Re: [Freesurfer] Reliability of labeling procedure in the same scan

[Bruce Fischl]

do you mean the hippocampal volume in the aseg or in the subfields?
On Sat, 
26 Aug 2017, anonymous anonymous wrote:



Hi all,
Without noticing I run recon-all twice on the same scan of the same subject and 
we noticed there are
some differences, at least in the hippocampal volume estimation.

Is it normal? If it is, why is it so? 


Thank you so much for your help

This is a great community!

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[Freesurfer] Reliability of labeling procedure in the same scan

[anonymous anonymous]

Hi all,

Without noticing I run recon-all twice on the same scan of the same subject
and we noticed there are some differences, at least in the hippocampal
volume estimation.

Is it normal? If it is, why is it so?


Thank you so much for your help

This is a great community!
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Re: [Freesurfer] Labels from Pial surface

[Fereshte]

What about volume? For surface, it
seems that it is ok.
On Tue, Aug 22, 2017 at 1:29 AM Douglas N Greve 
wrote:

>
> whatever annotation you give it (eg, aparc). There are not separate
> labels for the inner and the outer. The distinction is in the xyz
> coordinates. If you don't give it a surface, it will use the xyz coords
> from the inner (white) surface. If you give it --surface pial, it will
> use the xyz coords from the outer
>
>
>
> On 08/21/2017 04:33 PM, Fereshte wrote:
> > And what labels does this mri_annotation2label give? Does it give the
> > outer cortical boundary as well?
> > On Tue, Aug 22, 2017 at 12:19 AM Douglas N Greve
> > > wrote:
> >
> > when you run mri_annotation2label you can specify the surface
> > (--surface). By default, it uses white, but you can specify pial
> > instead
> >
> >
> > On 08/21/2017 11:33 AM, Fereshte wrote:
> > > Hello FreeSurfer developers,
> > > Is it possible to have the segmentation labels after the pial
> > surface
> > > is done in FreeSurfer? I mean once you do the topology
> > correction and
> > > expand the inner cortical boundary to make the pial surface ; is it
> > > possible to have the inner and outer cortical boundaries as labels
> > > from pial surface?
> > > Looking forward to hearing from you
> > > Sincerely,
> > > Fereshte Ramezani
> > >
> > >
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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
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
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> >
> >
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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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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Re: [Freesurfer] Change the template in Freesurfer

[Bruce Fischl]

Hi YQ

which template do you mean? We have many. What are you trying to achieve?

cheers
Bruce
On 
Wed, 23 Aug 2017, YQ Chen wrote:



Hi, 

I want to change the template when doing recon-all.
Is it possible? If it can, how can I do?

Tell me, please!
Thanks a lot!

YQ

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Re: [Freesurfer] dividing cortex into equal patches

[Bruce Fischl]

Hi Ani

using sphere is as close as we come to equal area. The difference in 
Gaussian curvature between the sphere and the cortex make this a 
non-trivial problem.


cheers
Bruce


On 
Fri, 25 Aug 2017, Aniqa Dalowr wrote:



Also I tried using both lh.sphere and lh.sphere.reg and in both cases, the 
patches arent equal in
surface area. There is a lot of variablility in surface area and the number of 
vertices. Please see
below. Is there a way to generate roughly equal size patches ?
Thank you,

Ani

USING lh.sphere in the mris_make_face_parcellation step

mris_anatomical_stats -a lh.ic1.annot -b bert lh

computing statistics for each annotation in lh.ic1.annot.

reading volume /Applications/freesurfer5.3/subjects//bert/mri/wm.mgz...

reading input surface 
/Applications/freesurfer5.3/subjects//bert/surf/lh.white...

reading input pial surface 
/Applications/freesurfer5.3/subjects//bert/surf/lh.pial...

reading input white surface 
/Applications/freesurfer5.3/subjects//bert/surf/lh.white...

reading colortable from annotation file...

colortable with 42 entries read (originally 
/Applications/freesurfer5.3/lib/bem/ic1.tri)


table columns are:

    number of vertices

    total surface area (mm^2)

    total gray matter volume (mm^3)

    average cortical thickness +- standard deviation (mm)

    integrated rectified mean curvature

    integrated rectified Gaussian curvature

    folding index

    intrinsic curvature index

    structure name


 3003   1916   5416  2.489 1.079     0.119     0.043       36     5.9  
ic1.tri_vertex_0

 1834   1136   3495  2.706 0.877     0.125     0.098       33     9.1  
ic1.tri_vertex_1

 3900   2607   7660  2.589 0.719     0.138     0.047       65     7.2  
ic1.tri_vertex_2

 2642   1817   6685  3.022 0.701     0.138     0.051       38     5.3  
ic1.tri_vertex_3

 2584   1723   4305  2.325 0.647     0.128     0.041       30     4.5  
ic1.tri_vertex_4

 2920   1857   5725  2.444 0.597     0.140     0.055       48     5.8  
ic1.tri_vertex_5

 3273   2153   5148  2.275 0.701     0.133     0.042       43     5.1  
ic1.tri_vertex_6

 3067   2057   5496  2.511 0.899     0.121     0.034       33     4.1  
ic1.tri_vertex_7

 3062   2032   5701  2.577 0.760     0.122     0.036       73     4.8  
ic1.tri_vertex_8

 2561   1711   4119  2.324 0.843     0.122     0.036       27     3.9  
ic1.tri_vertex_9

 3771   2485   5211  1.996 0.686     0.150     0.053       57     8.4  
ic1.tri_vertex_10

 3161   2056   5323  2.256 1.418     0.115     0.063       41    10.5  
ic1.tri_vertex_11

 2901   1843   5209  2.442 0.744     0.116     0.048       39     6.2  
ic1.tri_vertex_12

 2606   1597   4923  2.738 0.690     0.122     0.059       60     8.2  
ic1.tri_vertex_13

 3201   2024   5676  2.518 1.156     0.120     0.046       47     6.1  
ic1.tri_vertex_14

 2773   1820   5356  2.494 0.709     0.138     0.048       52     5.7  
ic1.tri_vertex_15

 3014   2009   5838  2.448 0.607     0.137     0.042       40     4.7  
ic1.tri_vertex_16

 2830   1831   4750  2.330 1.164     0.121     0.048       56     4.5  
ic1.tri_vertex_17

 2562   1688   4790  2.399 0.625     0.137     0.041       34     4.2  
ic1.tri_vertex_18

 3426   2311   6400  2.410 1.448     0.136     0.148      151    12.1  
ic1.tri_vertex_19

 3174   2114   7074  2.738 1.159     0.133     0.069       57     6.4  
ic1.tri_vertex_20

 4168   2800  10961  3.074 0.904     0.146     0.150      130     9.4  
ic1.tri_vertex_21

 3168   2152   6826  2.749 0.684     0.124     0.036       36     4.7  
ic1.tri_vertex_22

 4735   3193  10350  2.681 0.653     0.152     0.057       91    11.0  
ic1.tri_vertex_23

 2135   1433   3968  2.511 0.727     0.126     0.044       24     3.6  
ic1.tri_vertex_24

 2722   1839   5346  2.594 0.871     0.121     0.034       30     3.5  
ic1.tri_vertex_25

 2334   1517   3672  2.380 0.830     0.129     0.043      128     3.7  
ic1.tri_vertex_26

 3167   2082   5127  2.295 0.600     0.136     0.046       41     6.1  
ic1.tri_vertex_27

 3160   2112   5358  2.452 0.916     0.125     0.040       39     5.1  
ic1.tri_vertex_28

 4252   2749   6928  2.203 0.636     0.143     0.051       64     9.0  
ic1.tri_vertex_29

 4375   2865   6826  2.199 0.646     0.132     0.042       54     7.4  
ic1.tri_vertex_30

 5192   3235   7301  2.004 0.656     0.161     0.080       95    19.8  
ic1.tri_vertex_31

 2115   1377   3391  2.411 0.762     0.126     0.048       59     4.0  
ic1.tri_vertex_32

 2403   1622   5521  2.877 0.790     0.131     0.045       28     4.2  
ic1.tri_vertex_33

 2128   1400   3425  2.400 1.097     0.119     0.036       24     3.3  
ic1.tri_vertex_34

 4474   2989   9551  2.636 0.632     0.153     0.087     1057    21.4  
ic1.tri_vertex_35

 3590   2437   6230  2.517 0.832     0.128     0.037       40     5.4  
ic1.tri_vertex_36

 3845   2558   6271  2.349 1.188     0.112     0.046       56     8.7  
ic1.tri_vertex_37

 2913   2084   6148  2.577 1.276     0.129     0.069       51    10.8