[Freesurfer] CVS repository

[Melvin Robinson]

I am trying to checkout the development version of Freesurfer from the CVS 
repository.  I need to build against VTK 7.1 instead of 5.6 for freeview and am 
using these instructions:  https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS

Using this command:

 cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P 
dev


Results in the following error:


cvs server: cannot find module `dev' - ignored

Can you tell me the correct module name?


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[Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

If I run recon-all with both a T1 and a T2 scan and switch t2pial, does 
mri_info -tkr2scanner give me the transform to the T1 scanner frame of 
reference?

And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me 
then?

Thanks - Don

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Re: [Freesurfer] recon all

[Bruce Fischl]

Hi John

it means that the talairach transform that was computed was extremely 
unlikely and deemed to be probably incorrect. Frequently this happens if 
you start with images (like analyze) that don't contain accurate direction 
cosine information. You can check this by bringing one of the volumes in 
freeview and checking to make sure that the anatomical directions we show
(e.g. anterior/posterior) correspond to the true anatomy. Sometimes 
abnormal anatomiies like huge ventricles can also make it fail, but you 
need to figure out which one it is before deciding what to do


cheers
Bruce


On Fri, 11 Nov 2016, John 
Anderson wrote:



Dear Freesurfer experts,
I ran the following command on a T1 image
recon-all -subjid 089 -all -qcache
 
and I got the following error message:
 
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
 
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
 
 
I highly appreciate an explanation for the meaning of this error and how to
fix it.
 
 
Best
John 

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[Freesurfer] recon all

[John Anderson]

Dear Freesurfer experts,

I ran the following command on a T1 image

recon-all -subjid 089 -all -qcache

 

and I got the following error message:

 

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)

 

 

I highly appreciate an explanation for the meaning of this error and how to fix it.

 

 


Best
John 
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Thank you Douglas !

Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  a
écrit :

> You need to weight by the number of vertices
>
> n = [27805 2321 552];
>   m = [8.8194 10.3661 10.3365];
> sum(n.*m)/sum(n)
>
> ans =
>
>  8.9637
>
>
> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > Could anyone please explain me the difference I got with command line
> > in below mail ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> > >:
> >
> > Dear experts,
> >
> > I am in trouble with two ways of computing mean intensity with
> > mri_segstats.
> >
> > First I have used on .annot files with three different labels
> > inside (SegId 1 to 3) :
> >
> > /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> > /
> > /
> > which give me those results:
> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range
> > 1   1 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 2.4975
> >
> > Second I have created on .label files containing the three
> > segmented labels (SegId 1 to 3) and used this label with
> mri_segstats:
> >
> > /mri_segstats --slabel fsaverage lh
> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> > --excludeid 0 --sum lh.pet.label.sum /
> > /
> > /
> > which give me those results:/
> > /
> > /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range /
> > /  1   1 30678  15542.9  Seg0001 8.9637 1.4701 6.2105
> >  14.2947 8.0842 /
> > /
> > /
> > I verified if I obtained the same results with the two ways
> > (.annot or .label) and everything is fine comparing NVertices,
> > Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> > = 9.84066 and with .label file Mean = 8.9637.
> >
> > Did I have miss anything and how is computed mean intensity ?
> >
> > Many thanks in advance.
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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[Freesurfer] computing ICC with LME

[Tanmay Nath]

Hi,

I am trying to compute the between state ICC (using LME MATLAB toolbox) for
my data but the lme_fit fails to converge in most of the voxels and
thus  gives me ICC = 0.

Increasing the number of iterations have not helped me and it still does
not converge

Any suggestions? Am I missing anything?
Thanks
Warm Regards,
Tanmay Nath
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Re: [Freesurfer] reusing mri_surf2surf transformation

[Douglas N Greve]

I would have thought that it would have crashed without the right files. 
Or does it go out of the container to get the files it needs? btw, you 
can use reprozip to see all the files that a process touches to know 
exactly what it needs


On 11/10/2016 04:10 PM, Chris Filo Gorgolewski wrote:
> I found the problem. To save space I only included the 
> surf/{l,r}h.white and surf/{l,r}h.white.reg files in the ICBM2009c_fs6 
> subejct folder (to save space in my container). After including 
> everything the corregistration run under 10s.
>
> Do you have some ideas which files are speeding up the process?
>
> Best,
> Chris
>
> On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski 
> > wrote:
>
> There is only one frame in rh.sig.mgh file (see below). Most time
> seems to be spent in calculating forward and reverse loops. Ideas?
>
> root@36ddc1c5be86:/code# mri_info
> /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> Volume information for
> /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
>   type: MGH
> dimensions: 163842 x 1 x 1
>voxel sizes: 1.00, 1.00, 1.00
>   type: FLOAT (3)
>fov: 163842.000
>dof: 0
> xstart: -81921.0, xend: 81921.0
> ystart: -0.5, yend: 0.5
> zstart: -0.5, zend: 0.5
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
>  FieldStrength: 0.00
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0.,
> c_r = 0.
>   : x_a =   0., y_a =   0., z_a =   1.,
> c_a = 0.
>   : x_s =   0., y_s =  -1., z_s =   0.,
> c_s = 0.
>
> talairach xfm :
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>  -1.   0.   0. 81921.
> 0.   0.   1.-0.5000
> 0.  -1.   0. 0.5000
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>  -1.  -0.  -0. 81921.
>  -0.  -0.  -1. 0.5000
>  -0.   1.  -0. 0.5000
>  -0.  -0.  -0. 1.
>
>
> On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve
> > wrote:
>
> 16min is a very long time. How many frames are in rh.sig.mgh?
> For a
> single frame it should only take 10 or 20 sec
>
>
> On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
> > Thanks for a prompt reply. The command takes ~16 minutes per
> > hemisphere in my setting. Are those realistic numbers or is
> it longer
> > than it should take?
> >
> > mri_surf2surf --s fsaverage --hemi rh --sval
> > /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> > --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
> >
> > sysname  Linux
> > hostname 36ddc1c5be86
> > machine  x86_64
> > user root
> > srcsubject = fsaverage
> > srcval =
> /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> > srctype=
> > trgsubject = ICBM2009c_fs6
> > trgval = /tmp/out.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > UseDualHemi = 0
> > Reading source surface reg
> > /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
> > Done
> > Using surf2surf_nnfr()
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (157000)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (163842)
> > Reverse Loop had 117731 hits
> > Surf2Surf: Dividing by number of hits (157000)
> > INFO: nSrcLost = 0
> > nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
> > nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985,
> MnSrcMultiHits
> > = 4.69815
> > Saving target data
> > Saving to /tmp/out.mgh
> >
> > real16m25.129s
> > user16m24.160s
> > sys 0m0.260s
> 

Re: [Freesurfer] reusing mri_surf2surf transformation

[Chris Filo Gorgolewski]

I found the problem. To save space I only included the surf/{l,r}h.white
and surf/{l,r}h.white.reg files in the ICBM2009c_fs6 subejct folder (to
save space in my container). After including everything the corregistration
run under 10s.

Do you have some ideas which files are speeding up the process?

Best,
Chris

On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski <
chris.gorgolew...@gmail.com> wrote:

> There is only one frame in rh.sig.mgh file (see below). Most time seems to
> be spent in calculating forward and reverse loops. Ideas?
>
> root@36ddc1c5be86:/code# mri_info /d/drive/workspace/
> brainbrowser/examples/models/rh.sig.mgh
> Volume information for /d/drive/workspace/brainbrowser/examples/models/
> rh.sig.mgh
>   type: MGH
> dimensions: 163842 x 1 x 1
>voxel sizes: 1.00, 1.00, 1.00
>   type: FLOAT (3)
>fov: 163842.000
>dof: 0
> xstart: -81921.0, xend: 81921.0
> ystart: -0.5, yend: 0.5
> zstart: -0.5, zend: 0.5
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
> 0.
>   : x_a =   0., y_a =   0., z_a =   1., c_a =
> 0.
>   : x_s =   0., y_s =  -1., z_s =   0., c_s =
> 0.
>
> talairach xfm :
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>-1.   0.   0. 81921.
> 0.   0.   1.-0.5000
> 0.  -1.   0. 0.5000
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-1.  -0.  -0. 81921.
>-0.  -0.  -1. 0.5000
>-0.   1.  -0. 0.5000
>-0.  -0.  -0. 1.
>
>
> On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> 16min is a very long time. How many frames are in rh.sig.mgh? For a
>> single frame it should only take 10 or 20 sec
>>
>>
>> On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
>> > Thanks for a prompt reply. The command takes ~16 minutes per
>> > hemisphere in my setting. Are those realistic numbers or is it longer
>> > than it should take?
>> >
>> > mri_surf2surf --s fsaverage --hemi rh --sval
>> > /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
>> > --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
>> >
>> > sysname  Linux
>> > hostname 36ddc1c5be86
>> > machine  x86_64
>> > user root
>> > srcsubject = fsaverage
>> > srcval = /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
>> > srctype=
>> > trgsubject = ICBM2009c_fs6
>> > trgval = /tmp/out.mgh
>> > trgtype=
>> > srcsurfreg = sphere.reg
>> > trgsurfreg = sphere.reg
>> > srchemi= rh
>> > trghemi= rh
>> > frame  = 0
>> > fwhm-in= 0
>> > fwhm-out   = 0
>> > label-src  = (null)
>> > label-trg  = (null)
>> > OKToRevFaceOrder  = 1
>> > UseDualHemi = 0
>> > Reading source surface reg
>> > /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
>> > Loading source data
>> > Reading target surface reg
>> > /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
>> > Done
>> > Using surf2surf_nnfr()
>> > Mapping Source Volume onto Source Subject Surface
>> > surf2surf_nnfr: building source hash (res=16).
>> > Surf2Surf: Forward Loop (157000)
>> >
>> > surf2surf_nnfr: building target hash (res=16).
>> > Surf2Surf: Reverse Loop (163842)
>> > Reverse Loop had 117731 hits
>> > Surf2Surf: Dividing by number of hits (157000)
>> > INFO: nSrcLost = 0
>> > nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
>> > nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985, MnSrcMultiHits
>> > = 4.69815
>> > Saving target data
>> > Saving to /tmp/out.mgh
>> >
>> > real16m25.129s
>> > user16m24.160s
>> > sys 0m0.260s
>> >
>> > On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve
>> > > wrote:
>> >
>> > Years ago I used to have code that would cache this transform, but
>> we
>> > abandoned it because it would get out of synch whenever someone
>> > updated
>> > their recon, and, for ordinary apps, it does not take that much
>> time.
>> >
>> >
>> > On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
>> > > Thanks for a quick reply. I'm actually in a situation where I do
>> not
>> > > have all of the overlays at the same time so I cannot
>> > concatenate them.
>> > >
>> > > To put more contexts: I am building surface support into
>> neurovault.
>> > > When someone uploads a surface statistical map I want to
>> > automatically
>> > > calculate a projection of this map into MNI volume. To 

Re: [Freesurfer] reusing mri_surf2surf transformation

[Chris Filo Gorgolewski]

There is only one frame in rh.sig.mgh file (see below). Most time seems to
be spent in calculating forward and reverse loops. Ideas?

root@36ddc1c5be86:/code# mri_info
/d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
Volume information for
/d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
0.   0.   1.-0.5000
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
   -0.  -0.  -0. 1.


On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve  wrote:

> 16min is a very long time. How many frames are in rh.sig.mgh? For a
> single frame it should only take 10 or 20 sec
>
>
> On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
> > Thanks for a prompt reply. The command takes ~16 minutes per
> > hemisphere in my setting. Are those realistic numbers or is it longer
> > than it should take?
> >
> > mri_surf2surf --s fsaverage --hemi rh --sval
> > /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> > --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
> >
> > sysname  Linux
> > hostname 36ddc1c5be86
> > machine  x86_64
> > user root
> > srcsubject = fsaverage
> > srcval = /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> > srctype=
> > trgsubject = ICBM2009c_fs6
> > trgval = /tmp/out.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > UseDualHemi = 0
> > Reading source surface reg
> > /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
> > Done
> > Using surf2surf_nnfr()
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (157000)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (163842)
> > Reverse Loop had 117731 hits
> > Surf2Surf: Dividing by number of hits (157000)
> > INFO: nSrcLost = 0
> > nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
> > nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985, MnSrcMultiHits
> > = 4.69815
> > Saving target data
> > Saving to /tmp/out.mgh
> >
> > real16m25.129s
> > user16m24.160s
> > sys 0m0.260s
> >
> > On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve
> > > wrote:
> >
> > Years ago I used to have code that would cache this transform, but we
> > abandoned it because it would get out of synch whenever someone
> > updated
> > their recon, and, for ordinary apps, it does not take that much time.
> >
> >
> > On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
> > > Thanks for a quick reply. I'm actually in a situation where I do
> not
> > > have all of the overlays at the same time so I cannot
> > concatenate them.
> > >
> > > To put more contexts: I am building surface support into
> neurovault.
> > > When someone uploads a surface statistical map I want to
> > automatically
> > > calculate a projection of this map into MNI volume. To improve
> > the MNI
> > > volume surface mapping I have reconstructed the surface of the
> > > 2009c_asym_nlin template. For every incoming map I am doing
> > > fsaverage -> MNI2009c mri_surf2surf followed by mri_surf2vol.
> > However,
> > > the mri_surf2surf takes quite a bit of time to run and most of it
> is
> > > spend on coregistration - which is always the same. If only I could
> > > calculate the coregistration once and apply it to every incoming
> map
> > > it would speed things up tremendously.
> > >
> > > Let me know if you have any 

Re: [Freesurfer] reusing mri_surf2surf transformation

[Douglas N Greve]

16min is a very long time. How many frames are in rh.sig.mgh? For a 
single frame it should only take 10 or 20 sec


On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
> Thanks for a prompt reply. The command takes ~16 minutes per 
> hemisphere in my setting. Are those realistic numbers or is it longer 
> than it should take?
>
> mri_surf2surf --s fsaverage --hemi rh --sval 
> /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh 
> --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
>
> sysname  Linux
> hostname 36ddc1c5be86
> machine  x86_64
> user root
> srcsubject = fsaverage
> srcval = /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
> srctype=
> trgsubject = ICBM2009c_fs6
> trgval = /tmp/out.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> UseDualHemi = 0
> Reading source surface reg 
> /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
> Loading source data
> Reading target surface reg 
> /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
> Done
> Using surf2surf_nnfr()
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (157000)
>
> surf2surf_nnfr: building target hash (res=16).
> Surf2Surf: Reverse Loop (163842)
> Reverse Loop had 117731 hits
> Surf2Surf: Dividing by number of hits (157000)
> INFO: nSrcLost = 0
> nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
> nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985, MnSrcMultiHits 
> = 4.69815
> Saving target data
> Saving to /tmp/out.mgh
>
> real16m25.129s
> user16m24.160s
> sys 0m0.260s
>
> On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve 
> > wrote:
>
> Years ago I used to have code that would cache this transform, but we
> abandoned it because it would get out of synch whenever someone
> updated
> their recon, and, for ordinary apps, it does not take that much time.
>
>
> On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
> > Thanks for a quick reply. I'm actually in a situation where I do not
> > have all of the overlays at the same time so I cannot
> concatenate them.
> >
> > To put more contexts: I am building surface support into neurovault.
> > When someone uploads a surface statistical map I want to
> automatically
> > calculate a projection of this map into MNI volume. To improve
> the MNI
> > volume surface mapping I have reconstructed the surface of the
> > 2009c_asym_nlin template. For every incoming map I am doing
> > fsaverage -> MNI2009c mri_surf2surf followed by mri_surf2vol.
> However,
> > the mri_surf2surf takes quite a bit of time to run and most of it is
> > spend on coregistration - which is always the same. If only I could
> > calculate the coregistration once and apply it to every incoming map
> > it would speed things up tremendously.
> >
> > Let me know if you have any ideas.
> >
> > Best,
> > Chris
> >
> > On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve
> > 
>  >> wrote:
> >
> > You can use mri_concat to create a stack of overlays, then
> > mri_surf2surf
> > the entire stack, then split the stack.
> >
> >
> > On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
> > > Hi,
> > > I need to convert a big number of scalar surface maps from
> fsaverage
> > > to one particular subject space. This means running
> mri_surf2surf
> > > command many times. For each execution the same
> transformation is
> > > calculated and then applied. Since estimating the
> transformation
> > take
> > > a substantial amount of time I was wondering if I could
> > calculate the
> > > transformation once and just apply it (which is a common
> thing in
> > > volumetric registration). I perused the website and the
> command line
> > > options, but I could not find anything. Is it possible to
> save and
> > > reuse surface transformations?
> > >
> > > Best,
> > > Chris
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>  

Re: [Freesurfer] reusing mri_surf2surf transformation

[Chris Filo Gorgolewski]

Thanks for a prompt reply. The command takes ~16 minutes per hemisphere in
my setting. Are those realistic numbers or is it longer than it should take?

mri_surf2surf --s fsaverage --hemi rh --sval
/d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh --trgsubject
ICBM2009c_fs6 --tval /tmp/out.mgh

sysname  Linux
hostname 36ddc1c5be86
machine  x86_64
user root
srcsubject = fsaverage
srcval = /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
srctype=
trgsubject = ICBM2009c_fs6
trgval = /tmp/out.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg
/opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Loading source data
Reading target surface reg
/opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (157000)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (163842)
Reverse Loop had 117731 hits
Surf2Surf: Dividing by number of hits (157000)
INFO: nSrcLost = 0
nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
nSrc121 = 133857, nSrcLost = 0, nSrcMulti = 29985, MnSrcMultiHits =
4.69815
Saving target data
Saving to /tmp/out.mgh

real16m25.129s
user16m24.160s
sys 0m0.260s

On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve  wrote:

> Years ago I used to have code that would cache this transform, but we
> abandoned it because it would get out of synch whenever someone updated
> their recon, and, for ordinary apps, it does not take that much time.
>
>
> On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
> > Thanks for a quick reply. I'm actually in a situation where I do not
> > have all of the overlays at the same time so I cannot concatenate them.
> >
> > To put more contexts: I am building surface support into neurovault.
> > When someone uploads a surface statistical map I want to automatically
> > calculate a projection of this map into MNI volume. To improve the MNI
> > volume surface mapping I have reconstructed the surface of the
> > 2009c_asym_nlin template. For every incoming map I am doing
> > fsaverage -> MNI2009c mri_surf2surf followed by mri_surf2vol. However,
> > the mri_surf2surf takes quite a bit of time to run and most of it is
> > spend on coregistration - which is always the same. If only I could
> > calculate the coregistration once and apply it to every incoming map
> > it would speed things up tremendously.
> >
> > Let me know if you have any ideas.
> >
> > Best,
> > Chris
> >
> > On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve
> > > wrote:
> >
> > You can use mri_concat to create a stack of overlays, then
> > mri_surf2surf
> > the entire stack, then split the stack.
> >
> >
> > On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
> > > Hi,
> > > I need to convert a big number of scalar surface maps from
> fsaverage
> > > to one particular subject space. This means running mri_surf2surf
> > > command many times. For each execution the same transformation is
> > > calculated and then applied. Since estimating the transformation
> > take
> > > a substantial amount of time I was wondering if I could
> > calculate the
> > > transformation once and just apply it (which is a common thing in
> > > volumetric registration). I perused the website and the command
> line
> > > options, but I could not find anything. Is it possible to save and
> > > reuse surface transformations?
> > >
> > > Best,
> > > Chris
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > 

Re: [Freesurfer] reusing mri_surf2surf transformation

[Douglas N Greve]

Years ago I used to have code that would cache this transform, but we 
abandoned it because it would get out of synch whenever someone updated 
their recon, and, for ordinary apps, it does not take that much time.


On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
> Thanks for a quick reply. I'm actually in a situation where I do not 
> have all of the overlays at the same time so I cannot concatenate them.
>
> To put more contexts: I am building surface support into neurovault. 
> When someone uploads a surface statistical map I want to automatically 
> calculate a projection of this map into MNI volume. To improve the MNI 
> volume surface mapping I have reconstructed the surface of the 
> 2009c_asym_nlin template. For every incoming map I am doing 
> fsaverage -> MNI2009c mri_surf2surf followed by mri_surf2vol. However, 
> the mri_surf2surf takes quite a bit of time to run and most of it is 
> spend on coregistration - which is always the same. If only I could 
> calculate the coregistration once and apply it to every incoming map 
> it would speed things up tremendously.
>
> Let me know if you have any ideas.
>
> Best,
> Chris
>
> On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve 
> > wrote:
>
> You can use mri_concat to create a stack of overlays, then
> mri_surf2surf
> the entire stack, then split the stack.
>
>
> On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
> > Hi,
> > I need to convert a big number of scalar surface maps from fsaverage
> > to one particular subject space. This means running mri_surf2surf
> > command many times. For each execution the same transformation is
> > calculated and then applied. Since estimating the transformation
> take
> > a substantial amount of time I was wondering if I could
> calculate the
> > transformation once and just apply it (which is a common thing in
> > volumetric registration). I perused the website and the command line
> > options, but I could not find anything. Is it possible to save and
> > reuse surface transformations?
> >
> > Best,
> > Chris
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] Questions about outputs in Longitudinal Stream

[Tamara Tavares]

Thank you for the clarification Martin

I have a follow-up question. When I load the base to  make sure it doesn't
look blurry, should I check the norm.mgz or brainmask.mgz? Online says
norm.mgz but I just want to make sure. Also, would the "blurriness" be
obvious?

Similarly, when I open the base and the longitudinal runs to see whether
they align, again should I load the brainmask.mgz for these as well?

Thank you in advance for your help,
Tamara
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] reusing mri_surf2surf transformation

[Chris Filo Gorgolewski]

Thanks for a quick reply. I'm actually in a situation where I do not have
all of the overlays at the same time so I cannot concatenate them.

To put more contexts: I am building surface support into neurovault. When
someone uploads a surface statistical map I want to automatically calculate
a projection of this map into MNI volume. To improve the MNI volume surface
mapping I have reconstructed the surface of the 2009c_asym_nlin template.
For every incoming map I am doing fsaverage -> MNI2009c mri_surf2surf
followed by mri_surf2vol. However, the mri_surf2surf takes quite a bit of
time to run and most of it is spend on coregistration - which is always the
same. If only I could calculate the coregistration once and apply it to
every incoming map it would speed things up tremendously.

Let me know if you have any ideas.

Best,
Chris

On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve  wrote:

> You can use mri_concat to create a stack of overlays, then mri_surf2surf
> the entire stack, then split the stack.
>
>
> On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
> > Hi,
> > I need to convert a big number of scalar surface maps from fsaverage
> > to one particular subject space. This means running mri_surf2surf
> > command many times. For each execution the same transformation is
> > calculated and then applied. Since estimating the transformation take
> > a substantial amount of time I was wondering if I could calculate the
> > transformation once and just apply it (which is a common thing in
> > volumetric registration). I perused the website and the command line
> > options, but I could not find anything. Is it possible to save and
> > reuse surface transformations?
> >
> > Best,
> > Chris
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

(2005,100e) for MRI (Philips)
(0028,1053) for PET (Philips)

I understand the PET may not be intended to work, but it doesn't seem to 
be copying over or applying the scale for either modality.

On 11/10/2016 12:40 PM, Douglas N Greve wrote:
> What is the dicom tag for the scale?
>
>
> On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
>> As far as I can tell, mri_convert doesn't apply the scaling factor, and
>> also doesn't copy over the slope scale header entry, when converting
>> from dicom to nifti.
>>
>> By contrast, dcm2nii does not apply the scale either, however, it copies
>> over the slope scale header entry, enabling other software (eg
>> Freeview..) to apply the scaling..
>>
>> Hope this clarifies. Thanks for checking into this.
>>
>> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>>> Sorry, is it a scale in the dicom file or the nifti file that is not
>>> being applied properly?
>>>
>>>
>>> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
 Doug,

 Can you verify? The dicom and mri_covnert .nii are identical (integer
 values, as per dicom convention) when we inspect the matrix in MATLAB.

 The img matrices for mri_convert and dcm2nii are also identical, the
 difference appears to be that dcm2nii retains the slope scale in the
 header, allowing the viewer (freeview, pmod, etc..) to apply it.

 We have been trying to nail down this issue for the last couple days,
 any insight would be appreciated.

 Eli

 On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>  Subject: Re: [Freesurfer] mri_convert
> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed I think we
> actually apply the scaling, so including it in the output would be
> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>>> Hello,
>>>
>>> We have been using mri_convert to convert our dicoms into .nii
>>> niftis.
>>> There is an entry in the .nii header for the slope scale, but
>>> mri_convert appears to discard this value instead of copying it
>>> into the
>>> header (whereas mricron retains this value) We prefer to use
>>> mri_convert.
>>>
>>> Is there a way to have mri_convert carry this value over? Why is it
>>> being discarded?
>>>
>>> Thanks,
>>> Eli
>>>
>

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

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Re: [Freesurfer] mri_convert slope scale

[Douglas N Greve]

What is the dicom tag for the scale?


On 11/10/2016 01:29 PM, Rockers, Elijah D. wrote:
> As far as I can tell, mri_convert doesn't apply the scaling factor, and
> also doesn't copy over the slope scale header entry, when converting
> from dicom to nifti.
>
> By contrast, dcm2nii does not apply the scale either, however, it copies
> over the slope scale header entry, enabling other software (eg
> Freeview..) to apply the scaling..
>
> Hope this clarifies. Thanks for checking into this.
>
> On 11/10/2016 12:18 PM, Douglas N Greve wrote:
>> Sorry, is it a scale in the dicom file or the nifti file that is not
>> being applied properly?
>>
>>
>> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>>> Doug,
>>>
>>> Can you verify? The dicom and mri_covnert .nii are identical (integer
>>> values, as per dicom convention) when we inspect the matrix in MATLAB.
>>>
>>> The img matrices for mri_convert and dcm2nii are also identical, the
>>> difference appears to be that dcm2nii retains the slope scale in the
>>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>>
>>> We have been trying to nail down this issue for the last couple days,
>>> any insight would be appreciated.
>>>
>>> Eli
>>>
>>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
 Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
  Subject: Re: [Freesurfer] mri_convert
 slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
 <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
 Content-Type: text/plain; charset=utf-8; format=flowed I think we
 actually apply the scaling, so including it in the output would be
 inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>> Hello,
>>
>> We have been using mri_convert to convert our dicoms into .nii
>> niftis.
>> There is an entry in the .nii header for the slope scale, but
>> mri_convert appears to discard this value instead of copying it
>> into the
>> header (whereas mricron retains this value) We prefer to use
>> mri_convert.
>>
>> Is there a way to have mri_convert carry this value over? Why is it
>> being discarded?
>>
>> Thanks,
>> Eli
>>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Optseq2 - Repeating Stimuli and Contrasting the Repetitions

[Douglas N Greve]

Hi Ruth, there are no ways to constrain the order of the stimuli in this 
way in optseq. If the timing is fixed between these 3 items, then they 
are effectively one stimulus type, and you can optimize the order of 
that one stimulus type.


On 11/10/2016 01:31 PM, Ruthie Shaffer wrote:
> Hi all,
>
> I’m posting to ask for advice on setting up certain parameters in optseq2:
>
> Specifically, in optseq2, how can one set up parameters to best optimize a 
> task where there are say 20 items presented 3 times, where the relevant 
> contrasts are between the first, second, and third presentations of the same 
> items?  Meaning the second presentation must come sometime after the first 
> and the third presentation must come sometime after the second?
>
> Thank you so much for any help on this!
>
> Best wishes,
>
> Ruth
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] aparcstats2table

[Douglas N Greve]

This appears to be broken in 5.3. You can do 2 things: (1) specify the 
subjects in a different way, or (2) use the aparcstats2table below. I'm 
not 100% sure it will work in the 5.3 env, so make a backup of your 
aparcstats2table file.

https://gate.nmr.mgh.harvard.edu/safelinks/greve/aparcstats2table

For your other questions

a) average across what? Subject? You can use mri_glmfit --table ..., or 
you can load it into matlab with fast_ldtable and do your averages there

b) Are what in fsaverage space? When you run aparcstats2table you get 
averages in the parcellations of the individual, fsaverage does not come 
into it

c) We don't have anything that will do this easily (a harder problem 
than you might think). I would do it in matlab, loading the annotation 
using read_annotation.m, create a vector of values (one item per 
vertex), then assign all the vertices in a given parcellation the value 
for that parcellation from your average, then write it out as an mgh 
file  using MRIwrite.m




On 11/09/2016 08:27 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> Please find the attached qdec file, along with diagnosis file which I 
> used in QDEC, and this is the same qdec file I trying to use for 
> the aparcstats2table command.
>
> Thanks.
>
> PS: I was also wondering (a) how can I average thickness stats (b) are 
> these in fsaverage (standard) space and (c) how can I display it on 
> standard fsaverage for publications purpose?
>
> On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve 
> > wrote:
>
> can you send the qdec file with variables?
>
>
> On 11/09/2016 11:51 AM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > Somehow even after adding variables, it's not working, although same
> > qdec file works fine when I perform GLM in qdec.
> > So I replaced the flag with subjectsfile and provided subject
> list.txt
> > file. So in that way, it's working fine now.
> >
> > I was also wondering (a) how can I average these thickness stats (b)
> > are these in fsaverage (standard) space and (c) how can I display it
> > on standard fsaverage for publications purpose?
> >
> > Thanks a lot.
> >
> > On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve
> > 
>  >> wrote:
> >
> > Appears to be having problems reading the qdec table. It
> might be
> > expecting the qdec table to actually variables in it. Can
> you try
> > adding variables? Also, try it without the --qdec flag instead
> > specifying the subjects with --subjects HC003_1 HC004_1 ...
> >
> >
> > On 11/8/16 8:09 PM, Martin Juneja wrote:
> >> Hi everyone,
> >>
> >> I am trying to use following command to save stats from a
> set of
> >> subjects in a table format:
> >>
> >> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t
> >> zzz.txt
> >>
> >> But after I run this, I get following error:
> >>
> >> Traceback (most recent call last):
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line
> 353, in
> >> 
> >>
> >> subj_listoftuples = assemble_inputs(options)
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line
> 228, in
> >> assemble_inputs
> >>
> >> fsid=row['fsid'].strip()
> >>
> >> KeyError: 'fsid'
> >>
> >> My qdec.dat file looks like below:
> >>
> >> fsidHC003_1
> >> HC004_1
> >> HC006_1
> >> HC015_1
> >>
> >> This command works fine if I use subject IDs individually
> here e.g.
> >> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1
> >> HC015_1 --hemi lh --meas thickness -t zzz.txt
> >>
> >> Another question I have here is: How can I average these
> >> thickness stats and display it on standard fsaverage?
> >>
> >> Any help would be really appreciated.
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> 
> >>  >
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >>  >
> > ___ Freesurfer
> mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> 
>   

[Freesurfer] Optseq2 - Repeating Stimuli and Contrasting the Repetitions

[Ruthie Shaffer]

Hi all,

I’m posting to ask for advice on setting up certain parameters in optseq2:

Specifically, in optseq2, how can one set up parameters to best optimize a task 
where there are say 20 items presented 3 times, where the relevant contrasts 
are between the first, second, and third presentations of the same items?  
Meaning the second presentation must come sometime after the first and the 
third presentation must come sometime after the second?

Thank you so much for any help on this!

Best wishes,

Ruth
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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

As far as I can tell, mri_convert doesn't apply the scaling factor, and 
also doesn't copy over the slope scale header entry, when converting 
from dicom to nifti.

By contrast, dcm2nii does not apply the scale either, however, it copies 
over the slope scale header entry, enabling other software (eg 
Freeview..) to apply the scaling..

Hope this clarifies. Thanks for checking into this.

On 11/10/2016 12:18 PM, Douglas N Greve wrote:
> Sorry, is it a scale in the dicom file or the nifti file that is not 
> being applied properly?
>
>
> On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
>> Doug,
>>
>> Can you verify? The dicom and mri_covnert .nii are identical (integer
>> values, as per dicom convention) when we inspect the matrix in MATLAB.
>>
>> The img matrices for mri_convert and dcm2nii are also identical, the
>> difference appears to be that dcm2nii retains the slope scale in the
>> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>>
>> We have been trying to nail down this issue for the last couple days,
>> any insight would be appreciated.
>>
>> Eli
>>
>> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>>>  Subject: Re: [Freesurfer] mri_convert
>>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>>> actually apply the scaling, so including it in the output would be
>>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
> Hello,
>
> We have been using mri_convert to convert our dicoms into .nii 
> niftis.
> There is an entry in the .nii header for the slope scale, but
> mri_convert appears to discard this value instead of copying it 
> into the
> header (whereas mricron retains this value) We prefer to use 
> mri_convert.
>
> Is there a way to have mri_convert carry this value over? Why is it
> being discarded?
>
> Thanks,
> Eli
>
>

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

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Hospital and/or its relevant affiliates and may contain restricted and 
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use, distribution or disclosure by others is strictly prohibited. If you are 
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Re: [Freesurfer] reusing mri_surf2surf transformation

[Douglas N Greve]

You can use mri_concat to create a stack of overlays, then mri_surf2surf 
the entire stack, then split the stack.


On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
> Hi,
> I need to convert a big number of scalar surface maps from fsaverage 
> to one particular subject space. This means running mri_surf2surf 
> command many times. For each execution the same transformation is 
> calculated and then applied. Since estimating the transformation take 
> a substantial amount of time I was wondering if I could calculate the 
> transformation once and just apply it (which is a common thing in 
> volumetric registration). I perused the website and the command line 
> options, but I could not find anything. Is it possible to save and 
> reuse surface transformations?
>
> Best,
> Chris
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Douglas N Greve]

You need to weight by the number of vertices

n = [27805 2321 552];
  m = [8.8194 10.3661 10.3365];
sum(n.*m)/sum(n)

ans =

 8.9637


On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> Dear Freesurfer's experts,
>
> Could anyone please explain me the difference I got with command line 
> in below mail ?
>
> Best regards,
> Matthieu
>
> 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte 
> >:
>
> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different labels
> inside (SegId 1 to 3) :
>
> /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
> --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> /
> /
> which give me those results:
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> StdDev Min Max Range
> 1   1 2780514182.6  cluster-001  8.8194 1.4351
> 6.210514.2947 8.0842
> 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> 8.837512.9317 4.0942
> 3   3   552  313.1  cluster3  10.3365 0.4711
> 9.371911.8694 2.4975
>
> Second I have created on .label files containing the three
> segmented labels (SegId 1 to 3) and used this label with mri_segstats:
>
> /mri_segstats --slabel fsaverage lh
> lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> --excludeid 0 --sum lh.pet.label.sum /
> /
> /
> which give me those results:/
> /
> /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> StdDev Min Max Range /
> /  1   1 30678  15542.9  Seg0001 8.9637 1.4701 6.2105  
>  14.2947 8.0842 /
> /
> /
> I verified if I obtained the same results with the two ways
> (.annot or .label) and everything is fine comparing NVertices,
> Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> = 9.84066 and with .label file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_convert slope scale

[Douglas N Greve]

Sorry, is it a scale in the dicom file or the nifti file that is not 
being applied properly?


On 11/10/2016 11:01 AM, Rockers, Elijah D. wrote:
> Doug,
>
> Can you verify? The dicom and mri_covnert .nii are identical (integer
> values, as per dicom convention) when we inspect the matrix in MATLAB.
>
> The img matrices for mri_convert and dcm2nii are also identical, the
> difference appears to be that dcm2nii retains the slope scale in the
> header, allowing the viewer (freeview, pmod, etc..) to apply it.
>
> We have been trying to nail down this issue for the last couple days,
> any insight would be appreciated.
>
> Eli
>
> On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve
>>  Subject: Re: [Freesurfer] mri_convert
>> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID:
>> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed I think we
>> actually apply the scaling, so including it in the output would be
>> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
 Hello,

 We have been using mri_convert to convert our dicoms into .nii niftis.
 There is an entry in the .nii header for the slope scale, but
 mri_convert appears to discard this value instead of copying it into the
 header (whereas mricron retains this value) We prefer to use mri_convert.

 Is there a way to have mri_convert carry this value over? Why is it
 being discarded?

 Thanks,
 Eli


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

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

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Re: [Freesurfer] mri_convert slope scale

[Rockers, Elijah D.]

Doug,

Can you verify? The dicom and mri_covnert .nii are identical (integer 
values, as per dicom convention) when we inspect the matrix in MATLAB.

The img matrices for mri_convert and dcm2nii are also identical, the 
difference appears to be that dcm2nii retains the slope scale in the 
header, allowing the viewer (freeview, pmod, etc..) to apply it.

We have been trying to nail down this issue for the last couple days, 
any insight would be appreciated.

Eli

On 11/09/2016 05:51 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve 
>  Subject: Re: [Freesurfer] mri_convert 
> slope scale To: freesurfer@nmr.mgh.harvard.edu Message-ID: 
> <908818ac-156f-f6d2-1338-694626cde...@nmr.mgh.harvard.edu> 
> Content-Type: text/plain; charset=utf-8; format=flowed I think we 
> actually apply the scaling, so including it in the output would be 
> inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote:
>> >Hello,
>> >
>> >We have been using mri_convert to convert our dicoms into .nii niftis.
>> >There is an entry in the .nii header for the slope scale, but
>> >mri_convert appears to discard this value instead of copying it into the
>> >header (whereas mricron retains this value) We prefer to use mri_convert.
>> >
>> >Is there a way to have mri_convert carry this value over? Why is it
>> >being discarded?
>> >
>> >Thanks,
>> >Eli
>> >

-- 
Elijah Rockers
Research Data Analyst
Houston Methodist Research Institute
O: 713-363-7729

Houston Methodist. Leading Medicine.

U.S. News & World Report has recognized Houston Methodist as one of the 
nation’s top 20 hospitals, placing it for the second time on the magazine’s 
prestigious Honor Roll. It is also designated as a Magnet hospital for 
excellence in nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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Re: [Freesurfer] License on fsaverage datasets

[Bruce Fischl]

sure, that's fine. Thanks for asking
Bruce
On Thu, 10 Nov 2016, Marmaduke Woodman wrote:

> hi
> 
> As part of developing some tools [1] partly on the FreeSurfer ecosystem,
> we'd like to use the fsaverage5 dataset as a test data. In our workflow that
> would mean committing those files to our Git repo, pushing to GitHub,
> testing on Travis CI etc which makes them public in our repo. We have,
> however, no intention of otherwise redistributing the data.
> 
> If we place the FreeSurfer license file next to the fsaverage5 folder in our
> repo, is this OK? or would you have a strong preference against this?
> 
> 
> Thanks,
> Marmaduke
> 
> 
> [1] The project in question is here
> 
> https://github.com/ins-amu/bnm-recon-tools
> 
> though not well developed at its current stage.
> 
> 
>
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Re: [Freesurfer] Vertex-labeling

[Bruce Fischl]

Hi Foteini

if you threshold the surface map, the index of each nonzero value can be 
used to lookup the vertex coordinate in the relevant surface (e.g. white 
or pial) in matlab for example. What do you want to do with this 
information?

cheers
Bruce


On Thu, 10 Nov 2016, Foteini Protopapa wrote:

> Dear FS experts,
> I have a volume with specific clusters and I project it to a surface
> using mri_vol2surf. How can I determine the edges of my clusters now?
> By getting the surface I get a vector, but I don't know the "labels" of this
> vector. To which point (in mm) each value corresponds?
> 
> Thanks in advance,
> Foteini.
> 
>
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[Freesurfer] Vertex-labeling

[Foteini Protopapa]

Dear FS experts,

I have a volume with specific clusters and I project it to a surface
using mri_vol2surf. How can I determine the edges of my clusters now?
By getting the surface I get a vector, but I don't know the "labels" of
this vector. To which point (in mm) each value corresponds?

Thanks in advance,
Foteini.
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Re: [Freesurfer] FreeSurfer Dev Releases {Disarmed}

[Elia S.]

Dear Zeke,


Thank you for this clarification.


Best,

Elia.



Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Z K 

Inviato: martedì 8 novembre 2016 16.15
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: Re: [Freesurfer] FreeSurfer Dev Releases



On 11/07/2016 05:39 AM, Elia S. wrote:
> Dear FreeSurfer Developers,
>
>
> We have been trying out, for the past few months, the freesurfer dev
> releases, and in particular this one:
>
>
> freesurfer-X86_64-unknown-linux-gnu-dev5-20150924
>
>
> My question is, does the above version classify as a nightly version of
> FreeSurfer 5, or as an early beta of the 6?
>
> Or..do the dev versions fall in some kind of grey area that are
> neither 5 or 6?

This. dev versions are nightly builds that include latest features and
bug fixes, but are not adequately tested, and do not undergo the same
rigorous testing that a released version would get. We anticipate a v6
beta version before the end of this month.

-Zeke



>
>
> Thank you in advance,
>
> Elia.
>
>
>
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

Could anyone please explain me the difference I got with command line in
below mail ?

Best regards,
Matthieu

2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :

> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different labels inside
> (SegId 1 to 3) :
>
> *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i
> lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum*
>
> which give me those results:
> # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range
>   1   1 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 2.4975
>
> Second I have created on .label files containing the three segmented
> labels (SegId 1 to 3) and used this label with mri_segstats:
>
> *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i
> lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum *
>
> which give me those results:
> *# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean StdDev Min
> Max Range  *
> *  1   1 3067815542.9  Seg0001 8.9637 1.4701 6.2105
>  14.2947 8.0842 *
>
> I verified if I obtained the same results with the two ways (.annot or
> .label) and everything is fine comparing NVertices, Area_mm2 but Mean in
> first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label
> file Mean = 8.9637.
>
> Did I have miss anything and how is computed mean intensity ?
>
> Many thanks in advance.
>
> Best regards,
> Matthieu
>
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Re: [Freesurfer] FW: Manual pial and white matter corrections cause irregularities

[Cleo Vandervost]

Hi Bruce, 

I have to send you aWetransfer link because the original tar.gz files are too 
large to email.
Hope this is no problem for you. 

Link: https://we.tl/GTtu2iH5Fm

Cheers, 

Cleo 

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 namens Bruce Fischl 

Verzonden: dinsdag 8 november 2016 15:05
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] FW: Manual pial and white matter corrections cause 
irregularities

Hi Cleo

to check I need the actual subject directories. Can you tar, gzip and
upload the before and after ones?

cheers
Bruce


On Tue, 8 Nov 2016, Cleo
Vandervost wrote:

>
> Hi Bruce;
>
> Sorry to send this email once again but I didn't get an answer to my previous 
> one. As you asked, I uploaded the recon-all log-file for that subject, edited 
> and unedited.  We're using version 5.3. How can you check for sure that the 
> WM significantly gets  >110?
>
> I also uploaded the pictures once again.
>
> Thanks,
>
> Cleo
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>  namens Bruce Fischl 
> 
> Verzonden: vrijdag 21 oktober 2016 02:14
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Manual pial and white matter corrections cause 
> irregularities
>
> Hi Cleo
>
> can you upload a subject before and after editing so we can replicate what
> you are seeing? And what version of FreeSurfer are you using? Does the WM
> after editing get signifcantly >110? If so, you may have accidentally
> placed a control point in a gray matter voxel
>
> cheers
> Bruce
>
>
> On Thu, 20 Oct 2016, Cleo Vandervost wrote:
>
>>
>> ​Hello Freesurfer team,
>>
>>
>> For my thesis I'm researching the differences in grey and white matter and 
>> cortical thickness between
>> children with and without dyslexia. My supervisor advised me to manually 
>> edit the Freesurfer-generated
>> data. I've been editing my data as follows:
>>
>> - adding control points to (larger) WM-areas that FS did not include
>>
>> - manually editing (smaller) WM-areas through recon-editing
>>
>> - correcting the pial surface through recon-editing
>>
>>
>> After finishing and saving my edits I reran recon-all with this command: 
>> recon-all -autorecon2-cp
>> -autorecon -subjid (subject number). When I opened my data again in 
>> Freesurfer to check my edits, I saw
>> that there were two big problems:
>>
>> - 'distortions' in the pial surface
>>
>> - sometimes large areas of WM suddenly were excluded, even when I didn't 
>> make any edits in that area
>>
>> ​It makes the edited data look much worse than the original data, which is 
>> weird I suppose.
>>
>>
>> I've included some pictures so you can see what I mean.
>>
>> - Picture (a) is the original unedited version.
>>
>> - Picture (b) is the edited version: control points and WM edits. You can 
>> see that there's a large area
>> in the left hemisfere excluded from the original WM area
>>
>> - Picture (c) is the re-edited version of (b), control points added in that 
>> large area. This time it's
>> included but the pial surface shows a lot of irregularities.
>>
>>
>> Me and my supervisor tried a couple of times with other data, but we still 
>> had the same results. We also
>> tried by only adding control points and editing manually, without the 
>> pial-corrections.
>>
>>
>> Do you have any idea of what's going wrong in the editing proces?
>>
>>
>> Thank you very much,
>>
>>
>> Kind regards
>>
>>
>> Cleo Vandervost
>>
>> 1st master speech and language therapy
>>
>> Katholieke Universiteit Leuven
>>
>>
>>
>>
>>

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