[Freesurfer] FS dev install error at mri_surf2vol on mac

[Jonathan DuBois]

External Email - Use Caution

Hi Freesurfer developers

I’m trying to install the development package from github on my mac running osx 
10.14.6. I ran CMake with the OSX package without any issue, although when I 
ran make I got the following error:

[ 28%] Linking CXX executable surf2vol
ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq 
instruction is too different from dwarf stack size
…
"vnl_nonlinear_minimizer::is_a() const", referenced from:
      vtable for fs_powell in libutils.a(numerics.cpp.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [fem_elastic/surf2vol] Error 1
make[1]: *** [fem_elastic/CMakeFiles/surf2vol.dir/all] Error 2
make: *** [all] Error 2

The full error is copied in the attached text file. I have not been able to 
find anything useful on google so please let me know if you have any ideas. I 
don’t necessarily need MRI_surf2vol so I could exclude it from the install but 
I’m guessing that there are other programs that rely on it?

Best,
Jon
:~/freesurfer$ make
[  3%] Built target jpeg
[  3%] Built target expat
[  5%] Built target tiff
[  8%] Built target glut
[ 10%] Built target xml2
[ 11%] Built target minc
[ 12%] Built target dicom
[ 13%] Built target cephes
[ 13%] Built target netcdf
[ 13%] Built target tetgen
[ 15%] Built target nrrdio
[ 16%] Built target nifti
[ 16%] Built target gifti
[ 17%] Built target svm
[ 17%] Built target fsPrintHelp
[ 27%] Built target utils
[ 28%] Built target vtkutils
[ 28%] Built target lineprof
[ 28%] Linking CXX executable surf2vol
ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MatSetValuesBlockedLocal: 
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFinalize: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscError: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscOptionsInsertFile: stack 
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscSynchronizedFlush: stack 
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerDestroy_Binary: 
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for 
_PetscViewerFileSetName_Binary: stack subq instruction is too different from 
dwarf stack size
ld: warning: could not create compact unwind for _VecViewFromOptions: stack 
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for 
_PetscLogOpenHistoryFile.part.1: stack subq instruction is too different from 
dwarf stack size
ld: warning: could not create compact unwind for 
_PetscOptionsCheckInitial_Private: stack subq instruction is too different from 
dwarf stack size
ld: warning: could not create compact unwind for _MatMult_SeqCSRPERM: stack 
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MatMultAdd_SeqCSRPERM: stack 
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscLogDump: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscSharedTmp: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFileRetrieve: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscInfo_Private: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFOpen: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscPOpen: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscRandomViewFromOptions: 
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerDestroy_ASCII: 
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerStringSPrintf: 
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _VecStrideNormAll: stack subq 
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for 
_MPIDI_CH3I_VC_post_sockconnect: stack subq instruction is too different from 
dwarf stack size
ld: warning: could not create compact unwind for _connToStringKVS: stack subq 
instruction is 

[Freesurfer] Roundness of a surface label

[Jonathan DuBois]

Hi,

I was wondering if there was any existing freesurfer script to calculate
the roundness and/or the perimeter of a surface label? If anyone has ideas
on how to calculate this, I would appreciate it.

Thanks,
Jonathan
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Re: [Freesurfer] PET surface sampling

[Jonathan DuBois]

Hi Doug, 

Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although 
the resulting bp file seems to only have binary clusters (in the attached image 
the red cluster all have a value of 1 and everywhere else is 0). Is this the 
normal output? I expected a more varying map. 

Thanks 
Jonathan

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[Freesurfer] PET surface sampling

[Jonathan DuBois]

Hi, 

I’m trying to use the PETsurfer Pipeline to perform BP analysis, but I’m not 
sure at which point in the pipeline to sample the data to the surface and what 
registration to use? 

I tried running the pipeline using dynamic kinetic modeling as described here: 
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
, and then used the 
following command to try and sample the BP map the surface: 
mri_vol2surf --hemi lh --projfrac .5 --out_type mgh --cortex --mov 
mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o lh.bp_pf5.mgh

But got the following error: 
ERROR: source volume is neither source nor target of the registration

I also tried sampling the mrtm2/bp.nii.gz to the orig.mgz volume space and then 
to the surface using: 
mri_vol2vol --mov mrtm2/bp.nii.gz --reg aux/bbpet2anat.lta --o 
mrtm2/bp_2anat.nii.gz --targ $SUBJECTS_DIR/subject1/mri/orig.mgz; mri_vol2surf 
--hemi lh --projfrac .5 --out_type mgh --cortex --mov mrtm2/bp_2anat.nii.gz 
--regheader subject1 --o lh.bp_pf5.mgh

This worked, although the surface file did not have any values…

Could you please let me know what is the best way to sample the data to the 
surface, and if it should be down prior to mri_glmfit or after. 

Thanks 
Jonathan

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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[Freesurfer] PET processing seg fault with mri_glmfit --mrtm1

[Jonathan DuBois]

Hi Freesurfer developers, 

I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc 
without PVC, which finished without error. However, the km.hb.tac.nii.gz 
appears empty when I open it with fslview or tkmedit, although this may be due 
to the nature of the file (I’m not sure what it is supposed to show). The 
km.ref.tac.dat and km.hb.tac.dat are normal.
Please let me know what you think. 

The command and error: 
mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 
--no-est-fwhm --nii.gz
Segmentation fault (core dumped)

Where time.dat is a text file with the time (in seconds) of each frame:
0 30 60 90 120 150 180 240 300 360 420 540 660 780 900 1020 1140 1260 1380 1620 
1860 2100 2400 2700 3000 3300

I’m using the linux version 6 beta downloaded on Oct. 30th
freesurfer-Linux-centos4_x86_64-dev-20151030

Best, 
Jonathan
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Re: [Freesurfer] PET tools in FS dev v6.0

[Jonathan DuBois]

Hi Doug,

I uploaded the files you requested. I'm not sure if it matters, but one
thing I forgot to mention was that in order to get the pet file in the
right format and orientation, I ended up using (ecattominc pet.v pet.mnc)
and (itk_convert --inv-y --inv-x pet.mnc pet.nii). I couldn't find a good
tool to convert directly form ECAT to NIFTI, but perhaps this conversion
process interferes with the pet processing?

Best,
Jonathan


> Message: 7
> Date: Mon, 28 Sep 2015 18:07:18 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5609ba16.2090...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> Can you upload the FS subject, pet data, and .lta?
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 09/28/2015 12:08 PM, Jonathan DuBois wrote:
> > Hi Doug,
> >
> > I was told you were away last week so I'm reposting this message.
> > Thanks for sending me the information on the PET scripts. I
> > ran gtmseg, and bbregister successfully (I inspected both and they
> > look accurate), but I am getting a segfault with mri_gtmpvc at the
> > auto mask step.
> >
> > I copied the command and the error below. I thought that it could be a
> > memory issue due to the size of the matrix (I ran it on a mac with
> > 8gb) but I also tried to run it with the --tt-reduce and got the same
> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For the
> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is this
> > correct?
> >
> > Thanks
> > Jonathan
> >
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > Loading input pet.nii.gz
> >   done loading input 26 frames
> >
> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
> > cd /Volumes/my_passport/external/Documents/fssub2/test
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > sysname  Darwin
> > hostname Jons-MacBook-Air.local
> > machine  x86_64
> > user jonathandubois
> > vgthresh   0.001000
> > nReplace   18
> > 0. 0. 0. 0. 0. 0.
> > 4 avail.processors, using 1
> > Creating output directory gtmpvc.output
> > Loading seg for gtm
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
> > Loading seg ctab
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab
> > Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
> > Replacing 18
> > Pruning ctab
> > done with seg vol
> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
> > Computing auto mask
> > Segmentation fault: 11
> >
> >
> > Message: 13
> > Date: Tue, 08 Sep 2015 14:34:11 -0400
> > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>
> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> > To: freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>Message-ID:
> > <55ef2a23.3070...@nmr.mgh.harvard.edu
> > <mailto:55ef2a23.3070...@nmr.mgh.harvard.edu>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> > Yes there are both. For KM we have MRTM1 and MRTM2 so far. They
> > are not
> > well documented yet.
> > 1. To start, run
> > gtmseg --s subject
> > This will take a couple of hours and produces some files needed
> > for GTM
> > PVC (which is used for GTM, MG, RBV).
> > 2. You'd then register the PET to the anatomical with bbregister
> (with
> > --t2 weighting). Make sure to save the output as an LTA (--lta). I
> > usually use the mean TAC as the input. You can do this in parallel
> > with #1.
> > 3. You'd then run mri_gtmpvc, something like
> > mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
> > gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o
> > gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > PSF is t

Re: [Freesurfer] PET tools in FS dev v6.0

[Jonathan DuBois]

Hi Doug,

I was told you were away last week so I'm reposting this message. Thanks
for sending me the information on the PET scripts. I ran gtmseg, and
bbregister successfully (I inspected both and they look accurate), but I am
getting a segfault with mri_gtmpvc at the auto mask step.

I copied the command and the error below. I thought that it could be a
memory issue due to the size of the matrix (I ran it on a mac with 8gb) but
I also tried to run it with the --tt-reduce and got the same error. The
data is from an HRRT PET scanner with a PSF of 4mm. For the auto-mask input
I used 6 .01, as your instructions were PSF+2. Is this correct?

Thanks
Jonathan

mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11
12 13 50 51 52 --km-ref 8 47 --no-rescale
Loading input pet.nii.gz
  done loading input 26 frames

$Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
cd /Volumes/my_passport/external/Documents/fssub2/test
mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11
12 13 50 51 52 --km-ref 8 47 --no-rescale
sysname  Darwin
hostname Jons-MacBook-Air.local
machine  x86_64
user jonathandubois
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
4 avail.processors, using 1
Creating output directory gtmpvc.output
Loading seg for gtm
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
Loading seg ctab /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab
Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
Replacing 18
Pruning ctab
done with seg vol
maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Segmentation fault: 11


Message: 13
> Date: Tue, 08 Sep 2015 14:34:11 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <55ef2a23.3070...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> Yes there are both. For KM we have MRTM1 and MRTM2 so far. They are not
> well documented yet.
> 1. To start, run
> gtmseg --s subject
> This will take a couple of hours and produces some files needed for GTM
> PVC (which is used for GTM, MG, RBV).
> 2. You'd then register the PET to the anatomical with bbregister (with
> --t2 weighting). Make sure to save the output as an LTA (--lta). I
> usually use the mean TAC as the input. You can do this in parallel with #1.
> 3. You'd then run mri_gtmpvc, something like
> mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
> gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> PSF is the point-spread FWHM of the scanner; reg.lta is the registration
> from #2.  --km-hb specifies the highbinding region for MRTM2. --km-ref
> specifies the reference region.  --mgx specifies to output a
> muller-gartner map (not necessary for GTM ROI analysis).
> 4. For the GTM (ROI) MRTM1 KM analysis, you would then run
>   mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o
> mrtm1 --no-est-fwhm --nii.gz
> where time.dat is a text file withe acquisition time of each time point
> in the tac.
> 5. For the MRTM2 analysis
> set k2p = `cat mrtm1/k2prime.dat`
> mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o
> mrtm1 --no-est-fwhm --nii.gz
> If you want to run a voxel-wise analysis, then you can use the mgx
> volume as input (--y). Probably you'll want to sample this to the
> surface using mri_vol2surf and the registration file aux/anat2pet.lta,
> then smooth on the surface.
>
>
> doug
>
>
>
> On 09/08/2015 02:11 PM, Jonathan DuBois wrote:
> > Hi FS experts,
> >
> > In FS development package I see that there have been tools added for
> > partial volume correction of PET data, but I was wondering if there
> > were also kinetic modeling tools similar to those described in Doug's
> > 2014 paper? If you could let me know what PET processing tools have
> > been included in the dev package, I would be interested to test and
> > compare them.
> >
> > Thanks,
> > Jonathan
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] PET tools in FS dev v6.0

[Jonathan DuBois]

Hi Doug,

Thanks for sending me this information. I ran gtmseg, and bbregister
successfully (I inspected both and they look accurate), but I am getting a s
egfault with mri_gtmpvc at the auto mask step.

I copied the command and the error below. I thought that it could be a
memory issue due to the size of the matrix (I ran it on a mac with 8gb) but
I also tried to run it with the --tt-reduce and got the same error. The
data is from an HRRT PET scanner with a PSF of 4mm. For the auto-mask input
I used 6 .01, as your instructions were PSF+2. Is this correct?

Thanks
Jonathan

mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11
12 13 50 51 52 --km-ref 8 47 --no-rescale
Loading input pet.nii.gz
  done loading input 26 frames

$Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
cd /Volumes/my_passport/external/Documents/fssub2/test
mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11
12 13 50 51 52 --km-ref 8 47 --no-rescale
sysname  Darwin
hostname Jons-MacBook-Air.local
machine  x86_64
user jonathandubois
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
4 avail.processors, using 1
Creating output directory gtmpvc.output
Loading seg for gtm
/Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
Loading seg ctab /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab
Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
Replacing 18
Pruning ctab
done with seg vol
maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Segmentation fault: 11


Message: 13
> Date: Tue, 08 Sep 2015 14:34:11 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <55ef2a23.3070...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> Yes there are both. For KM we have MRTM1 and MRTM2 so far. They are not
> well documented yet.
> 1. To start, run
> gtmseg --s subject
> This will take a couple of hours and produces some files needed for GTM
> PVC (which is used for GTM, MG, RBV).
> 2. You'd then register the PET to the anatomical with bbregister (with
> --t2 weighting). Make sure to save the output as an LTA (--lta). I
> usually use the mean TAC as the input. You can do this in parallel with #1.
> 3. You'd then run mri_gtmpvc, something like
> mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
> gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> PSF is the point-spread FWHM of the scanner; reg.lta is the registration
> from #2.  --km-hb specifies the highbinding region for MRTM2. --km-ref
> specifies the reference region.  --mgx specifies to output a
> muller-gartner map (not necessary for GTM ROI analysis).
> 4. For the GTM (ROI) MRTM1 KM analysis, you would then run
>   mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o
> mrtm1 --no-est-fwhm --nii.gz
> where time.dat is a text file withe acquisition time of each time point
> in the tac.
> 5. For the MRTM2 analysis
> set k2p = `cat mrtm1/k2prime.dat`
> mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o
> mrtm1 --no-est-fwhm --nii.gz
> If you want to run a voxel-wise analysis, then you can use the mgx
> volume as input (--y). Probably you'll want to sample this to the
> surface using mri_vol2surf and the registration file aux/anat2pet.lta,
> then smooth on the surface.
>
>
> doug
>
>
>
> On 09/08/2015 02:11 PM, Jonathan DuBois wrote:
> > Hi FS experts,
> >
> > In FS development package I see that there have been tools added for
> > partial volume correction of PET data, but I was wondering if there
> > were also kinetic modeling tools similar to those described in Doug's
> > 2014 paper? If you could let me know what PET processing tools have
> > been included in the dev package, I would be interested to test and
> > compare them.
> >
> > Thanks,
> > Jonathan
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://

[Freesurfer] PET tools in FS dev v6.0

[Jonathan DuBois]

Hi FS experts,

In FS development package I see that there have been tools added for
partial volume correction of PET data, but I was wondering if there were
also kinetic modeling tools similar to those described in Doug's 2014
paper? If you could let me know what PET processing tools have been
included in the dev package, I would be interested to test and compare
them.

Thanks,
Jonathan
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[Freesurfer] adjust pial surface outward for abnormally thick cortex

[Jonathan DuBois]

Hi Freesurfers,

I am having trouble manually correcting the surface of brain with an
abnorally thick cortex due to a malformation. It seems as though there is a
thickness threshold that constrains the pial surface reconstruction. I have
added control points to the white matter but the problem seems to be due to
the adnormally thick cortex or the abnormal gyrification. Is there an
option I can change when running recon-all or a manual edit I can make in
these cases? I understand that it may not be perfect but I would like to
get it good as possible.

Thanks in advance,
Jonathan

[image: Inline image 1]
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[Freesurfer] fscalc.fsl bad dim error

[Jonathan DuBois]

Hi Freesurfers,

I am trying to use fscalc.fsl to do calculations on an fsaverage vertex map
of values (mgh files). In some of these files, but not all, I get the
following error:

** ERROR: nifti_convert_nhdr2nim: bad dim[1]
** ERROR (nifti_image_read): cannot create nifti image from header
'./tmp.fscalc.fsl.57121/s1.nii.gz'
** ERROR: nifti_image_open(./tmp.fscalc.fsl.57121/s1): bad header info
ERROR: failed to open file ./tmp.fscalc.fsl.57121/s1
Cannot open volume ./tmp.fscalc.fsl.57121/s1 for reading!

I saw a similar list serve question in 2008 where Doug responded: How many
vertices does that subject have and is there a prime factor less than
2^15?” However, these surface maps have around 300k vertices, not less than
2^15.

I would really appreciate any advice with this. Thanks!

Jon
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[Freesurfer] aparcstats2table for functional overlay

[Jonathan DuBois]

Hi all,

I was wondering if there was a script like aparcstats2table that would
accept a functional overlay file that has been sampled to the surface as a
measure instead of the available options for structural measures?

In tksurfer there is a manual way to average over an ROI using the sig.mgh
and the y.fsgd file, marking the label and exporting the average graph. I
would like to do something similar. Is there anything like this avaiable?

Thanks,
Jonathan
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Re: [Freesurfer] PET Partial volume correction

[Jonathan DuBois]

Hi Doug,

Thanks for replying. We are currently working on this analysis, is there
anyway you could provide a beta version of the PVC code?

Thanks,
Jonathan
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[Freesurfer] PET Partial volume correction

[Jonathan DuBois]

Hi Freesurfer experts,

I have been using freesurfer for surface-based PET analysis and was
wondering if the method for   voxel-based partial volume correction, used
in the recent paper (Cortical surface-based analysis reduces bias and
variance in kinetic modeling of brain PET data), was implemented with
scripts available in the freesurfer package? If so, would you mind
providing more details on what tools were used?

As in the paper, I have 3T MRIs (reconstructed with FS) and BP data from
controls scanned in a HRRT PET and reconstructed with a similar method.

Thank you,
Jonathan
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[Freesurfer] Modifying cortical surface for large dysplasia

[Jonathan DuBois]

Hi All,

I have run recon-all on a subject with a large cortical dysplasia, and
while the segmentation (aseg) seems to be relatively correct, there is a
large region of dysplasia not included by the pail surface. The normalized
intensity values for the cortex and the excluded region are very similar so
it seems that there is a threshold related to the distance from the white
matter surface to the pial surface, or perhaps normal gyrification that is
constraining the pial surface.

Is there a recon-all or expert option for surface reconstruction of
abnormally thick cortex?

Thanks in advance,
Jonathan
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[Freesurfer] z-test differences from fscalc and mri_glmfit

[Jonathan DuBois]

Hi All,

In a previous post Doug suggested two methods for generating voxel-wise
z-score maps, one using glmfit with one subject in one group and the second
using fscalc.fsl. Link to post:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html


I have tried both methods using PET data registered to the surface, but get
very different results from fscalc and mri_glmfit. The results I expect are
given by fscalc, but I would also like to run the Monte Carlo-based MCC,
which requires a glmdir. Is there another way to run MC MCC on the z-map
generated by fscal or alternatively, is the code that I am using for glmfit
wrong? A simplified version of the code for both analyses is below. I am
using FS 5.3 with the fsl binaries from the release notes on mac OS 10.8.


Thanks for your help
Jon

--mri_glmfit:
for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv
nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv
nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --iv
pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 --out
${h}.pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh

for h in rh lh; do mri_surf2surf --hemi $h --s fsaverage --fwhm 10 --cortex
--sval ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh --tval
${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh; done

for h in rh lh; do mri_glmfit --y
${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh --fsgd
patient1_allcontrols_ztest.fsgd dods --C group2_cov0_diff.mtx --surf
fsaverage $h --cortex --glmdir
${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.glmdir

*patient1_allcontrols_ztest.fsgd*:
GroupDescriptorFile 1
Title patient01_ztest
Class Patient
Class Control
Input pat01 Patient
Input nc01 Control
Input nc02 Control
Input nc03 Control

*group2_cov0_diff.mtx*:
-1 1

--fscalc.fsl:
for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv
nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv
nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --pf 0.5 --out
${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh

for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5 --out
${h}.patient01_pet_ztest_pf05_fsaverage.mgh

for h in rh lh; do for stat in mean std; do mri_concat
${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh --o
${h}.allcontrols_pet_ztest_pf05_fsaverage_${stat}.mgh --${stat}; done; done

for h in rh lh; do fscalc.fsl --surf fsaverage $h
${h}.patient01_pet_ztest_pf05_fsaverage.mgh -sub
${h}.allcontrols_pet_ztest_pf05_fsaverage_mean.mgh -div
${h}.allcontrols_pet_ztest_pf05_fsaverage_std.mgh
${h}.patient01_vs_allcontrols_pet_ztest_pf05_fsaverage_zmap.mgh; done
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[Freesurfer] flip hemisphere of manual label

[Jonathan DuBois]

Hi,

Is there a way to transpose a manual surface label in fsaverage space onto
the contralateral hemisphere? With tksurfer it opens in the opposite
hemisphere but it does not correspond to the contralateral region.
Thanks in advance.

Best,
Jonathan
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Re: [Freesurfer] Binary volume to surface label

[Jonathan DuBois]

Hi Bruce,

Thanks for your help yesterday. I was able to create the .mgh file using
the -output_type mgh option, but I am still unable to load it in tksurfer
as label or anything else. If you or Doug have any other suggestions, I
would really appreciate it. Thanks!

Jonathan


On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Jonathan

 try -output_type mgh. It should create a volume that is nvertices long.
 Not sure if it can directly create a label file, maybe Doug knows?


 Bruce


 On Sun, 12 May 2013, Jonathan DuBois wrote:

  I used the following options: mri_vol2surf --hemi lh --regheader subject01
 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could

 not open the resulting file in tksurfer as either a label or an overlay:
 -
 /Applications/freesurfer/**tktools/tksurfer.bin: no data in label file
 /Users/label.mgh
 tkmedit: Trying to open /Users/label.dat
 surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar
 volume

 Best,
 Jonathan


 On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 
 wrote:
   try using --regheader

   cheers
   Bruce
   On Sun, 12 May 2013, Jonathan DuBois wrote:

 Hi Bruce,
 I would like to convert the .mgz label volume to a
 surface label for that
 subject, but mri_vol2surf requires a registration
 file.

 Best,
 Jonathan



 On Sunday, May 12, 2013, Bruce Fischl wrote:
   Hi Jonathan

   you don't need to register it if it's shown
 properly in tkmedit
   or freeview. Can you tell us more about what
 you are trying to
   do?
   Bruce


   On Sun, 12 May 2013, Jonathan DuBois wrote:

 Hi Bruce,
 Thanks for the quick response. The label
 is a
 manually traced area of the
 cortex. It is in subject scanner space
 and has a
 single value, so it
 probably would not work with bbregister.
 I can load
 it in tkmedit as a
 segmentation and the alignment is
 correct. I
 attached a screenshot. Is there
 a way to select the values greater than
 zero in
 tkmedit and save as a label
 that could be used in vol2surf? I have
 other labels
 that are larger so I
 would prefer not to retrace them if
 possible.

 Inline image 2
 Best,
 Jonathan


 On Sun, May 12, 2013 at 10:11 AM, Bruce
 Fischl
 fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Jonathan

   what is the label? What space is
 it in? If it
 has gray/white
   contrast you could try bbregister.

   cheers
   Bruce
   On Sat, 11 May 2013, Jonathan
 DuBois wrote:

 Hi Freesurfer Experts,
 I have a binary volume label
 in subject
 space that I
 converted from MINC to MGZ.
 I would like
 to register
 it to
 the surface of that subject
 as a flat
 label. I
 thought I would be able to
 do so with
 mri_vol2surf
 but I am not
 sure how to generate the
 required
 registration file.
 Is that the correct command,
 and if so,
 which
 registration
 file should I use?

 Thanks
 Jonathan




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 intended only for
 the person to whom
 it is
 addressed. If you believe this e-mail
 was sent to
 you in error and the
 e-mail
 contains patient information, please

Re: [Freesurfer] Binary volume to surface label

[Jonathan DuBois]

Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks
for your help!

Best,
Jonathan


On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:

 you should be able to load it into tksurfer as an overlay.

 cheers
 Bruce

 On Mon, 13 May 2013, Jonathan DuBois wrote:

  Hi Bruce,
 Thanks for your help yesterday. I was able to create the .mgh file using
 the -output_type mgh option, but I am still unable to
 load it in tksurfer as label or anything else. If you or Doug have any
 other suggestions, I would really appreciate it. Thanks!

 Jonathan


 On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Jonathan

   try -output_type mgh. It should create a volume that is nvertices
 long. Not sure if it can directly create a label
   file, maybe Doug knows?

   Bruce


   On Sun, 12 May 2013, Jonathan DuBois wrote:

   I used the following options: mri_vol2surf --hemi lh --regheader
 subject01
 --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could
 not open the resulting file in tksurfer as either a label or an overlay:
 -
 /Applications/freesurfer/**tktools/tksurfer.bin: no data in label file
 /Users/label.mgh
 tkmedit: Trying to open /Users/label.dat
 surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar
 volume

 Best,
 Jonathan


 On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 
 wrote:
   try using --regheader

   cheers
   Bruce
   On Sun, 12 May 2013, Jonathan DuBois wrote:

 Hi Bruce,
 I would like to convert the .mgz label volume to a
 surface label for that
 subject, but mri_vol2surf requires a registration
 file.

 Best,
 Jonathan



 On Sunday, May 12, 2013, Bruce Fischl wrote:
   Hi Jonathan

   you don't need to register it if it's shown
 properly in tkmedit
   or freeview. Can you tell us more about what
 you are trying to
   do?
   Bruce


   On Sun, 12 May 2013, Jonathan DuBois wrote:

 Hi Bruce,
 Thanks for the quick response. The label
 is a
 manually traced area of the
 cortex. It is in subject scanner space
 and has a
 single value, so it
 probably would not work with bbregister.
 I can load
 it in tkmedit as a
 segmentation and the alignment is
 correct. I
 attached a screenshot. Is there
 a way to select the values greater than
 zero in
 tkmedit and save as a label
 that could be used in vol2surf? I have
 other labels
 that are larger so I
 would prefer not to retrace them if
 possible.

 Inline image 2
 Best,
 Jonathan


 On Sun, May 12, 2013 at 10:11 AM, Bruce
 Fischl
 fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Jonathan

   what is the label? What space is
 it in? If it
 has gray/white
   contrast you could try bbregister.

   cheers
   Bruce
   On Sat, 11 May 2013, Jonathan
 DuBois wrote:

 Hi Freesurfer Experts,
 I have a binary volume label
 in subject
 space that I
 converted from MINC to MGZ.
 I would like
 to register
 it to
 the surface of that subject
 as a flat
 label. I
 thought I would be able to
 do so with
 mri_vol2surf
 but I am not
 sure how to generate the
 required
 registration file.
 Is that the correct command,
 and if so,
 which
 registration
 file should I use?

 Thanks
 Jonathan




 The information

Re: [Freesurfer] Binary volume to surface label

[Jonathan DuBois]

Hi Bruce,

Thanks for the quick response. The label is a manually traced area of the
cortex. It is in subject scanner space and has a single value, so it
probably would not work with bbregister. I can load it in tkmedit as a
segmentation and the alignment is correct. I attached a screenshot. Is
there a way to select the values greater than zero in tkmedit and save as a
label that could be used in vol2surf? I have other labels that are larger
so I would prefer not to retrace them if possible.

[image: Inline image 2]
Best,
Jonathan


On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:

 Hi Jonathan

 what is the label? What space is it in? If it has gray/white contrast you
 could try bbregister.

 cheers
 Bruce

 On Sat, 11 May 2013, Jonathan DuBois wrote:

  Hi Freesurfer Experts,
 I have a binary volume label in subject space that I converted from MINC
 to MGZ. I would like to register it to
 the surface of that subject as a flat label. I thought I would be able to
 do so with mri_vol2surf but I am not
 sure how to generate the required registration file. Is that the correct
 command, and if so, which registration
 file should I use?

 Thanks
 Jonathan




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

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Re: [Freesurfer] Binary volume to surface label

[Jonathan DuBois]

Hi Bruce,

I would like to convert the .mgz label volume to a surface label for that
subject, but mri_vol2surf requires a registration file.

Best,
Jonathan



On Sunday, May 12, 2013, Bruce Fischl wrote:

 Hi Jonathan

 you don't need to register it if it's shown properly in tkmedit or
 freeview. Can you tell us more about what you are trying to do?
 Bruce


 On Sun, 12 May 2013, Jonathan DuBois wrote:

  Hi Bruce,
 Thanks for the quick response. The label is a manually traced area of the
 cortex. It is in subject scanner space and has a single value, so it
 probably would not work with bbregister. I can load it in tkmedit as a
 segmentation and the alignment is correct. I attached a screenshot. Is
 there
 a way to select the values greater than zero in tkmedit and save as a
 label
 that could be used in vol2surf? I have other labels that are larger so I
 would prefer not to retrace them if possible.

 Inline image 2
 Best,
 Jonathan


 On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Jonathan

   what is the label? What space is it in? If it has gray/white
   contrast you could try bbregister.

   cheers
   Bruce
   On Sat, 11 May 2013, Jonathan DuBois wrote:

 Hi Freesurfer Experts,
 I have a binary volume label in subject space that I
 converted from MINC to MGZ. I would like to register
 it to
 the surface of that subject as a flat label. I
 thought I would be able to do so with mri_vol2surf
 but I am not
 sure how to generate the required registration file.
 Is that the correct command, and if so, which
 registration
 file should I use?

 Thanks
 Jonathan




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




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Re: [Freesurfer] Binary volume to surface label

[Jonathan DuBois]

I used the following options: mri_vol2surf --hemi lh --regheader subject01
--cortex --mov label.mgz --o ./label.mgh
It ran without error, but I could not open the resulting file in tksurfer
as either a label or an overlay:
-
/Applications/freesurfer/tktools/tksurfer.bin: no data in label file
/Users/label.mgh
tkmedit: Trying to open /Users/label.dat
surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar
volume

Best,
Jonathan


On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 try using --regheader

 cheers

 Bruce
 On Sun, 12 May 2013, Jonathan DuBois wrote:

  Hi Bruce,
 I would like to convert the .mgz label volume to a surface label for that
 subject, but mri_vol2surf requires a registration file.

 Best,
 Jonathan



 On Sunday, May 12, 2013, Bruce Fischl wrote:
   Hi Jonathan

   you don't need to register it if it's shown properly in tkmedit
   or freeview. Can you tell us more about what you are trying to
   do?
   Bruce


   On Sun, 12 May 2013, Jonathan DuBois wrote:

 Hi Bruce,
 Thanks for the quick response. The label is a
 manually traced area of the
 cortex. It is in subject scanner space and has a
 single value, so it
 probably would not work with bbregister. I can load
 it in tkmedit as a
 segmentation and the alignment is correct. I
 attached a screenshot. Is there
 a way to select the values greater than zero in
 tkmedit and save as a label
 that could be used in vol2surf? I have other labels
 that are larger so I
 would prefer not to retrace them if possible.

 Inline image 2
 Best,
 Jonathan


 On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Jonathan

   what is the label? What space is it in? If it
 has gray/white
   contrast you could try bbregister.

   cheers
   Bruce
   On Sat, 11 May 2013, Jonathan DuBois wrote:

 Hi Freesurfer Experts,
 I have a binary volume label in subject
 space that I
 converted from MINC to MGZ. I would like
 to register
 it to
 the surface of that subject as a flat
 label. I
 thought I would be able to do so with
 mri_vol2surf
 but I am not
 sure how to generate the required
 registration file.
 Is that the correct command, and if so,
 which
 registration
 file should I use?

 Thanks
 Jonathan




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Re: [Freesurfer] Longitudinal comparison of thickness data

[Jonathan DuBois]

Thanks Martin!
I will look into why we are not getting a sphere.reg file. Everything else
seems pretty straight forward, although it sounds like the processing will
be a lot easier with FS 5.1. Do you know when we could expect that to be
released?

Best,
Jonathan



On Tue, Mar 29, 2011 at 1:39 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:

 Hi Jonathan,

 sorry, missed your mail completely.

 Anyway, in 5.1 there will be tools to do all this automatically for you
 (also for more than 2 time points). Everything below is only for 2 time
 points.

 Also about your questions:
 Something is wrong with you data, you should have the ?h.shpere.reg in
 the surf directories. Make sure your long runs finish without error.
 Make sure each subject has its own base (template).

 You would usually divide by the time difference in any case if your time
 points are differently spaced between subjects:
 mris_calc -o new.mgh whatever.mgh div 1.2
 (for example if time delta is 1.2 years)

 average thickness is (for 2 time points):
 mris_calc -o avg.mgh tp1.mgh add tp2.mgh
 mris_calc -o avg.mgh avg.mgh div 2

 and dividing by avg thickness
 mris_calc -o spc.mgh  diff.mgh div avg.mgh

 Note that spc (symmetrized percent change) is recommended over percent
 change with respect to time 1. Time 1 can be outlier and you get more
 power using the symmetrized version (with respect to the average).

 Also note that mris_calc cannot deal with different input types (mgh and
 curv files),therefore use mri_convert to convert a curv file into mgh
 format, e.g. mri_convert lh.thickness lh.thick1.mgh

 For more than 2 time points you could fit a GLM within each subject to
 compute the average and slope per time unit. But it depends on what you
 are trying to achieve, one could also compare rate of change in first
 year vs. rate of change in second year for a 3 tp study (each a year
 apart). Or more complex longitudinal models

 Best, Martin

 On Wed, 2011-03-09 at 14:44 -0500, Jonathan DuBois wrote:
  Hi Freesurfer users,
 
 
  I have been working from the list posting below for vertex comparison
  of longitudinal thickness data, although there are a couple issues I
  was hoping someone could help with.
 
  Using FS v5.0 with the fixed binaries
 , I have put together the following steps for data comparison following
 the third step of the longitudinal stream with their associated commands
 and questions (highlighted in bold). I am sorry if it is a lot of
 information, although I thought it might be useful for other users
 working with longitudinal analysis.
 
 
  Thanks
 
  Jonathan
 
 
  --
 
 
  Martin Reuter mreuter at nmr.mgh.harvard.edu
 
  Tue Jun 29 16:23:20 EDT 2010
 
 
  Hi Sandra,
 
  (and the list, I think this might be interesting for others)
 
 
  1. the longitudinal ?h.thickness files are in registration (within
  subject)
 
  so in order to compute the difference or the rate you can simply use:
 
  mris_calc -o lh.outdiff sdir2/surf/lh.thickness
  sdir1/surf/lh.thickness
 
  and for the rate, you can divide by time 1 thickness or by the average
 
  thickness. If the time points are not equally spaced across subjects,
 
  you can also divide by difference in time.
 
  It is best to smooth the thickness files before you do all this (i.e.
 
  within time point smooth the ?h.thickness files with mri_surf2surf).
 
 
  2. then map everything to your template (e.g. fsaverage) with
  mri_surf2surf
 
 
  3. there you can stack the thick-differences or thick-rates with
 
  mri_concat
 
 
  4. do the glm
 
 
  Best
 
  Gruesse, Martin
 
 
  --
 
 
  1. Smooth surface data:
 
 
  mri_surf2surf --s subj1_tp1.long.template --sval
  subj1_tp1.long.template/surf/lh.thickness --tval
  subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh --fwhm-src 10
  --hemi lh
 
 
  mri_surf2surf: could not read
  surface
 /space/mdeh2/1/halgdev/emcbkp/1/halgdev/projects/nyuproj/subjects/subj1_tp1.long.template/surf/lh.sphere.reg
 
  No such file or directory
 
 
  --The longitudinal processing does not create a ?h.sphere.reg or
  a ?h.sphere for running mri_register. While, the registration is
  specific to the longitudinal analysis, could I simply copy over
  the ?h.sphere.reg from the original subject, since it is the same
  brain? If not, how should this be generated?
 
 
 
  2. Compare time point differences within subjects using mris_calc and
  one of the three options:
 
 
  a. divide tp2 by tp1 - [mris_calc -o lh.NC024_thick_diff_fwhm10.mgh
  subj1_tp2.long.template/surf/lh.thickness.fwhm10.mgh div
  subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh]
 
  b. divide by average thickness
 
  c. divide by between scan time difference
 
 
  --Option (a) is straight forward, although option (c) would be ideal
  given that our subjects vary in time between scans. How would option
  (b) or © be set up with mris_calc? Would mris_calc work for more than
  two time points?
 
 
 
  3

[Freesurfer] Longitudinal comparison of thickness data

[Jonathan DuBois]

Hi Freesurfer users,


I have been working from the list posting below for vertex comparison of
longitudinal thickness data, although there are a couple issues I was hoping
someone could help with.

Using FS v5.0 with the fixed binaries, I have put together the following
steps for data comparison following the third step of the longitudinal
stream with their associated commands and questions (highlighted in bold). I
am sorry if it is a lot of information, although I thought it might be
useful for other users working with longitudinal analysis.


Thanks

Jonathan


--


Martin Reuter mreuter at nmr.mgh.harvard.edu
freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Longitudinal%20processingIn-Reply-To=%3C1277843000.24825.221.camel%40riemann.nmr.mgh.harvard.edu%3E

Tue Jun 29 16:23:20 EDT 2010


Hi Sandra,

(and the list, I think this might be interesting for others)


1. the longitudinal ?h.thickness files are in registration (within subject)

so in order to compute the difference or the rate you can simply use:

mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness

and for the rate, you can divide by time 1 thickness or by the average

thickness. If the time points are not equally spaced across subjects,

you can also divide by difference in time.

It is best to smooth the thickness files before you do all this (i.e.

within time point smooth the ?h.thickness files with mri_surf2surf).


2. then map everything to your template (e.g. fsaverage) with mri_surf2surf


3. there you can stack the thick-differences or thick-rates with

mri_concat


4. do the glm


Best

Gruesse, Martin


--


1. Smooth surface data:


mri_surf2surf --s subj1_tp1.long.template --sval
subj1_tp1.long.template/surf/lh.thickness --tval
subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh --fwhm-src 10 --hemi lh


mri_surf2surf: could not read surface
/space/mdeh2/1/halgdev/emcbkp/1/halgdev/projects/nyuproj/subjects/subj1_tp1.long.template/surf/lh.sphere.reg

No such file or directory


*--The longitudinal processing does not create a ?h.sphere.reg or a
?h.sphere for running mri_register. While, the registration is specific to
the longitudinal analysis, could I simply copy over the ?h.sphere.reg from
the original subject, since it is the same brain? If not, how should this be
generated?*


**

2. Compare time point differences within subjects using mris_calc and one of
the three options:


 a. divide tp2 by tp1 - [mris_calc -o lh.NC024_thick_diff_fwhm10.mgh
subj1_tp2.long.template/surf/lh.thickness.fwhm10.mgh div
subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh]

b. divide by average thickness

c. divide by between scan time difference


*--Option (a) is straight forward, although option (c) would be ideal given
that our subjects vary in time between scans. How would option (b) or © be
set up with mris_calc? Would mris_calc work for more than two time points?*



3. Register subjects' between scan difference map to fsaverage


mri_surf2surf --s lh.NC024_thickness_diff_fwhm10.mgh --trgsubject fsaverage
--tval lh.NC024_thickness_diff_fsaverage.fwhm10.mgh --fwhm-src 10 --hemi lh


*--I haven't gotten to this step yet, but I'm not sure that it will work
given that there is only a .mgh file without an associated subject? Also,
similar problem to question one (no sphere.reg).*

**

4. Stack subjects' difference maps using mri_concat


5. Run GLM using mri_glmfit
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[Freesurfer] Bonferroni multiple comparison correction

[Jonathan DuBois]

When correcting for multiple comparisons with Bonferroni for FS parcilation
statistics, is it necessary to adjust for all parcellations (35) or just the
variables (in our case mean thickness and surface area)? Assuming that no
prior hypothesis is used to constrain the number of parcellations.

Thanks for you input!

Jon
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