to remove intensity inhomogeneities is with control points 
usually. The wm.mgz gives us an initial estimate of the surface locations, 
but we then deform it based on the intensities in the brain.mgz volume. So 
if it looks like wm extends that far out in the brain your wm.mgz edits are 
unliekly to fix things


cheers
Bruce


On Sun, 26 Apr 2020, Zeng, Victor  (BIDMC - Keshavan - 
Psychiatry) 
wrote:





Hi Freesurfer developers,


I have a subsample of a FS dataset that have scanner-originated 
hyperintensities in the bilateral
supramarginal/temporal lobes. I've manually removed these hyperintensities by 
editing the wm.mgz, yet FS
seems to be unable to recognize these edits when looking at the ?h.white and 
aparc+aseg.mgz. Is there a
possible way to rectify these errors? 


I am using FS6 for linux


Here are some pictures: 


[IMAGE]​[IMAGE]


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



This message is intended for the use of the person(s) to whom it may be 
addressed. It may contain
information that is privileged, confidential, or otherwise protected from 
disclosure under applicable
law. If you are not the intended recipient, any dissemination, distribution, 
copying, or use of this
information is prohibited. If you have received this message in error, please 
permanently delete it and
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Re: [Freesurfer] Generating Surfaces Meshes

[Bruce Fischl]

Hi Jonah

no, I don't think that would be very accurate. In our cortical surface 
stream we do partial volume modeling in the surface deformation so that 
the surface settles at the right point between gray/white and gray/csf. 
We never wrote anything comparable for the aseg structs like hippocampus, 
but a quick-and-dirty solution would be to settle at the 0.5 posterior 
probablity level of something like samseg


cheers
Bruce



On Fri, 24 Apr 
2020, Peter, Jonah wrote:



Hi Bruce,
I'm interested in generating meshes for the whole brain,and individual regions 
of the prefrontal cortex
and the hippocampus.

It seems that freesurfer doesn't generate meshes with physical volumes 
corrected for partial volume
effects, but instead performs an a posteriori calculation that is output to the 
aseg.stats file (is this
correct?). What I meant before was: do you think it would be reasonable to take 
the surface meshes and
simply scale down their volumes such that the physical mesh volume then 
corresponds to the partial
volume corrected volume?

As an example, suppose the actual physical volume of the hippocampal mesh is 
5000 mm3, whereas the
aseg.stats lists the volume as 4000 mm3 after correcting for partial volume 
effects. Would it be correct
to just scale the mesh volume to 4000 mm3?

Thanks again,
Jonah

On Fri, Apr 24, 2020 at 10:35 AM Bruce Fischl  
wrote:
  Hi Jonah

  I'm not positive I understand, but I doubt partial volume effects are
  isotropic given the geometric complexity of a lot of brain structures.
  Maybe the easiest thing for you to do is to use something like SAMSEG in
  the upcoming V7 and try deforming the surface to pass through the p=0.5
  isosurface. Not sure how hard that would be to implement, maybe others
  (Doug? Eugenio? Viviana?) can comment? Are there any specific structures
  you are interested in?

  cheers
  Bruce


  On Thu, 23 Apr 2020, Peter, Jonah wrote:

  > Hi Bruce,
  > The issue is that I want the surface mesh itself to reflect the correct 
(partial volume
  corrected)
  > volume as I will be simulating the passage of high energy particles 
through it. Do you
  think it would
  > suffice to take the (smoothed) mesh and simply scale its volume in an 
application like
  blender? My
  > thinking is that the partial volume effects are probably isotropic so a 
uniform scaling
  would leave the
  > geometry unchanged.
  >
  > Best,
  > Jonah
  >
  > On Thu, Apr 23, 2020 at 9:53 PM Bruce Fischl 
 wrote:
  >       HI Jonah
  >
  >       it depends how you compute volume. mris_volume for example will 
compute the
  >       volume of the interior without any partial volume correction.
  >
  >       And yes, I would expect you want to smooth the surface a bit. You 
might try
  >       the Taubin smoothing built into freeview as it won't shrink the 
surface,
  >       but you can also try mris_smooth
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Thu, 23 Apr 2020, Peter, Jonah wrote:
  >
  >       > Hi Bruce,
  >       > I tried mri_tessellate which worked well in that the surface 
seems to follow the
  aseg
  >       projections
  >       > exactly. Does the volume of this mesh account for partial 
volume effects? Also, is
  there a
  >       need to run
  >       > mri_pretess or some sort of smoothing procedure?
  >       >
  >       > For reference, what I am trying to do is import these surface 
meshes into a Geant4
  >       simulation for proton
  >       > therapy, and want to make sure I'm using as realistic geometry 
as possible.
  Ideally I'd be
  >       able to
  >       > generate a mesh for the whole brain as well as individual 
segmentations.
  >       >
  >       > Thanks again for your help,
  >       > Jonah
  >       >
  >       > On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl 
 wrote:
  >       >       no, they are definitely not negligible. It depends on 
structure geometry,
  >       >       but I bet for something like the hippocampus a large 
fraction of voxels in
  >       >       it are partial volumed.
  >       >
  >       >       You can use mri_mc or mri_tessellate to generate a mesh. 
It will be closed
  >       >       but may not have a simple topology
  >       >
  >       >       On Thu, 23 Apr 2020, Peter, Jonah
  >       >       wrote:
  >       >
  >       >       > Hi all,
  >       >       > Thanks for the response. 

Re: [Freesurfer] Generating Surfaces Meshes

[Bruce Fischl]

Hi Jonah

I'm not positive I understand, but I doubt partial volume effects are 
isotropic given the geometric complexity of a lot of brain structures. 
Maybe the easiest thing for you to do is to use something like SAMSEG in 
the upcoming V7 and try deforming the surface to pass through the p=0.5 
isosurface. Not sure how hard that would be to implement, maybe others 
(Doug? Eugenio? Viviana?) can comment? Are there any specific structures 
you are interested in?


cheers
Bruce


On Thu, 23 Apr 2020, Peter, Jonah wrote:


Hi Bruce,
The issue is that I want the surface mesh itself to reflect the correct 
(partial volume corrected)
volume as I will be simulating the passage of high energy particles through it. 
Do you think it would
suffice to take the (smoothed) mesh and simply scale its volume in an 
application like blender? My
thinking is that the partial volume effects are probably isotropic so a uniform 
scaling would leave the
geometry unchanged.

Best,
Jonah

On Thu, Apr 23, 2020 at 9:53 PM Bruce Fischl  wrote:
  HI Jonah

  it depends how you compute volume. mris_volume for example will compute 
the
  volume of the interior without any partial volume correction.

  And yes, I would expect you want to smooth the surface a bit. You might 
try
  the Taubin smoothing built into freeview as it won't shrink the surface,
  but you can also try mris_smooth

  cheers
  Bruce


  On Thu, 23 Apr 2020, Peter, Jonah wrote:

  > Hi Bruce,
  > I tried mri_tessellate which worked well in that the surface seems to 
follow the aseg
  projections
  > exactly. Does the volume of this mesh account for partial volume 
effects? Also, is there a
  need to run
  > mri_pretess or some sort of smoothing procedure?
  >
  > For reference, what I am trying to do is import these surface meshes 
into a Geant4
  simulation for proton
  > therapy, and want to make sure I'm using as realistic geometry as 
possible. Ideally I'd be
  able to
  > generate a mesh for the whole brain as well as individual segmentations.
  >
  > Thanks again for your help,
  > Jonah
  >
  > On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl 
 wrote:
  >       no, they are definitely not negligible. It depends on structure 
geometry,
  >       but I bet for something like the hippocampus a large fraction of 
voxels in
  >       it are partial volumed.
  >
  >       You can use mri_mc or mri_tessellate to generate a mesh. It will 
be closed
  >       but may not have a simple topology
  >
  >       On Thu, 23 Apr 2020, Peter, Jonah
  >       wrote:
  >
  >       > Hi all,
  >       > Thanks for the response. I'm familiar with partial volume 
effects within the
  context of
  >       PET imaging, but
  >       > wouldn't you expect these effects to be negligible in MRI for 
structures on the
  order of
  >       mm?
  >       >
  >       > With respect to the mesh type, I'd like to get closed meshes 
for each
  >       segmentation/parcellation.
  >       >
  >       > Is there a way to do this in freesurfer?
  >       >
  >       > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl 
 wrote:
  >       >       Hi Jonah
  >       >
  >       >       when we compute volumes we typically use a partial-volume 
model, which we
  >       >       have found improves accuracy and repeatability. That may 
be the source of
  >       >       your discrepancy
  >       >
  >       >       cheers
  >       >       Bruce
  >       >       On Wed, 22 Apr 2020, Peter, Jonah wrote:
  >       >
  >       >       > Hello,
  >       >       > I'm trying to generate surface meshes for different 
brain regions that can
  >       >       > be imported into a software like MeshLab or Blender 
(i.e. .STL, .PLY,
  .OBJ,
  >       >       > etc.). I ran recon-all on my T1 images, and the 
parcellation/segmentation
  >       >       > looks fine. However, I noticed that when I imported 
this data into
  3DSlicer,
  >       >       > the volumes of these regions did not match the volumes 
in the aseg.stats
  >       >       > file. In some cases, the differences were quite 
substantial. I tried
  >       >       > removing all smoothing filters in 3DSlicer but the 
outcome was the same.
  >       >       >
  >       >       > Do you know what could be going wrong here? 
Alternatively, is there an
  >       >       > easier way to generate surface meshes from the aparc 

Re: [Freesurfer] Generating Surfaces Meshes

[Bruce Fischl]

HI Jonah

it depends how you compute volume. mris_volume for example will compute the 
volume of the interior without any partial volume correction.


And yes, I would expect you want to smooth the surface a bit. You might try 
the Taubin smoothing built into freeview as it won't shrink the surface, 
but you can also try mris_smooth


cheers
Bruce


On Thu, 23 Apr 2020, Peter, Jonah wrote:


Hi Bruce,
I tried mri_tessellate which worked well in that the surface seems to follow 
the aseg projections
exactly. Does the volume of this mesh account for partial volume effects? Also, 
is there a need to run
mri_pretess or some sort of smoothing procedure?

For reference, what I am trying to do is import these surface meshes into a 
Geant4 simulation for proton
therapy, and want to make sure I'm using as realistic geometry as possible. 
Ideally I'd be able to
generate a mesh for the whole brain as well as individual segmentations.

Thanks again for your help,
Jonah

On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl  wrote:
  no, they are definitely not negligible. It depends on structure geometry,
  but I bet for something like the hippocampus a large fraction of voxels in
  it are partial volumed.

  You can use mri_mc or mri_tessellate to generate a mesh. It will be closed
  but may not have a simple topology

  On Thu, 23 Apr 2020, Peter, Jonah
  wrote:

  > Hi all,
  > Thanks for the response. I'm familiar with partial volume effects 
within the context of
  PET imaging, but
  > wouldn't you expect these effects to be negligible in MRI for 
structures on the order of
  mm?
  >
  > With respect to the mesh type, I'd like to get closed meshes for each
  segmentation/parcellation.
  >
  > Is there a way to do this in freesurfer?
      >
  > On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl 
 wrote:
  >       Hi Jonah
  >
  >       when we compute volumes we typically use a partial-volume model, 
which we
  >       have found improves accuracy and repeatability. That may be the 
source of
  >       your discrepancy
  >
  >       cheers
  >       Bruce
  >       On Wed, 22 Apr 2020, Peter, Jonah wrote:
  >
  >       > Hello,
  >       > I'm trying to generate surface meshes for different brain 
regions that can
  >       > be imported into a software like MeshLab or Blender (i.e. .STL, 
.PLY, .OBJ,
  >       > etc.). I ran recon-all on my T1 images, and the 
parcellation/segmentation
  >       > looks fine. However, I noticed that when I imported this data 
into 3DSlicer,
  >       > the volumes of these regions did not match the volumes in the 
aseg.stats
  >       > file. In some cases, the differences were quite substantial. I 
tried
  >       > removing all smoothing filters in 3DSlicer but the outcome was 
the same.
  >       >
  >       > Do you know what could be going wrong here? Alternatively, is 
there an
  >       > easier way to generate surface meshes from the aparc or aseg 
atlases?
  >       >
  >       > I'm using the ICBM 2009c Nonlinear Asymmetric
  >       > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain 
volume
  >       > (though alternative suggestions are welcome).
  >       >
  >       > Thanks!
  >       > Jonah
  >       >
  >       > --
  >       > Jonah PeterGraduate Student in The Biophysics ProgramHarvard 
University
  >       > P: 646-306-0848
  >       > E: jonahpe...@g.harvard.edu
  >       >
  >       >___
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  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >
  > --
  > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
  > P: 646-306-0848
  > E: jonahpe...@g.harvard.edu
  >
  >___
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--
Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
P: 646-306-0848
E: jonahpe...@g.harvard.edu

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Re: [Freesurfer] Generating Surfaces Meshes

[Bruce Fischl]

no, they are definitely not negligible. It depends on structure geometry, 
but I bet for something like the hippocampus a large fraction of voxels in 
it are partial volumed.


You can use mri_mc or mri_tessellate to generate a mesh. It will be closed 
but may not have a simple topology


On Thu, 23 Apr 2020, Peter, Jonah 
wrote:



Hi all,
Thanks for the response. I'm familiar with partial volume effects within the 
context of PET imaging, but
wouldn't you expect these effects to be negligible in MRI for structures on the 
order of mm?

With respect to the mesh type, I'd like to get closed meshes for each 
segmentation/parcellation.

Is there a way to do this in freesurfer?

On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl  
wrote:
  Hi Jonah

  when we compute volumes we typically use a partial-volume model, which we
  have found improves accuracy and repeatability. That may be the source of
  your discrepancy

  cheers
  Bruce
  On Wed, 22 Apr 2020, Peter, Jonah wrote:

  > Hello,
  > I'm trying to generate surface meshes for different brain regions that 
can
  > be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, 
.OBJ,
  > etc.). I ran recon-all on my T1 images, and the 
parcellation/segmentation
  > looks fine. However, I noticed that when I imported this data into 
3DSlicer,
  > the volumes of these regions did not match the volumes in the aseg.stats
  > file. In some cases, the differences were quite substantial. I tried
  > removing all smoothing filters in 3DSlicer but the outcome was the same.
  >
  > Do you know what could be going wrong here? Alternatively, is there an
  > easier way to generate surface meshes from the aparc or aseg atlases?
  >
  > I'm using the ICBM 2009c Nonlinear Asymmetric
  > template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume
  > (though alternative suggestions are welcome).
  >
  > Thanks!
  > Jonah
  >
  > --
  > Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
  > P: 646-306-0848
  > E: jonahpe...@g.harvard.edu
  >
  >___
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--
Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
P: 646-306-0848
E: jonahpe...@g.harvard.edu

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Re: [Freesurfer] ROIs to surface overlays / Arithmetic on surface overlays

[Bruce Fischl]

Hi Quentin

if you import it as a surface label you should be able to use morphological 
operations to smooth it (open, close, dilate, erode)


cheers
Bruce


On Thu, 23 Apr 2020, Funk, Quentin wrote:



External Email - Use Caution

Freesurfer experts,

I have a volumetric ROI (integer valued) in MNI space. I'd really like to
display them on the fsaverage brain as a surface overlay so that it's clear
what regions I'm looking at. 

Using something like this, I get pretty good results:

mri_vol2surf --mov ROI_integers.nii  --regheader fsaverage  --hemi lh --out
left_overlay.mgh --projfrac-max 0.15 .17 .01

but the edges are kind of a mess, see: https://imgur.com/a/53RVGCM

Is there any way to smooth these edges while maintaining the "lookup table'
nature of the surface overlay? Any kind of interpolation ruins that, so it's
a bit hard (you can't see in that image, but there are multiple regions
shown).

Alternatively, is there any way I can do arithmetic with surfaces? If there
were a tool like fslmaths for surface overlays, solving this problem would
be relatively straightforward.

Thanks for any help you can provide!

-quentin funk

Houston Methodist. Leading Medicine.

Houston Methodist is ranked by U.S. News & World Report as the No. 1
hospital in Texas and among the top 20 hospitals nationwide. Houston
Methodist is the only nationally ranked Honor Roll hospital in the state and
is designated as a Magnet hospital for excellence in nursing.


houstonmethodist.org | twitter.com/MethodistHosp |
facebook.com/HoustonMethodist

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Re: [Freesurfer] Cortical thickness measure for external analysis.

[Bruce Fischl]

you should be fine with the subject metrics we generate. Typically 
thickness doesn't need much if any eTIV correction
On Thu, 23 Apr 2020, 
Miguel Ángel Rivas Fernández wrote:




External Email - Use Caution

Dear Freesurfer experts,

We are interested in running external analysis with thickness measurements
of two brain regions. Can we use safely the metrics exported or by contrary
a previous transformation is required before export the stats of each
subject?

Thanks for your time.

Best regards,

--
Miguel Ángel Rivas Fernández

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Re: [Freesurfer] Generating Surfaces Meshes

[Bruce Fischl]

Hi Jonah

when we compute volumes we typically use a partial-volume model, which we 
have found improves accuracy and repeatability. That may be the source of 
your discrepancy


cheers
Bruce
On Wed, 22 Apr 2020, Peter, Jonah wrote:


Hello,
I'm trying to generate surface meshes for different brain regions that can
be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ,
etc.). I ran recon-all on my T1 images, and the parcellation/segmentation
looks fine. However, I noticed that when I imported this data into 3DSlicer,
the volumes of these regions did not match the volumes in the aseg.stats
file. In some cases, the differences were quite substantial. I tried
removing all smoothing filters in 3DSlicer but the outcome was the same.

Do you know what could be going wrong here? Alternatively, is there an
easier way to generate surface meshes from the aparc or aseg atlases?

I'm using the ICBM 2009c Nonlinear Asymmetric
template (http://nist.mni.mcgill.ca/?p=904) as a generic brain volume
(though alternative suggestions are welcome).

Thanks!
Jonah

--
Jonah PeterGraduate Student in The Biophysics ProgramHarvard University
P: 646-306-0848
E: jonahpe...@g.harvard.edu

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Re: [Freesurfer] Most effective way to compute stats/aseg.stats

[Bruce Fischl]

yes, careg is required. In general you should run things all the way to 
the end of recon-all as the surfaces are used to improve the accuracy of 
the aseg.


cheers
Bruce
On Sun, 19 Apr 2020, Ерохин Александр wrote:



External Email - Use Caution

Hello together,
 
Could you please suggest the most effective way (in terms of time) for
computation of statistics on segmented volumes from .nii source file?
 
So far I went though the following steps:
 
recon-all -autorecon1 -no-isrunning -subjid test
recon-all -gcareg -no-isrunning -subjid test
recon-all -canorm -no-isrunning -subjid test
 
And seem to be stuck on -careg as transforms/talairach.m3z is needed to
proceed.
 
As far as I can tell — there is no way around recon-all -careg which seems
to be the most time consuming in the chain of invocations based on Step-wise
Directives (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all).
 
But I might be wrong and hoping for your expertise here.
 
Many thanks,
Aleksandr Erokhin.

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Re: [Freesurfer] Data on the Freesurfer surface

[Bruce Fischl]

oh, then you probably want to use bbreg to register it and mri_vol2surf 
to sample it onto the surface. Doug is the expert on this and can 
add/correct if this is not the whole story :)


cheers
Bruce
On Fri, 17 Apr 2020, Mason 
Wells wrote:



   External Email - Use Caution

Hi Bruce,

The only pre-processing I have done is the motion correction, high pass 
filtering and distortion correction. So, as far as I know it is still in the 
volume and in the original functional space.

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   is your filtered_func file already sampled onto the surface or is it a
   volume?

   cheers
   Bruce
   On Fri, 17 Apr 2020, Mason Wells wrote:

   >
   > External Email - Use Caution
   >
   > Hi all,
   >
   >
   >
   > I am trying to use an analysis package that works on surface based data
   > (SamSrf). I have ran Feat and have a filtered_func file which is of course
   > the motion corrected/unwarped version of my EPI. However, I need some 
advice
   > on how to get these data onto the Freesurfer surface. I have found this
   > page, but I wanted to double check this is the most up-to-date pipeline. On
   > the page it suggests using the same DOF as used in Feat, I use BBR so this
   > seems a little redundant. Has anyone on these lists got any experience of
   > getting filtered_func onto the Freesurfer surface?
   >
   >
   >
   > Thanks in advance,
   >
   > Mason
   >
   >
   >
   >
   >
   > Mason T Wells, MSc
   >
   > PhD student
   >
   > School of Optometry and Vision Sciences
   >
   > & Cardiff University Brain Research
   >
   > Imaging Centre (CUBRIC), School of Psychology
   >
   > Cardiff University
   >
   > Cardiff
   >
   > CF24 4HQ
   >
   > UK
   >
   >
   >
   > Email: wells...@cardiff.ac.uk
   >
   > Tel: 02920 879628
   >
   > Web: Cardiff University webpage
   >
   > Mason T Wells, MSc
   >
   > Myfyriwr PhD
   >
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   >
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol
   > Seicoleg
   >
   > Prifysgol Caerdydd
   >
   > Heol Maindy
   >
   > Caerdydd
   >
   > CF24 4HQ
   >
   > DU
   >
   >
   >
   > E-bost: wells...@caerdydd.ac.uk
   >
   > Ffôn: 02920 879628
   >
   >
   >
   >
   >


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Re: [Freesurfer] Data on the Freesurfer surface

[Bruce Fischl]

Hi Mason

is your filtered_func file already sampled onto the surface or is it a 
volume?


cheers
Bruce
On Fri, 17 Apr 2020, Mason Wells wrote:



External Email - Use Caution

Hi all,

  

I am trying to use an analysis package that works on surface based data
(SamSrf). I have ran Feat and have a filtered_func file which is of course
the motion corrected/unwarped version of my EPI. However, I need some advice
on how to get these data onto the Freesurfer surface. I have found this
page, but I wanted to double check this is the most up-to-date pipeline. On
the page it suggests using the same DOF as used in Feat, I use BBR so this
seems a little redundant. Has anyone on these lists got any experience of
getting filtered_func onto the Freesurfer surface?

 

Thanks in advance,

Mason

 

 

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff   

CF24 4HQ

UK

 

Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd   

CF24 4HQ 

DU

 

E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628

 


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Re: [Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

[Bruce Fischl]

Hi Marina

can you include command line and full screen output (in text!) so we can 
understand what you mean by "it doesn't work". Also, note that 
.mgh/.nii.gz are volume formats, not surface ones, so you can't convert a 
surface to them. You will need to use our surface format


cheers
Bruce
On Fri, 17 Apr 
2020, Marina Fernández wrote:




External Email - Use Caution

Hi experts,
How can I convert a surface in .gii format to a surface in .mgh or nii.gz
format?

I tried with mris_convert but it doesn't work.


Best regards,
Marina

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Re: [Freesurfer] Queries on the Function of Freesurfer

[Bruce Fischl]

they aren't released yet, but we are working on them
On Tue, 14 Apr 2020, 
Koustav Chatterjee wrote:




External Email - Use Caution

Dear Sir,I am afraid I am yet to find pedunculopontine nucleus and locus
coeruleus in particular through FS dev versions of labelings volume.
Could you please help me out?
Best Regards,
KC


On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl 
wrote:
  Hi Koustav

  the current version of FS requires a T1-weighted input but could
  also use
  a T2 to improve accuracy and automaticity. Future versions will
  relax
  this constraint.

  As for 2D/3D, you have to distinguish the acquisition type
  (which almost
  always should be a 3D sequence like an MP-RAGE or a 3D
  FLASH/SGPR) from
  the model. When we say "2d cortical surface" we are talking
  about
  extracting that model ("reconstructing" it) from the 3D data

  As for the structures you mention, we have dev versions of
  labelings for
  all of them I believe, but I defer to Doug on the details

  cheers
  Bruce


  On Sun, 12 Apr 2020, Koustav Chatterjee wrote:

  >
  > External Email - Use Caution
  >
  > Dear all,
  > I am a beginner in FreeSurfer world.
  > I have 4 questions. It would be kind enough if you could
  clarify my
  > confusions.
  >  *  I have came across that 'Freesurfer can reconstruct 2D
  cortical surface
  >     from 3D T1 MRI brain image'. However, I know that T1 2D
  brain images are
  >     being fed to freesurfer for 'Recon-all...-all' to function
  all its
  >     pre-processing steps. 
  > Whether "...reconstruct 2D cortical surface from 3D T1 MRI
  image" this
  > statement is true? Is there any step where FreeSurfer make a
  3D image from
  > 2D T1 images and again reconstruct them into 2D
  > cortical surface through preprocessing steps?
  >
  >  *  Can FreeSurfer only recognize 'T1 weighted images' for
  processing? Why
  >     only T1, why not T2 or Flair etc?
  >  *  Can we estimate the volume of substantia nigra,
  pedunculopontine nucleus
  >     and locus cereleus using FreeSurfer? If so any specific
  version
  >     of Freesurfer is required?
  >  *  If I have Freesurfer installed in my PC; I also have T1
  and diffusion
  >     weighted image sequence of a subject. Can I use 'Tracula'
  to analyse
  >     tracts of that subject's brain directly? How could I
  analyse tracts in
  >     Freesurfer?
  > Thank you for your time and effort.
  > Regards,
  > Koustav
  >
  >
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Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

yes, that should be doable if you process in the order I suggested below
cheers
Bruce
On 
Mon, 13 Apr 2020, Amar Shukla wrote:




External Email - Use Caution

Dear Sir,

Thank you for your precious reply  

Actually i am working on to the study of Disease which have the effect on
the brain.

1) First i am using t1 image for analysis of the same subject of that
disease.

2) I am using Diffussion image for the analysis  for the same subject.

So can i make any relation between trac based analysis of diffusion image
and Volumetric analysis of T1 weighted image of same subject.

regards
Amar Shukla


On Mon, 13 Apr 2020, 19:09 Bruce Fischl,  wrote:
  Hi Amar

  I'm not quite sure I understand your question, but in FS you
  would use
  the T1 as input to recon-all, then the outputs of that and the
  diffusion
  data would let you run tracula

  cheers
  Bruce
  On Mon, 13 Apr 2020, Amar Shukla wrote:

  >
  > External Email - Use Caution
  >
  > Hello Freesurfer,
  >
  > Can we go through the volumetric  [surface area and many more
  ] through DTI
  > images and  T1 or t2 weighted images of the same subject. Can
  we provide
  > common study and can we develop any analysis on these studies.
  > My research is focused on these direction o or any kind of
  corelation
  > through different Images .
  > basis of diffusion images and  T1 or t2 weighted images,
  >
  > so please give suggestions and comment on these.
  >
  >
  >
  > --
  > With Regards,
  > Amar Shukla
  >
  >
  >___
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Re: [Freesurfer] DTI and T1 AND T2 WEIGHTED IMAGES

[Bruce Fischl]

Hi Amar

I'm not quite sure I understand your question, but in FS you would use 
the T1 as input to recon-all, then the outputs of that and the diffusion 
data would let you run tracula


cheers
Bruce
On Mon, 13 Apr 2020, Amar Shukla wrote:



External Email - Use Caution

Hello Freesurfer,

Can we go through the volumetric  [surface area and many more ] through DTI
images and  T1 or t2 weighted images of the same subject. Can we provide
common study and can we develop any analysis on these studies.
My research is focused on these direction o or any kind of corelation
through different Images .
basis of diffusion images and  T1 or t2 weighted images,

so please give suggestions and comment on these.



--
With Regards,
Amar Shukla


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Re: [Freesurfer] Atlas for subcortical segmentation

[Bruce Fischl]

Hi Javier

our atlas includes a broad range of ages and is intended to work across 
the lifespan except for <=5 or so


cheers
Bruce
On Mon, 13 Apr 2020, javier quilis wrote:



External Email - Use Caution

Dear Freesurfer developers, 

I'm interested in trying different possible atlas to do the subcortical
segmentation in order to see which one is more accurate in my dataset. Is
there a list of atlas somewhere and the explanation of how to use them? The
only example I found is InfantFS
(https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS), but I would be
interested in something focused in elderly people. In any case, if there is
a list it would be useful to see which one suits better.

Thank you very much, 
Bests regards, 

Javier Quilis


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Re: [Freesurfer] Hello Respected Community,

[Bruce Fischl]

Hi Safi

have you tried loading the label file into freeview? You should be able 
to type the ras coordinates from the label into the freeview info window 
and it will go to that point (not that there are different types of ras 
displayed by freeview


cheers
Bruce
On Mon, 13 Apr 2020, Safi 
Ullah . wrote:




External Email - Use Caution

Hello Respected Community,
I generated a label file using the command 
mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173
--l midbrain.label 
the content of the label file is probably in RAS format. My question is how
to locate a point in freeview using the given coordinates of the label
file? 
i.e the label file content is as follows
-1  4.000  -20.750  33.750 0.00
-1  3.500  -20.750  33.750 0.00
I am unable to locate 4.0, -20.750, 33.750 in the volume shown through
freeview. 

I also want to find out the overlapping planes of two label files, for which
I need to convert the label file into voxal coordinates (or may be there is
any other simpler way, i dont know) 

Any help shall be highly appreciated.

Regards, 
Safi

[icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
Virus-free. www.avast.com

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Re: [Freesurfer] Queries on the Function of Freesurfer

[Bruce Fischl]

yes, if you run your T1 through FreeSurfer's recon-all you should be able 
to use tracula afterwards to reconstruct tract models from your dwi data.


We use T1 because it is by far the most common anatomical sequence and 
historically has had better cnr/unit-time


cheers
Bruce

On 
Mon, 13 Apr 2020, Koustav Chatterjee wrote:




External Email - Use Caution

Thank you very much Sir for your effort and time to answer my questions.
I am afraid I have not got the answer for the following:

 *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
weighted image sequence of a subject. Can I use 'Tracula' to analyse
tracts of that subject's brain directly? How could I analyse tracts in
Freesurfer?  

It would also be kind enough why T1 weighted or T2 can only be read by
FreeSurfer? Is this because of the algorithm they use.

On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl 
wrote:
  Hi Koustav

  the current version of FS requires a T1-weighted input but could
  also use
  a T2 to improve accuracy and automaticity. Future versions will
  relax
  this constraint.

  As for 2D/3D, you have to distinguish the acquisition type
  (which almost
  always should be a 3D sequence like an MP-RAGE or a 3D
  FLASH/SGPR) from
  the model. When we say "2d cortical surface" we are talking
  about
  extracting that model ("reconstructing" it) from the 3D data

  As for the structures you mention, we have dev versions of
  labelings for
  all of them I believe, but I defer to Doug on the details

  cheers
  Bruce


  On Sun, 12 Apr 2020, Koustav Chatterjee wrote:

  >
  > External Email - Use Caution
  >
  > Dear all,
  > I am a beginner in FreeSurfer world.
  > I have 4 questions. It would be kind enough if you could
  clarify my
  > confusions.
  >  *  I have came across that 'Freesurfer can reconstruct 2D
  cortical surface
  >     from 3D T1 MRI brain image'. However, I know that T1 2D
  brain images are
  >     being fed to freesurfer for 'Recon-all...-all' to function
  all its
  >     pre-processing steps. 
  > Whether "...reconstruct 2D cortical surface from 3D T1 MRI
  image" this
  > statement is true? Is there any step where FreeSurfer make a
  3D image from
  > 2D T1 images and again reconstruct them into 2D
  > cortical surface through preprocessing steps?
  >
  >  *  Can FreeSurfer only recognize 'T1 weighted images' for
  processing? Why
  >     only T1, why not T2 or Flair etc?
  >  *  Can we estimate the volume of substantia nigra,
  pedunculopontine nucleus
  >     and locus cereleus using FreeSurfer? If so any specific
  version
  >     of Freesurfer is required?
  >  *  If I have Freesurfer installed in my PC; I also have T1
  and diffusion
  >     weighted image sequence of a subject. Can I use 'Tracula'
  to analyse
  >     tracts of that subject's brain directly? How could I
  analyse tracts in
  >     Freesurfer?
  > Thank you for your time and effort.
  > Regards,
  > Koustav
  >
  >
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Re: [Freesurfer] Queries on the Function of Freesurfer

[Bruce Fischl]

Hi Koustav

the current version of FS requires a T1-weighted input but could also use 
a T2 to improve accuracy and automaticity. Future versions will relax 
this constraint.


As for 2D/3D, you have to distinguish the acquisition type (which almost 
always should be a 3D sequence like an MP-RAGE or a 3D FLASH/SGPR) from 
the model. When we say "2d cortical surface" we are talking about 
extracting that model ("reconstructing" it) from the 3D data


As for the structures you mention, we have dev versions of labelings for 
all of them I believe, but I defer to Doug on the details


cheers
Bruce


On Sun, 12 Apr 2020, Koustav Chatterjee wrote:



External Email - Use Caution

Dear all,
I am a beginner in FreeSurfer world.
I have 4 questions. It would be kind enough if you could clarify my
confusions.
 *  I have came across that 'Freesurfer can reconstruct 2D cortical surface
from 3D T1 MRI brain image'. However, I know that T1 2D brain images are
being fed to freesurfer for 'Recon-all...-all' to function all its
pre-processing steps. 
Whether "...reconstruct 2D cortical surface from 3D T1 MRI image" this
statement is true? Is there any step where FreeSurfer make a 3D image from
2D T1 images and again reconstruct them into 2D
cortical surface through preprocessing steps?

 *  Can FreeSurfer only recognize 'T1 weighted images' for processing? Why
only T1, why not T2 or Flair etc?
 *  Can we estimate the volume of substantia nigra, pedunculopontine nucleus
and locus cereleus using FreeSurfer? If so any specific version
of Freesurfer is required?
 *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
weighted image sequence of a subject. Can I use 'Tracula' to analyse
tracts of that subject's brain directly? How could I analyse tracts in
Freesurfer?
Thank you for your time and effort.
Regards,
Koustav


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Re: [Freesurfer] Error running recon-all

[Bruce Fischl]

Hi David

did you check the skull stripping as suggested? Seems like the input 
volume given to the CC finder was empty. Work backwards and find the 
earliest volume where something is wrong


cheers
Bruce
On Fri, 10 Apr 2020, David 
Schwantner wrote:




External Email - Use Caution

Thank you in advance for the assistance!

I am running the following command:

             recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all

The log isat 
https://github.com/dschwant/mri_to_3d/blob/master/202004090853_error_rec
on-all.log, and the nii file isat 
https://github.com/dschwant/mri_to_3d/blob/master/202004_DS_Brain_MRI/11
31_T2_raw.nii.gz.
 
Here is the tail of the log. As you can see, I am running it in Ubuntu
18.04.4 under the Windows Subsystem for Linux.

  ...
searching rotation angles z=[-9  5], y=[-22 -8]
searching scale 1 Z rot 5.3  global minimum found at slice 139.0,
rotations (-14.14, -1.42)
final transformation (x=139.0, yr=-14.141, zr=-1.420):
 0.96940   0.02478  -0.24423   8.04082;
-0.02403   0.99969   0.00605  -41.07934;
 0.24430   0.0   0.96970   18.40543;
 0.0   0.0   0.0   1.0;
mri_cc: no WM voxels found with norm > 40 -- check skull stripping

No such file or directory
Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07
15:22:00 PST 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s DS_T2 exited with ERRORS at Thu Apr  9 11:19:24 DST 2020
...


Is it just not enough "details" in the nifti file? I am trying the next
larger one now.
 David - dschw...@gmail.com


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Re: [Freesurfer] Recon-all Note Completing

[Bruce Fischl]

Hi Jason

looks like it is not finding your license file. Did you get one?

cheers
Bruce
On Tue, 7 
Apr 2020, Ledesma, Jason wrote:




External Email - Use Caution

Hi,


I am receiving an error when performing recon-all.  See attached for recon-all 
log. Thanks. 


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@lundquist.org






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Re: [Freesurfer] Chorid-plexus in Freesurfer reconall

[Bruce Fischl]

Hi An Lijun

The choroid is a plexus of ependymal cells that produce CSF. it is pretty 
tough to segment and mostly we include it to get more accurate segmenations 
of the hippocampus where it is adjacent to ventricle and the ventricles 
themselves. I'm not sure I've ever seen any normative stats on it though.


You can read more here:

https://en.wikipedia.org/wiki/Choroid_plexus

cheers
Bruce

On Tue, 7 Apr 2020, Lijun An 
wrote:




External Email - Use Caution

Dear Freesurfer experts, 

I have a little question about the structure 'chorid-plexus', I am not very 
deep in brain
anatomy and function. Could anyone have a sense of what is the normal range of 
this
structure volume from Freesurfer reconall?

I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran 
reconall for my
local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 
800 mm^3.

Could anyone give an explanation or a paper I could refer to for this 
'chorid-plexus'
structure?

Thanks  so much!   

Best Regards,An Lijun

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Re: [Freesurfer] Converting .mgz (or .nii) file to .hdr file (.hdr and .img)

[Bruce Fischl]

Hi Kim

are you really sure that you want to use analyze format? I doesn't keep 
track of the direction cosines properly so once you go to it it is hard to 
know left from right.  SPM should be fine with nifti. In any case 
conversion should be something like:


mri_convert file.mgz file.nii

or

mri_convert file.mgz file.img

although again, I wouldn't recommend using analyze

cheers
Bruce


On Sat, 4 Apr 2020, Kim, Gwang-Won wrote:



Dear expert,

 

I'd like to convert .mgz (or .nii) file to .hdr file (.hdr and .img) to use 
.hdr in SPM
software.

I tried to convert the file using "mri_convert". But, there were the error 
messages below.

Please, let me know how to onvert  .mgz (or .nii) file to .hdr file (.hdr and 
.img).

 

1) convert  .nii file to .hdr file (.hdr and .img) 

[latifah:kim] (nmr-stable6-env) mri_convert -it nii -ot spm BB.nii RE
mri_convert.bin -it nii -ot spm BB.nii RE
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from BB.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to RE...
ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768

 

 

2) convert  .mgh file to .hdr file (.hdr and .img)

[latifah:kim] (nmr-stable6-env) mri_convert -it mgh -ot spm AA.mgh RE.hdr
mri_convert.bin -it mgh -ot spm AA.mgh RE.hdr
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from AA.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to RE.hdr...
ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768

 


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Re: [Freesurfer] Recon-all exited with errors

[Bruce Fischl]

Hi Lily

yes, some brains are harder (and longer to process) than others.

glad it worked out

cheers
Bruce
On Wed, 1 
Apr 2020, Wang, Lily wrote:



Hi Bruce,

I re-ran it without running anything else on the machine. Took almost three 
times as long as my
recons usually take but it finished without error. Thank you for your help!

Best,
Lily

_
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Monday, March 30, 2020 5:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all exited with errors  
Hi Lily

that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you can tar and gzip the whole subject dir and
ftp it to us and we will take a look, but I would try rerunning when
nothing else is taking up significant chunks of memory on your machine and
see if that fixes it
cheers
Bruce

On Mon, 30 Mar 2020, Wang, Lily wrote:

> Hi Dr. Greve,
>
> I'm not seeing any glaring issues with inclusion of cerebellum or skull in
> the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
> the wm.mgz. However, two things that do seem strange are 1. a portion of the
> subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
> looks like the ventricles are supposed to be white, but a big portion of
> this subject's ventricles are not included and it seems that it's messing up
> the lh.orig.nofix surface as well. Could this possibly be an issue? Please
> see attached screenshot.
>
> Thank you,
> Lily
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> Sent: Monday, March 30, 2020 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] Recon-all exited with errors  
> It looks like there might be a very large defect. Try looking at the wm.mgz
> and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
> part of skull or cerebellum that is encompassed in the orig.nofix surface
>
> On 3/30/2020 11:26 AM, Wang, Lily wrote:
>   Hi All,
>
> I have a subject whose T1 quality is quite good but reconstruction
> exited with errors so I am not sure what the issue could be. Attached
> is the recon-all.log. Could it be that the subject is very old and has
> a lot of degeneration?
>
> Thank you,
> Lily
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>

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Re: [Freesurfer] Color map - color bar

[Bruce Fischl]

Hi Adam

if you are using freeview to display a colormap you can just click the 
colorbar button in the top row near the middle to toggle it on/off


cheers
Bruce

On Wed, 1 Apr 2020, Adam Rytina wrote:



External Email - Use Caution

Hello all,

I did the post-processing on brain images in Freesurfer. I changed the color 
coding to display where
MR signals values are higher or lower. I need to add the color bar onto the 
image in order to easily
identify what "blue" or "red" color means. Please, in which program is it 
possible to change the
color map and to add the color bar as well? I tried to implement it in ITK-SNAP 
but the option of
adding the color bar is not implemented there.

Thanks a lot
Regards
Adam

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Re: [Freesurfer] kill recon-all programatically/remotely

[Bruce Fischl]

ps aux | grep recon-all

To get the pid, then 

kill -9 pid

Or 

killall recon-all

If it is the only one running on that box

Cheers
Bruce

> On Mar 31, 2020, at 10:10 PM, Octavian Lie  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear All, 
> 
> Is there a way to kill a  recon-all run on linux via ssh/putty. Ctrl+C is not 
> working, obviously, and it is not easy to figure out which process encodes 
> the recon-all runs with commands such as ps aux, top etc. One gross way may 
> be removing the subject directory all together midway, but not sure how this 
> affects FS, subsequent runs
> Thank you, 
> Octavian
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Re: [Freesurfer] Reducing FreeSurfer recon-all time

[Bruce Fischl]

Hi Xiaojiang

do you have multiple cores? If so, you can use -openmp 4  or something to 
reduce the recon time even on your linux box


cheers
Bruce
On Tue, 31 Mar 2020, Xiaojiang 
Yang wrote:




External Email - Use Caution

Freesurfer experts:

I know in my powerful Linux machine, recon-all needs about 10 hours to finish 
all computation. What
is the possible way I can use to greatly reduce this computation time from 10 
hours to, say 1-3
hours?

Is Sun Grid Engine (SGE), or GPU/CUDA, or any other technique, helpful?

Thank you!
Xiaojiang


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Re: [Freesurfer] Recon-all exited with errors

[Bruce Fischl]

Hi Lily

that looks ok I think, although it's hard to tell for sure. The 
cerebellum shouldn't be included in the surface. Are you sure you have 
enough ram on your machine? It looked like half of it was in use when you 
ran recon-all. If you want you can tar and gzip the whole subject dir and 
ftp it to us and we will take a look, but I would try rerunning when 
nothing else is taking up significant chunks of memory on your machine and 
see if that fixes it

cheers
Bruce

On Mon, 30 Mar 2020, Wang, Lily wrote:


Hi Dr. Greve,

I'm not seeing any glaring issues with inclusion of cerebellum or skull in
the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
the wm.mgz. However, two things that do seem strange are 1. a portion of the
subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
looks like the ventricles are supposed to be white, but a big portion of
this subject's ventricles are not included and it seems that it's messing up
the lh.orig.nofix surface as well. Could this possibly be an issue? Please
see attached screenshot.

Thank you,
Lily


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Douglas N. Greve

Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all exited with errors  
It looks like there might be a very large defect. Try looking at the wm.mgz
and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
part of skull or cerebellum that is encompassed in the orig.nofix surface

On 3/30/2020 11:26 AM, Wang, Lily wrote:
  Hi All,

I have a subject whose T1 quality is quite good but reconstruction
exited with errors so I am not sure what the issue could be. Attached
is the recon-all.log. Could it be that the subject is very old and has
a lot of degeneration?

Thank you,
Lily

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Re: [Freesurfer] mri_vol2surf projections for subcortical structures

[Bruce Fischl]

Hi Niels

I don't see why not. vol2surf takes the surface location and the surface 
normal and sampled from the volume onto the surface using those two pieces 
of local information. Global surface topology shouldn't matter

cheers
Bruce

On Sun, 
29 Mar 2020, Niels Janssen . wrote:




External Email - Use Caution

Dear list

I am working on a project in which we want to extract hippocampal surfaces
using mri_tessellate and then overlay these surfaces with fmri activations
from nifti files using mri_vol2surf. However, I am unclear whether
mri_vol2surf can be used for surfaces derived from subcortical structures
like the hippocampus. Crucially, these structures are unlike the cortex in
that they have a closed shape and therefore the projection of activation to
a surface may be more complex than in the case of cortex (which surface
normal should one take?). So I guess my question is whether mri_vol2surf
works for these kinds of surfaces or whether some other approach should be
used. Thanks!

Niels

--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/

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Re: [Freesurfer] thalamic segmentation analysis

[Bruce Fischl]

Hi VP

you need to give us more information! What is going wrong? What kind of 
system are you installing/running on? Send us the commands you are running 
and their output including any error messages.


cheers
Bruce



On Sat, 28 Mar 2020, Parisi Veronica 
wrote:




External Email - Use Caution

Hi there,

I have been trying to learn and set-up Freesurfer for a research project I a
m working on, but I am having trouble with the set-up/installation process.

Once Freesurfer is set-up, I will be using it to measure thalami and define 
their sub nuclei.


I have followed the instructions online to the best of my ability but can't 
seem to figure this out. Any assistance would be very much appreciated. 


Thank you.

Best,

VP


Rispetta l’ambiente: non stampare questa mail se non è necessario.
Respect the environment: print this email only if necessary.


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Re: [Freesurfer] Hippocampal Volume Extraction

[Bruce Fischl]

Hi Devika

the volumes should be in the stats/aseg.stats file for each subject.

cheers
Bruce
On Thu, 
26 Mar 2020, Devika K wrote:




External Email - Use Caution

Hi,

I want to extract hippocampal volume from longitudinal samples. I am less
aware of it. I ran recon-all-all with longitudinal pipeline for all those
samples.

How I need to process further (Commands that I need to follow).
Would you please help me out?



Thanks and Regards
Devika K


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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

[Bruce Fischl]

Hi Mason

not sure we can help if everything looks good in freeview. Doesn't that 
make it a SamSrf issue? Or an interface between the two packages? Have you 
checked with their support?


cheers
Bruce


On Thu, 26 Mar 2020, Mason Wells wrote:


   External Email - Use Caution

In the event that Bruce might not be able to help. I ask if anyone else on the 
list has experience with the problem described in this thread? Any help would 
be greatly appreciated.

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 18:38, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:

   External Email - Use Caution

   HI Bruce,

   Ok, great. I just thought some sections of white matter had not been traced 
in their entirety (see red crosshair in attached image). If you think this all 
looks reasonable, please can you advise on the misaligned as outlined in the 
original post?

   Best wishes,
   Mason

   Mason T Wells, MSc
   PhD student
   School of Optometry and Vision Sciences
   & Cardiff University Brain Research
   Imaging Centre (CUBRIC), School of Psychology
   Cardiff University
   Cardiff
   CF24 4HQ
   UK

   Email: wells...@cardiff.ac.uk
   Tel: 02920 879628
   Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
   Mason T Wells, MSc
   Myfyriwr PhD
   Yr Ysgol Optometreg a Gwyddorau’r Golwg
   & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
   Prifysgol Caerdydd
   Heol Maindy
   Caerdydd
   CF24 4HQ
   DU

   E-bost: wells...@caerdydd.ac.uk
   Ffôn: 02920 879628


   On 25/03/2020, 17:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   I can't tell from those images except that it looks reasonable
   cheers
   Bruce
   On Wed, 25
   Mar 2020, Mason Wells wrote:

   >External Email - Use Caution
   >
   > Hi again Bruce,
   >
   > I have now installed the relevant libpng packages and have freeview 
open. The segmentation doesn’t look brilliant in some areas. What do you think?
   >
   > Mason T Wells, MSc
   > PhD student
   > School of Optometry and Vision Sciences
   > & Cardiff University Brain Research
   > Imaging Centre (CUBRIC), School of Psychology
   > Cardiff University
   > Cardiff
   > CF24 4HQ
   > UK
   >
   > Email: wells...@cardiff.ac.uk
   > Tel: 02920 879628
   > Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
   > Mason T Wells, MSc
   > Myfyriwr PhD
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
   > Prifysgol Caerdydd
   > Heol Maindy
   > Caerdydd
   > CF24 4HQ
   > DU
   >
   > E-bost: wells...@caerdydd.ac.uk
   > Ffôn: 02920 879628
   >
   >
   > On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:
   >
   >External Email - Use Caution
   >
   >Hi Bruce,
   >
   >I get the following error message when I try to load freeview
   >
   >Setting up environment for FreeSurfer/FS-FAST (and FSL)
   >FREESURFER_HOME   /usr/local/freesurfer
   >FSFAST_HOME   /usr/local/freesurfer/fsfast
   >FSF_OUTPUT_FORMAT nii.gz
   >SUBJECTS_DIR  /usr/local/freesurfer/subjects
   >MNI_DIR   /usr/local/freesurfer/mni
   >FSL_DIR   /usr/local/fsl
   >masontwells@masontwells-VIG800S:~$ freeview
   >freeview.bin: error while loading shared libraries: libpng12.so.0: 
cannot open shared object file: No such file or directory
   >
   >Mason T Wells, MSc
   >PhD student
   >School of Optometry and Vision Sciences
   >& Cardiff University Brain Research
   >Imaging Centre (CUBRIC), School of Psychology
   >Cardiff University
   >Cardiff
   >CF24 4HQ

Re: [Freesurfer] training set

[Bruce Fischl]

Have you checked the original aseg paper? If not, then it will be in 
Rahul's cortical parcellation one as it is the same data


cheers
Bruce

On Thu, 26 Mar 2020, javier quilis wrote:



External Email - Use Caution

Hi Bruce, 

thanks for the answer. Is there any paper where this is explained? I want to
detail this in my paper and I would like to refer to the source. 

Thanks again, 
Javier


De: freesurfer-boun...@nmr.mgh.harvard.edu
 en nombre de Bruce Fischl

Enviado: miércoles, 25 de marzo de 2020 14:40
Para: Freesurfer support list 
Asunto: Re: [Freesurfer] training set  
Hi Javier

no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).

cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:

>
> External Email - Use Caution
>
> Thanks for the answer. 
>
> I can not open the power point for some reason. Is there any paper where I
> can check this? I think the dataset used by freesurfer is in the MNI
Average
> Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from
young
> people, is this correct?
>
> Thanks again.
> Bests, 
> Javier
>
>
>
>
>
>___
_
> De: freesurfer-boun...@nmr.mgh.harvard.edu
>  en nombre de Douglas N. Greve
> 
> Enviado: viernes, 20 de marzo de 2020 15:39
> Para: freesurfer@nmr.mgh.harvard.edu 
> Asunto: Re: [Freesurfer] training set  
> Try the tutorial slides
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
> It does not go into a lot of detail, but it will give you the relevant
> lectures
>
>
> On 3/17/2020 8:54 AM, javier quilis wrote:
>
>   External Email - Use Caution
>
>   Hello everyone, 
>
> I'm trying to do a study of a comparison between the automated methods
> to analyze structural MRI from FSL and Freesurfer. I am interested in
> the training set used by Freesurfer to do the brain segmentation and I
> can not find a detailed description of it. Is there any source where
> this set is described?
>
> Thanks in advance.
> Bests, 
> Javier Quilis
>
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>
>
>
>

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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

[Bruce Fischl]

Hi Mason

I can't tell from those images except that it looks reasonable
cheers
Bruce
On Wed, 25 
Mar 2020, Mason Wells wrote:


   External Email - Use Caution 


Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The 
segmentation doesn’t look brilliant in some areas. What do you think?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:

   External Email - Use Caution

   Hi Bruce,

   I get the following error message when I try to load freeview

   Setting up environment for FreeSurfer/FS-FAST (and FSL)
   FREESURFER_HOME   /usr/local/freesurfer
   FSFAST_HOME   /usr/local/freesurfer/fsfast
   FSF_OUTPUT_FORMAT nii.gz
   SUBJECTS_DIR  /usr/local/freesurfer/subjects
   MNI_DIR   /usr/local/freesurfer/mni
   FSL_DIR   /usr/local/fsl
   masontwells@masontwells-VIG800S:~$ freeview
   freeview.bin: error while loading shared libraries: libpng12.so.0: cannot 
open shared object file: No such file or directory

   Mason T Wells, MSc
   PhD student
   School of Optometry and Vision Sciences
   & Cardiff University Brain Research
   Imaging Centre (CUBRIC), School of Psychology
   Cardiff University
   Cardiff
   CF24 4HQ
   UK

   Email: wells...@cardiff.ac.uk
   Tel: 02920 879628
   Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
   Mason T Wells, MSc
   Myfyriwr PhD
   Yr Ysgol Optometreg a Gwyddorau’r Golwg
   & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
   Prifysgol Caerdydd
   Heol Maindy
   Caerdydd
   CF24 4HQ
   DU

   E-bost: wells...@caerdydd.ac.uk
   Ffôn: 02920 879628


   On 25/03/2020, 16:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   something like

   freeview -v $SUBJECTS_DIR//mri/norm.mgz \
 -f $SUBJECTS_DIR//surf/?h.white

   cheers
   Bruce


   On Wed, 25 Mar 2020, Mason Wells wrote:

   >External Email - Use Caution
   >
   > Hi Bruce,
   >
   > Thanks for getting back to me. Sorry, but I am not sure I follow what 
you mean here.
   > Could you please explain how I would check this?
   >
   > Thanks again for your help.
   > Mason
   >
   > Mason T Wells, MSc
   > PhD student
   > School of Optometry and Vision Sciences
   > & Cardiff University Brain Research
   > Imaging Centre (CUBRIC), School of Psychology
   > Cardiff University
   > Cardiff
   > CF24 4HQ
   > UK
   >
   > Email: wells...@cardiff.ac.uk
   > Tel: 02920 879628
   > Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
   > Mason T Wells, MSc
   > Myfyriwr PhD
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
   > Prifysgol Caerdydd
   > Heol Maindy
   > Caerdydd
   > CF24 4HQ
   > DU
   >
   > E-bost: wells...@caerdydd.ac.uk
   > Ffôn: 02920 879628
   >
   >
   > On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:
   >
   >Hi Mason
   >
   >can you confirm that things look ok within FreeSurfer if you look 
at the
   >surface over the volume in freeview?
   >
   >cheers
   >Bruce
   >On Wed, 25 Mar 2020, Mason Wells wrote:
   >
   >>
   >> External Email - Use Caution
   >>
   >> Hello Freesurfer developers,
   >>
   >>
   >>
   >> I am using Freesurfer and SamSrf for prf mapping. I have ran the 
recon-all
   >> command which finished without errors. However, the white/grey 
matter
   >> boundaries are significantly misaligned with the subjects T1 
(images
   >> attached).  Below are the steps I have taken to reach this point 
in the
   > 

Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

[Bruce Fischl]

something like

freeview -v $SUBJECTS_DIR//mri/norm.mgz \
 -f $SUBJECTS_DIR//surf/?h.white

cheers
Bruce


On Wed, 25 Mar 2020, Mason Wells wrote:


   External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean 
here.
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   can you confirm that things look ok within FreeSurfer if you look at the
   surface over the volume in freeview?

   cheers
   Bruce
   On Wed, 25 Mar 2020, Mason Wells wrote:

   >
   > External Email - Use Caution
   >
   > Hello Freesurfer developers,
   >
   >
   >
   > I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
   > command which finished without errors. However, the white/grey matter
   > boundaries are significantly misaligned with the subjects T1 (images
   > attached).  Below are the steps I have taken to reach this point in the
   > analysis:
   >
   >
   >
   >  1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
   >  2. Ran Feat
   >
   > · Distortion correction of the EPI
   >
   > · Motion correction
   >
   > · No smoothing
   >
   > · Highpass filter
   >
   > · No registration to whole brain
   >
   > · Register to T1_biascorr_brain
   >
   > · Register to standard space
   >
   >  3. Ran recon-all on T1_biascorr
   >  4. Convert T1/T1_brain/orig(001) from mgz to nii
   >  5. Check registration (using the SurfaceProjection command from the SamSrf
   > package) which leads to the attached images named S1 and S1.
   >
   >
   >
   > Freesurfer version:
   > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
   >
   > Platform: Linux 5.3.0-40-generic x86_64
   >
   > Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP 
Mon
   > Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
   >
   >
   >
   > As you can see, the registration is significantly misaligned.
   >
   > Can anyone offer any advice on this/suggest a way to rectify it?
   >
   >
   >
   >
   >
   > Thanks in advance,
   >
   > Mason
   >
   >
   >
   > Mason T Wells, MSc
   >
   > PhD student
   >
   > School of Optometry and Vision Sciences
   >
   > & Cardiff University Brain Research
   >
   > Imaging Centre (CUBRIC), School of Psychology
   >
   > Cardiff University
   >
   > Cardiff
   >
   > CF24 4HQ
   >
   > UK
   >
   >
   >
   > Email: wells...@cardiff.ac.uk
   >
   > Tel: 02920 879628
   >
   > Web: Cardiff University webpage
   >
   > Mason T Wells, MSc
   >
   > Myfyriwr PhD
   >
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   >
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol
   > Seicoleg
   >
   > Prifysgol Caerdydd
   >
   > Heol Maindy
   >
   > Caerdydd
   >
   > CF24 4HQ
   >
   > DU
   >
   >
   >
   > E-bost: wells...@caerdydd.ac.uk
   >
   > Ffôn: 02920 879628
   >
   >
   >
   >
   >


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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

[Bruce Fischl]

Hi Mason

can you confirm that things look ok within FreeSurfer if you look at the 
surface over the volume in freeview?


cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:



External Email - Use Caution

Hello Freesurfer developers,

 

I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
command which finished without errors. However, the white/grey matter
boundaries are significantly misaligned with the subjects T1 (images
attached).  Below are the steps I have taken to reach this point in the
analysis:

 

 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
 2. Ran Feat

· Distortion correction of the EPI

· Motion correction

· No smoothing

· Highpass filter

· No registration to whole brain

· Register to T1_biascorr_brain

· Register to standard space

 3. Ran recon-all on T1_biascorr
 4. Convert T1/T1_brain/orig(001) from mgz to nii
 5. Check registration (using the SurfaceProjection command from the SamSrf
package) which leads to the attached images named S1 and S1.

 

Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux 5.3.0-40-generic x86_64

Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon
Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

 

As you can see, the registration is significantly misaligned.

Can anyone offer any advice on this/suggest a way to rectify it?

 

 

Thanks in advance,

Mason

 

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff   

CF24 4HQ

UK

 

Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd   

CF24 4HQ 

DU

 

E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628

 


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Re: [Freesurfer] training set

[Bruce Fischl]

Hi Javier

no, that's not correct, depending on which training set you mean. For the 
Bayesian segmentation (aseg) we used 40 datasets distributed in age and 
pathology (10 each for young, middle age, elderly and AD).


cheers
Bruce
On Wed, 25 Mar 
2020, javier quilis wrote:




External Email - Use Caution

Thanks for the answer. 

I can not open the power point for some reason. Is there any paper where I
can check this? I think the dataset used by freesurfer is in the MNI Average
Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young
people, is this correct?

Thanks again.
Bests, 
Javier






De: freesurfer-boun...@nmr.mgh.harvard.edu
 en nombre de Douglas N. Greve

Enviado: viernes, 20 de marzo de 2020 15:39
Para: freesurfer@nmr.mgh.harvard.edu 
Asunto: Re: [Freesurfer] training set  
Try the tutorial slides
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
It does not go into a lot of detail, but it will give you the relevant
lectures


On 3/17/2020 8:54 AM, javier quilis wrote:

  External Email - Use Caution

  Hello everyone, 

I'm trying to do a study of a comparison between the automated methods
to analyze structural MRI from FSL and Freesurfer. I am interested in
the training set used by Freesurfer to do the brain segmentation and I
can not find a detailed description of it. Is there any source where
this set is described?

Thanks in advance.
Bests, 
Javier Quilis

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Re: [Freesurfer] Segmentation Issues

[Bruce Fischl]

Hi Harriet

it's tough to diagnose from just this, but that is pretty bad! Can you give 
us some details about the editing? Or tar/gzip the whole subject dir and 
upload it and we will take a look


cheers
Bruce
 On Tue, 24 Mar 2020, Harriet Cornwell 
wrote:




External Email - Use Caution

Hello,

 

We are using FreeSurfer v5.3. and are sometimes finding that a brain can
seem okay when it is first run through the recon-all process and is edited,
but then when it is re-run the segmentation seems to deteriorate hugely. I
have screenshotted an example below. 

 

Are you able to advise us on why this might be happening and what we could
do about this? One of the options I had thought about was to re-run the
recon-all from scratch but it doesn’t seem very time efficient to do this
for multiple brains. Any suggestions would be gratefully received!

 

Thank you.



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Re: [Freesurfer] format bvalues bvectors tracula

[Bruce Fischl]

Hi Renew

please have patience. We are all dealing with a lot. Transitioning to 
working at home and trying to figure out how to be productive and such.


cheers
Bruce

On Tue, 17 Mar 2020, Renew Andrade wrote:

   External Email - Use Caution 


Dear Yendiki Anastasia:

I am replying for second time. I haven’t received an answer about this issue. I 
don’t know if it is silly but I don’t know how to fix it. It is not / slashes 
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Re: [Freesurfer] Troubleshooting fix topology lh stall

[Bruce Fischl]

Hi Ricky

how did you try to load the defect_labels? The end of the recon-all.log 
file lists a defect with 26K vertices, which is probably too big to fix 
(it's about 1/5 of a normal surface). You should be able to visualize it 
by loading the lh.defect_labels file as an overlay on the 
lh.inflated.nofix and lh.orig.nofix surfaces. Make sure to change the 
threshold for the overlay to 0, then finde defect #116, which is the one it 
is stuck on. I think we actually add 1 to the index in the labels file so 
that non-defective vertices show as 0, so it may be 117. It should be clear 
though as it will be a lot bigger than others


cheers
Bruce


On Sat, 
14 Mar 2020, Hoang, Ricky wrote:




External Email - Use Caution

Hello Freesurfer experts,
I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C
scan. The run keeps timing out during the fix topology lh step. I have
looked at the resulting images and I am not sure whether I need to fix the
white matter, add control points, or do something else entirely to fix the
problem. The lh.inflated.nofix does not seem to have anything unwanted still
attached and the lh.defect_label will not load. The lh.inflated.nofix does
show some areas that have strands/spikes, which I think might be due to the
gadolinium contrast. I wanted to ask for opinions on how to proceed. I have
attached the recon-all.log.

This is also a link to the output folder:
https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?us
p=sharing

Thank you!
Ricky

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Re: [Freesurfer] error when running recon-all

[Bruce Fischl]

Hi Bo

looks like you are running out of memory, no?

cheers
Bruce
On Fri, 13 Mar 2020, ZhangBo 
wrote:




External Email - Use Caution

Hi team,
I encountered an error when running the test "Candal" dataset.
For some patients' files, I found the error information in the log file. So,
after "recon-all" finished, I re-run recall for these files with errors.
However, error still happened? What's wrong? Thanks. log file for a patient
is in the attachment. 

Best wishes.
Bo


 


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Re: [Freesurfer] Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere

[Bruce Fischl]

Hi Fraser

if you look at the mris_register help there is an option to specify a 
manual label that corresponds to an atlas parcel:


   -L 
Specify a manual label to align with atlas label 

in the past I have used this to draw a central sulcus and force it to align 
using the Destrieux atlas (since Desikan/Killiany is gyral). There are some 
very nice tools in freeview that make this pretty trivial. Overlay sulc on 
the inflated surface, make sure that the dark gray of the central sulcus 
(or red) isn't connected to anything else. If it is make a line using the 
custom fill tool, then fill and save. Once you are familiar with the tools 
it will take you about 60 seconds


cheers
Bruce


On Fri, 13 Mar 2020, 
Fraser Smith wrote:




External Email - Use Caution

Hi there

I have a clear parcellation error with one participant who does look to have
an atypical structure around the right post-central gyrus (looks split in
two).

Both the pre and post central gyri are shifted significantly backwards – but
only for the right not the left hemisphere.

I see this has been mentioned before in the archives – but I have been
unable to find a fix for this.

Could you provide any tips on what to try? I am using v6.0.0.

Best wishes

Fraser Smith


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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Bruce Fischl]

Hi Frank

sorry, I've been busy with local deadlines that are over now. Can you send 
us the recon-all.log file? Or tar and gzip the entire subject dir and 
upload it to our ftp site? Apologies if any of this has been done.


cheers
Bruce


On Thu, 12 Mar 2020, Frank Chau wrote:


   External Email - Use Caution

Dear Douglas ,

How could I find out the root cause of this recon-all "exited with ERRORS"?
Does it mean there are flaws in the generated output? Or I could ignore this 
error warning? Thank you.

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N. Greve 
Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

it should not really affect it

On 3/10/2020 10:22 AM, Tim Schäfer wrote:

 External Email - Use Caution

Maybe Doug or Bruce should comment on that, but afaik that should not affect 
your analysis at all: recon-all will resample your data to 256x256x256 (as part 
of creating what FreeSurfer calls the 'conformed' version of the image) anyways.

The error you get, if I understand correctly from the logs, is that *after* the 
resampling, the FOV *still* is not 256.

Best,

Tim


On March 9, 2020 at 7:34 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Frank Chau 
Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim


On March 4, 2020 at 4:47 PM Frank Chau  wrote:


 External Email - Use Caution

Dear Tim,

I have checked the orig.mgz file and nothing usual was found (please see the 
attachment image)

For downloading my orig.mgz: 
https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0

Regards

Frank


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Tim Schäfer 
Sent: 04 March 2020 23:27
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

 External Email - Use Caution

Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:


ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Did you have a look at the orig.mgz?

Best,

Tim



On March 4, 2020 at 2:59 PM Frank Chau  wrote:


 External Email - Use Caution

Hello FreeSurfer Developers,

I ran a recon-all on a recent batch of T1 Nifti files and all ended with "exited with 
ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited with ERRORS at Sat Jan 11 
01:32:55 HKT 2020".

I've searched the email archive list and I found other researcher encountered same 
problem before. However, I am quite sure their root causes are not same as my case. 3 
possible causes were found in the email archive which about "exited with 
ERRORS":

   1.  The version of freesurfer (I have already used the latest 6.0.0 version)
   2.  Hard disk space (My computer have enough hard disk space)
   3.  sharing folder between virtual machine and original platform. (I use 
freesurfer in Mac OS which do not have this problem)

I uploaded the recon-all.log to my dropbox in case it's of any use.


1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

2) Platform: MAC OS X 10.11.6

3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: 
Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

4) recon-all.log, please download at:

https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0



Regards

Frank

---

FRANK  C Y CHAU



Research assistant

Division of Neurology

Department of Medicine



Tel: +852 6340 2553

Fax: 2872 5828



E-mail : cyfr...@hku.hk





Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102

Re: [Freesurfer] 8 Gb of ram

[Bruce Fischl]

I don't think our memory requirements change dramatically on a 
per-subject basis. The one exception might be topology fixing, but if it 
requires that much ram there are probably to many (or too large) defects to 
succeed in any case.


cheers
Bruce


On Thu, 5 Mar 2020, Ian wrote:



External Email - Use Caution

Hey guys.

I'm running Freesurfer on an AWS EC2 instance, in a docker container
(t3.large specifically.)

Would you expect 8Gb of ram to *always* be enough to run recon-all on a
280x280x240 T1 image?

The instance is running Ubuntu; the container image is based on Ubuntu; and
nothing else is being explicitly run on the instance while recon-all is
running.

Thanks,
Ian

--

Ian Hardingham



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Re: [Freesurfer] ubuntu: run freesurfer in two terminal

[Bruce Fischl]

sure, as long as you have more than one core. You can run them in the same
terminal as long as you put & at the end of the line

On Thu, 5 Mar 2020, ZhangBo wrote:



External Email - Use Caution

Hello FreeSurfer Developers,

My computer doesn't support cuda. To speed up data processing, could I open
two terminal, and in each of them, I first runing:

$> export FREESURFER_HOME=/usr/local/freesurfer
$> export FREESURFER_HOME=/SetUpFreeSurfer.sh
$> export SUBJECTS_DIR=/usr/local/freesurfer/subjects/

then running:
recon-all -s sub-01 -i sub-01_T1w.nii.gz -all (for terminal 1)
recon-all -s sub-02 -i sub-02_T1w.nii.gz -all (for terminal 2)

Thanks.




 



 


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Re: [Freesurfer] Control Points

[Bruce Fischl]

Hi Doro

it's hard to tell from your image, but it looks like at least one of your 
cps is not in wm but in the gm. This will mess everything up. Make sure 
that they are in unpartial-volumed wm

cheers
Bruce
On Tue, 3 Mar 2020, Meike Hettwer 
wrote:

>External Email - Use Caution 
>
> Dear Freesurfer Team,
>
> I am currently performing manual edits using freesurfer v. 6.0.1. (on Debian 
> /Linux 7). While brainmask edits work perfectly, the control points i set 
> (mainly in temporal and frontopolar regions, running recon-all -autorecon2-cp 
> -autorecon3) either have no effect at all or even make the situation worse 
> (see screenshots attached). Do you have any idea why that might be and how I 
> could fix that? I also tried editing the wm.mgz, but it didn't improve the 
> segmentation.
>
> Thanks a lot,
>
> Doro
>
>
>
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Re: [Freesurfer] registrations

[Bruce Fischl]

I think most of these questions are for Doug and Martin, but why don't 
you try them both and see if either works out of the box? I would not use 
the brain.mgz or T1.mgz as they are aggressively normalized, unless you 
have run both the preop and postop scans through recon-all. You'll want the 
"same" images pre and post. Both should have or not have the skull and 
such.

cheers
Bruce


On Sat, 29 Feb 2020, 
Octavian Lie wrote:

>External Email - Use Caution
>
> Dear Bruce, thank you for your replies.
>
> I planned using this line for intrasubject pre to postop
> (postresection) MRI T1 registration
> 1. with mri_robust_register:
>
> mri_robust_register --mov postop.mgz --dst preop.mgz --lta
> posttopre.lta --mapmov posttopre.mgz --weights posttopre-weights.mgz
> --iscale --satit -- maskmov itksnap_rezvol.nii
>
> 2.  with bbregister
> bbregister --s sbj --mov postop.mgz --init-fsl --reg register.lta --o
> posttopre.mgz --t1
>
> Here are follow-up questions and clarifications:
> 1. With bb register, I do not see an optional flag to accommodate a
> custom mask volume, such as a mask of the resection volume; if this is
> true, then one is not required, please advise
> 2. If one wants to try mri_robust_register for pre to postop MRI
> alignment, which pre volume from the FS recon pipeline would be
> indicated for best results? T1.mgz, brain.mgz, or another?
> 3. With bbregister, which of the several init options (coreg, header,
> spm, or fsl) are recommended (I have all external packages installed,
> so that is not an issue), or there is no rule?
> 4. With mri_robust_register, since the vol of resection is small
> (sublobar, at most lobar) in size, does a mask of the resection volume
> for 6 DOF registration improve registration? Or the mask refers more
> to more partial volumes such as slices, or hemi alignment, as in
> example 3 here 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register)?
> 5. A very rookie question: if one has to use a resection volume mask,
> do the inside-resection voxels have to be 1, and all outside 0, or the
> other way around?
> 6. I then need to mask the coregistered postop volume (posttopre.mgz)
> with a mask derived from FS preop pipeline, to include all cerebrum
> (ribbon.mgz) (no cerebellum) but also mesial temporal structures
> hippocampus/amygdala etc; is there such a mask in the recon pipeline,
> or it has to be constructed?
> Thank you,
> OL
>
> On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl  
> wrote:
>>
>> Hi Octavian
>>
>> 1. Not sure - you should try them. If you have reasonable surfaces I
>> think bbreg lets you specify masks to ignore, which should be giant help
>> in this scenario. On the other hand, mri_robust_register does this
>> automatically. They are both relatively fast so why not try and see?
>>
>> 2. Same answer as before. mri_robust_register has flags to tell it to use
>> an inter-modal similarity function, but you can also tell bbregister it is
>> a T2 and it should do a good job (and implicitly register to the T1 since
>> it is already aligned with the surface).
>>
>> 3. I'm not sure what you mean - can you explain further?
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Sun,
>> 23 Feb 2020, Octavian Lie wrote:
>>
>>>External Email - Use Caution
>>>
>>> Dear All,
>>>
>>> I need to register:
>>> 1. T1.mgz to a T1 postresection volume (no contrast), with large
>>> resection. Which one should I use, mri_robust_register, or bbregister,
>>> if the latter, which is the better initiator (nmi, spm, fsl)?
>>>
>>> 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
>>> recon-all flag), which FS registration tool should I use?
>>>
>>> 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
>>>
>>> I would appreciate commands (either names, or full command lines),
>>> please advise.
>>>
>>> Thank you,
>>> Octavian
>>>
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>>>
>>>
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>
>
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Re: [Freesurfer] Full analysis chain without Topology fix, Talairach check?

[Bruce Fischl]

Hi Dylan

I think you could probably do a recon without topology fixing although of 
course the spherical mapping will then be multi-valued. It will take a bit 
of hacking at recon-all to get it to work though as it is not a use-case 
that we explicitly support.


cheers
Bruce
 On Thu, 27 Feb 2020, 
hs...@mskcc.org wrote:




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Dear Freesurfers,


I am attempting to run the full reconstruction in Freesurfer on several
hundred patient images with diseased areas of the brain.

Without skipping any steps of the analysis chain, I am able to complete the
full reconstruction for about 50% of said patients. When the analysis is
able to complete, the disease sites are generally not included in the white
or gray segmentation labels, which is ideal for my use case. However, when
the disease is far from the cortical surface, it generally results in a
large topological defect. (In other cases, the Talairach check fails.) I
would like to know, does it really make sense to try to analyze the images
with a "real" topological defect, and if so, how to accomplish it?


I have tried to run the reconstruction with flags "-nofix" and
"-notal-check" to accept an imperfect Talairach transform and avoid crashes
trying to fix these unfixable topological defects. Unfortunately, the step
"mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a
file "surf/lh.orig.premesh" which is not found, causing a crash. From what I
can understand, that file is produced by the so-called old topology fix [1],
so it would imply that a full analysis chain is not supported if you
eschew topology-fixing. Is this a feature, or do you recommend modifying
the logic of the script to work around it? This is as far as I got, but I
suppose there may be steps later in the analysis chain that will also look
for files only produced if the topology fix runs.


For your information, I am currently using the nightly build from February
12 for CentOS7, and I am amenable to switching to an older or newer build.
Thank you for taking the time to help me.


Best regards,

Dylan Hsu, Ph.D

Memorial Sloan-Kettering Cancer Center


[1] https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807
349f21d9e4bc794/scripts/recon-all#L3128-L3139



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you are hereby notified that any reading, dissemination, distribution,
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Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Gabriel

they are in the subject's directory. Have you gone through the FS 
tutorials on our wiki? That would be a good place to start


cheers
Bruce
On Tue, 25 Feb 2020, Gabriel Tapia wrote:



External Email - Use Caution

Hello Bruce thank you for your quick reply,
Where should I look to get all these files?
The idea to check them is to confirm that the MRI went wrong at some point,
right?
Thanks,

Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67


Le mar. 25 févr. 2020 à 04:09, Bruce Fischl  a
écrit :
  Hi Gabriel,

  that is a huge defect and generally means something major has
  gone wrong.
  Look at the lh or rh.orig.nofix and the corresponding
  ?h.inflated.nofix
  over the wm.mgz file to see what is wrong (usually something
  like a big
  chunk of skull is left over and connected to the surface,
  sometimes
  through orbital fat in the eye sockets)

  If you can't sort it out let us know and we will help
  cheers
  Bruce

  On Tue, 25 Feb 2020, Gabriel Tapia
  wrote:

  >
  > External Email - Use Caution
  >
  > Hello dear Freesurfer developers, nice to e-meet you and thank
  you for
  > working on this open source software!
  >
  > I am trying to produce a 3D file of a brain.
  > The command I am trying to run is recon-all and here is the
  error I get:
  > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
  > Excessive topologic defect encountered: could not allocate
  140742253
  > edges for retessellation
  > Cannot allocate memory
  >
  > The version I am using is:
  freesurfer-Linux-centos4-stable-pub-v5.3.0
  > The platform is Red Hat 64-bit running in a Virtual box with
  7835mb
  > allocated memory.
  > You will find the corresponding log file attached.
  >
  > Isn't it surprising that I don't have enough memory with
  7835mb allocated?
  > Sorry, I am new to Freesurfer and there might be something I
  didn't get.
  > Thank you very much in advance for your help,
  > Regards,
  >
  > Gabriel Tapia
  > www.Partage3D.fr
  > +33 6 62 90 11 67
  >
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Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Gabriel,

that is a huge defect and generally means something major has gone wrong. 
Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix 
over the wm.mgz file to see what is wrong (usually something like a big 
chunk of skull is left over and connected to the surface, sometimes 
through orbital fat in the eye sockets)


If you can't sort it out let us know and we will help
cheers
Bruce

On Tue, 25 Feb 2020, Gabriel Tapia 
wrote:




External Email - Use Caution

Hello dear Freesurfer developers, nice to e-meet you and thank you for
working on this open source software!

I am trying to produce a 3D file of a brain.
The command I am trying to run is recon-all and here is the error I get:
CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
Excessive topologic defect encountered: could not allocate 140742253
edges for retessellation
Cannot allocate memory

The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
The platform is Red Hat 64-bit running in a Virtual box with 7835mb
allocated memory.
You will find the corresponding log file attached.

Isn't it surprising that I don't have enough memory with 7835mb allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get.
Thank you very much in advance for your help,
Regards,

Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67

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Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

[Bruce Fischl]

Hi Kate

the .lta format is for a linear registration (in ascii). YOu can just cat 
it to see the contents - it is not a PET image (which will be stored in 
.mgz or .nii). mri_convert or mri_vol2vol can be used to apply the 
registration and/or change the output format (if you specify file.nii or 
file.nii.gz it will write in Nifti)


cheers
Bruce


On Mon, 24 Feb 2020, Kate Marvel wrote:



External Email - Use Caution

Hi Douglas,
Is there a way to save the registered PET image in NIfTi format instead of
.lta?

Kate

On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve 
wrote:
  Not sure what you are trying to do. An lta file is a matrix and
  nifti is a format for storing images.

  On 2/21/2020 7:52 AM, Kate Marvel wrote:

  External Email - Use Caution

  Hi All,
How do you convert the registered file (.lta) into NIfTI format
in PETsurfer.

Thanks,


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--
kate

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Re: [Freesurfer] registrations

[Bruce Fischl]

Hi Octavian

1. Not sure - you should try them. If you have reasonable surfaces I 
think bbreg lets you specify masks to ignore, which should be giant help 
in this scenario. On the other hand, mri_robust_register does this 
automatically. They are both relatively fast so why not try and see?

2. Same answer as before. mri_robust_register has flags to tell it to use 
an inter-modal similarity function, but you can also tell bbregister it is 
a T2 and it should do a good job (and implicitly register to the T1 since 
it is already aligned with the surface).

3. I'm not sure what you mean - can you explain further?

cheers
Bruce



On Sun, 
23 Feb 2020, Octavian Lie wrote:

>External Email - Use Caution
>
> Dear All,
>
> I need to register:
> 1. T1.mgz to a T1 postresection volume (no contrast), with large
> resection. Which one should I use, mri_robust_register, or bbregister,
> if the latter, which is the better initiator (nmi, spm, fsl)?
>
> 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
> recon-all flag), which FS registration tool should I use?
>
> 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
>
> I would appreciate commands (either names, or full command lines),
> please advise.
>
> Thank you,
> Octavian
>
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>
>
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Re: [Freesurfer] tksurfer

[Bruce Fischl]

Hi Emalie

tksurfer and tkmedit have been deprecated for a long time. Can you try 
using freeview instead?


cheers
Bruce
On Fri, 21 Feb 2020, Emalie McMahon wrote:



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Hello, 
I get an error (see below) when opening tksurfer and tkmedit. Is there
anyway to resolve this? 

tksurfer s001 lh inflated
/Applications/freesurfer/tktools/tksurfer.bin: Bad CPU type in executable.

Freesurfer Details: 
freesurfer-i386-apple-darwin11.4.2-stable6-20170119


OS Details: 
Computer: 2019 Macbook Pro
OS: macOS 10.15.2 Catalin
Processor: 2.4 GHz 8-Core Intel Core i9 

Best, 
Emalie McMahon
PhD Student
Johns Hopkins University

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