Re: [Freesurfer] automatically save the selected plane

[Sadia Sheikh]

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Hello

My purpose is to get the specific(required) plane of axial view that lies
in the midbrain region. For that i m thinking firstly to get all the planes
of axial view from the midbrain region and then choose the best plane.i
want to get the mickey mouse sign that lies in the axial direction from
large number of data.
So, i want to do this automatically.

Thanks
Sadia

On Sat, Feb 16, 2019 at 12:17 AM Bruce Fischl 
wrote:

> Hi Sadia
>
> can you elaborate what you are trying to do. What seleected plane?
>
> cheers
> Bruce
>
> On Fri, 15
> Feb 2019, Sadia Sheikh wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear FreeSurfer experts
> >
> > It is possible to automatically save the selected planes or set of
> planes from the specific region?
> > Since I have a large number of data and I want to save all the planes
> that lie in the midbrain region.
> >
> > Regards
> > Sadia
> > Research Student
> >
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Re: [Freesurfer] surf2vol ERROR

[Barletta, Valeria]

Oh I just used that option instead of providing a registration file, which I 
don't have.
I need to turn the two surfaces into a single volume.

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Saturday, February 16, 2019 6:58:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR

Hi Vale

mri_surf2vol is to take take from the surface to the volume within one
subject. Why do you need a trgsubject? You can compute the registration
with e.g. bbregister. Maybe I'm not understanding what you are trying to
do

cheers
Bruce

On Sat, 16 Feb 2019, Barletta, Valeria wrote:

>
> Dear all,
>
> I am trying to register surfaces to a volume by this command:
>
> mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh 
> --hemi lh --surfval
> lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge 
> combined-CL.nii.gz --trgsubj
> MS089_R01_29
>
>
> And am obtaining this error:
>
> ERROR: Option --trgsubject unknown
>
>
> That is actually the name of my subject in $FREESURFER_HOME
>
> Also, I do not have a registration file so I used the option --trgsubject
>
> Is this correct? Why am I getting that error?
>
> Thanks,
>
> Vale
>
>
>
>
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Re: [Freesurfer] surf2vol ERROR

[Bruce Fischl]

Hi Vale

mri_surf2vol is to take take from the surface to the volume within one 
subject. Why do you need a trgsubject? You can compute the registration 
with e.g. bbregister. Maybe I'm not understanding what you are trying to 
do


cheers
Bruce

On Sat, 16 Feb 2019, Barletta, Valeria wrote:



Dear all, 

I am trying to register surfaces to a volume by this command:

mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh 
--hemi lh --surfval
lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge 
combined-CL.nii.gz --trgsubj
MS089_R01_29


And am obtaining this error:

ERROR: Option --trgsubject unknown


That is actually the name of my subject in $FREESURFER_HOME

Also, I do not have a registration file so I used the option --trgsubject

Is this correct? Why am I getting that error?

Thanks,

Vale



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[Freesurfer] Extracting stats from palm results (.mgz)

[Daniel Leopold]

External Email - Use Caution

Hi all,

Do you have any suggestions on how I could extract stats (e.g., thickness,
area, LGI, etc.) from a cluster(s) identified via palm? I've tried
mri_label2label in order to turn the palm output .mgz into a paint .label
file, but mri_label2label cannot seem to read the .mgz, .mgz.nii (i.e.,
.mgz mri_converted to .nii), or .mgz.nii.gz files. My inputs to palm are 4D
.mgh files, hence the .mgz results, which are in a data-per-vertex format.
Here are the errors I get when trying convert/input .mgz and .mgz.nii files:

G??M{?Kӭ7?xK/i?Mb4Ե??(???.!?t:6>|???ѧ???+F??c\Ϟ??U}??m?/8q?~ي???\???C??n?h+???~?}?w*jo???ʵS_??_??w?>ԏ??N?no+?8w
mri_label2label: could not scan # of lines from label file
ERROR reading
wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz

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[Freesurfer] surf2vol ERROR

[Barletta, Valeria]

Dear all,

I am trying to register surfaces to a volume by this command:

mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh 
--hemi lh --surfval lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz 
--merge combined-CL.nii.gz --trgsubj MS089_R01_29


And am obtaining this error:

ERROR: Option --trgsubject unknown


That is actually the name of my subject in $FREESURFER_HOME

Also, I do not have a registration file so I used the option --trgsubject

Is this correct? Why am I getting that error?

Thanks,

Vale


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[Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Douglas,

I wanted just to compute rescaled PET image without any PVC but following the 
same process as if I would have applied PVC. Moreover, I didn’t want to reduce 
FOV with auto mask generated (to still be in the gtmseg space). So I ran the 
following command:

mri_gtmpvc --i PET.lps.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --no-reduce-fov --rbv 
--o nopvc_nGMcerebpons --threads 4 --rescale 8 47 174

1) However, in the output directory rbv.nii.gz file still had a reduced fov:
  type: nii
dimensions: 297 x 381 x 363
   voxel sizes: 0.50, 0.50, 0.50
  type: FLOAT (3)
   fov: 148.500

Compared to the gtmseg.mgz:
 type: MGH
dimensions: 334 x 452 x 424
   voxel sizes: 0.50, 0.50, 0.50
  type: INT (1)
   fov: 226.000

I tried also to remove the —auto-mask option without success. Did I miss 
something?

2) I wonder why the process took so much time while there is just a rescaling 
to apply when using --psf 0 --no-tfe?

Best,
Matthieu___
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Re: [Freesurfer] Fix topology correcting defect

[Bruce Fischl]

Hi Yi-Fang

the topology fixing time complexity is square in the convex hull of the 
largest defect. So small defects are quick and big ones take forever. That 
said, for any defects that can be fixed reliably the run time isn't too 
bad. Almost always if it is taking this long it means something 
catastrophic has happened - skull is attached to brain, or the hemis are 
connected or some such.  It is usually immediately obvious if you look at 
the ?h.inflated.nofix and/or the ?h.orig.nofix over the wm.mgz/norm.mgz


cheers
Bruce


 On Sat, 16 Feb 2019, Yi-Fang Chuang wrote:



External Email - Use Caution

I would like to follow-up this thread.
I've encountered similar problem about the recon-all process is stuck at fix 
topology for a long time (10+
hours) [Centos 6, Freesurfer 6.0.0]
I can't see any problem from log files, just as follows
1.

#@# Fix Topology Copy rh Fri Feb 15 00:34:11 CST 2019

/home/yfc/subjects/BK036/scripts


 cp ../surf/rh.orig.nofix ../surf/rh.orig 



 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 


#@# Fix Topology lh Fri Feb 15 00:34:11 CST 2019


 mris_fix_topology -rusage 
/home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere
qsphere.nofix -ga -seed 1234 BK036 lh 


#@# Fix Topology rh Fri Feb 15 00:34:11 CST 2019


 mris_fix_topology -rusage 
/home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere
qsphere.nofix -ga -seed 1234 BK036 rh 


Waiting for PID 15635 of (15635 15638) to complete...


2.


#@# Fix Topology Copy rh Fri Feb 15 21:23:50 CST 2019

/home/yfc/subjects/BK151/scripts


 cp ../surf/rh.orig.nofix ../surf/rh.orig 



 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 


#@# Fix Topology lh Fri Feb 15 21:23:50 CST 2019


 mris_fix_topology -rusage 
/home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere
qsphere.nofix -ga -seed 1234 BK151 lh 


#@# Fix Topology rh Fri Feb 15 21:23:50 CST 2019


 mris_fix_topology -rusage 
/home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere
qsphere.nofix -ga -seed 1234 BK151 rh 


Waiting for PID 16471 of (16471 16474) to complete...



Intriguingly, I've run through these subjects before on MacOS, Freesurfer 5.3.0 
without error or being
stuck.

What's the problem here?

Yi-Fang


Bruce Fischl  於 2019年2月15日 週五 下午11:13寫道：
  Hi Milène

  did you edit in freeview? Or something else? If you load the wm.mgz on
  top of the norm.mgz, does is still look to be in the same space? If so,
  feel free to tar and gzip the entire subject dir and upload it and we will
  take a look

  cheers
  Bruce



  On Fri, 15
  Feb 2019, Milene Buerger wrote:

  >
  > External Email - Use Caution
  >
  > Thank you Bruce for your answer!
  > I figured out how to edit the wm.mgz. Indeed some parts of the skull 
were not properly
  removed from the
  > brainmask and therefor considered as white matter. I manually removed 
voxels from the wm.mgz
  and then I
  > tried to reintegrate the wm.mgz to the recon-all command by doing the 
mri_fill 
  .
  > Unfortunately I got this error:
  >  
  
>mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2017042

  > 5_T1/mri $ mri_fill wm.mgz filled.mgz
  > reading input volume...done.
  > searching for cutting planes...talairach transform
  >  1.18336   0.13264   0.04891   10.53902;
  > -0.11077   0.95044   0.09947  -11.50818;
  > -0.00953  -0.18656   1.07681  -50.07034;
  >  0.0   0.0   0.0   1.0;
  > INFO: Modifying talairach volume c_(r,a,s) based on average_305
  > voxel to talairach voxel transform
  >  1.18336   0.04891  -0.13264  -14.02849;
  > -0.00953   1.07681   0.18656   15.85732;
  >  0.11077  -0.09947   0.95044   6.22865;
  >  0.0   0.0   0.0   1.0;
  > mri_fill: could not find valid seed for the cc
  > Looking for area (min, max) = (350, 1400)
  > area[0] = 9142 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max 
= 0.75)
  > need search nearby
  > using +/- offset search region where offset is 3.
  > using +/- offset search region where offset is 6.
  > using +/- offset search region where offset is 9.
  > using +/- offset search region where offset is 12.
  > area[0] = 597 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 
0.75)
  > min_slice = -1, min_area = 65536
  > Looking for area (min, max) = (350, 1400)
  > area[0] = 1874 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max 
= 0.75)
  > need search nearby
  > using +/- offset search region where offset is 3.
  > using +/- offset search region where offset is 6.
  > using +/- offset search region where offset is 9.
  > using +/- offset search region where offset is 12.
  > using +/- offset search