Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

2019-01-28 Thread Boris Rauchmann 
External Email - Use Caution

Hi Bruce,

thank you for your quick answer. I managed it now to create cannot files based 
on the atlas volumetric segmentations.

I first created:

mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii --out 
.../Hammers_AVG.nii --out_type mgh --hemi lh --mni152reg

then applied:

mris_apply_reg --src .../hammers_lh_avg_surf.mgh --trg 
.../hammers_lh_INDI_0021.mgh --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
 .../0021/surf/lh.sphere 

and:

mris_seg2annot --seg /.../hammers_lh_INDI_0021.mgh   --s 0021 --h lh --ctab 
/.../ExploreDTI_Pcode/Source/Misc/My_FS_LUT.txt  --o 
.../lh.hammersmithINDI.annot

My question now is how can I create a suitable LUT with the correct labels for 
the cortical parcellations? I have only a .csv file with the labels for the 
volumetric atlas? 

My goal is to use 

mris_anatomical_stats -a .../0021/label/lh.hammersmithINDI.annot -b 0021 lh

to get the cortical thickness values of each segment in the annot for every 
participant file.

Thanks again, 
Boris




> Am 27.01.2019 um 23:58 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> vol2surf samples a scalar overlay in the volume to be a scalar overlay on the 
> surface. This is NOT the same as a surface itself - it contains no geometry 
> or topology information. Try giving freeview a surface (which I guess you 
> have for subject 0021). Something like
> 
> freeview -f \
> 0021/surf/lh.inflated:overlay=lhHammers_mith_atlas_n30r83_SPM5surf.mgh
> 
> cheers
> Bruce
> 
> 
> On Sun, 27 Jan 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Hi,
>> I used the following commands:
>>  mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
>> lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> --out_type mgh --hemi lh --regheader 0021
>> srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Computing registration from header.
>>   Using .../0021/mri/orig.mgz as target reference.
>> Reading surface .../0021/surf/lh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 76207
>> Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> Dim: 125545 1 1
>> it creates the .mgh file but when I try to open in in Freeview or tksurfer 
>> to check the surface file I get the
>> following error message:
>> my_computer$ freeview
>> ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
>> vertices!
>> Probably trying to use a scalar data file as a surface!
>> nquads=65537,  nvertices=0
>> ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 
>> many more faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see 
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
>> find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
>> run 
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: - Error Message 
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
>> CDT 2008 HG revision:
>> 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
>> Sun Jan 27 23:12:45 2019
>> [0]PETSC ERROR: Libraries linked from
>> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
>> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
>> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
>> --with-fc=0 --download-f-blas-lapack=0
>> --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
>> --with-shared=0 COPTFLAGS=-O3
>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: User

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

2019-01-27 Thread Bruce Fischl 

Hi Boris

vol2surf samples a scalar overlay in the volume to be a scalar overlay on 
the surface. This is NOT the same as a surface itself - it contains no 
geometry or topology information. Try giving freeview a surface (which I 
guess you have for subject 0021). Something like


freeview -f \
0021/surf/lh.inflated:overlay=lhHammers_mith_atlas_n30r83_SPM5surf.mgh

cheers
Bruce


On 
Sun, 27 Jan 2019, Boris 
Rauchmann wrote:




External Email - Use Caution

Hi,
I used the following commands:

 mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
lhHammers_mith_atlas_n30r83_SPM5surf.mgh
--out_type mgh --hemi lh --regheader 0021
srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using .../0021/mri/orig.mgz as target reference.
Reading surface .../0021/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 76207
Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
Dim: 125545 1 1


it creates the .mgh file but when I try to open in in Freeview or tksurfer to 
check the surface file I get the
following error message:


my_computer$ freeview
ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
vertices!
Probably trying to use a scalar data file as a surface!


nquads=65537,  nvertices=0
ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has many 
more faces than vertices!
Probably trying to use a scalar data file as a surface!

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision:
4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
Sun Jan 27 23:12:45 2019
[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0
--download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
--with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault


Hoe can I actually check the surface file?

Thanks,
Boris 

  Am 25.01.2019 um 17:45 schrieb Greve, Douglas N.,Ph.D. 
:

Those are the commands. Can you send the command lines you used and a fuller 
description of exactly how it is
not working?

On 1/25/19 10:56 AM, Boris Rauchmann wrote:

  External Email - Use Caution

  Dear FreeSurfer Developers,

   

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an
hammersmith n30r83 atlas segmentation. I have this atlas only in as a 
volumetric file. I already run
recon-all on all subjects. I tried mri_vol2surf and then mris_seg2annot but 
without success so far.
What commands would you recommend me to run?

 

Thanks,

Boris


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Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

2019-01-27 Thread Boris Rauchmann 
External Email - Use Caution

Hi,

I used the following commands:

 mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
lhHammers_mith_atlas_n30r83_SPM5surf.mgh --out_type mgh --hemi lh --regheader 
0021
srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using .../0021/mri/orig.mgz as target reference.
Reading surface .../0021/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 76207
Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
Dim: 125545 1 1


it creates the .mgh file but when I try to open in in Freeview or tksurfer to 
check the surface file I get the following error message:


my_computer$ freeview
ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
vertices!
Probably trying to use a scalar data file as a surface!


nquads=65537,  nvertices=0
ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has many 
more faces than vertices!
Probably trying to use a scalar data file as a surface!

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
Sun Jan 27 23:12:45 2019
[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 
FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault


Hoe can I actually check the surface file?

Thanks,
Boris 

> Am 25.01.2019 um 17:45 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> Those are the commands. Can you send the command lines you used and a fuller 
> description of exactly how it is not working?
> 
> On 1/25/19 10:56 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>>  <>Dear FreeSurfer Developers,
>> 
>>  
>> I´m trying to extract the cortical thickness of individuals from a study 
>> cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas 
>> only in as a volumetric file. I already run recon-all on all subjects. I 
>> tried mri_vol2surf and then mris_seg2annot but without success so far. What 
>> commands would you recommend me to run?
>> 
>>  
>> Thanks,
>> 
>> Boris
>> 
>> 
>> 
>> ___
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>> 
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Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

2019-01-25 Thread Greve, Douglas N.,Ph.D. 
Those are the commands. Can you send the command lines you used and a fuller 
description of exactly how it is not working?

On 1/25/19 10:56 AM, Boris Rauchmann wrote:

External Email - Use Caution
Dear FreeSurfer Developers,

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as 
a volumetric file. I already run recon-all on all subjects. I tried 
mri_vol2surf and then mris_seg2annot but without success so far. What commands 
would you recommend me to run?

Thanks,
Boris



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

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[Freesurfer] cortical thickness calculation based on hammersmith segmentation

2019-01-25 Thread Boris Rauchmann 
External Email - Use Caution

 <>Dear FreeSurfer Developers,

 

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as 
a volumetric file. I already run recon-all on all subjects. I tried 
mri_vol2surf and then mris_seg2annot but without success so far. What commands 
would you recommend me to run?

 

Thanks,

Boris___
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