Hello all,

How do I get aparc stats (area) using the pial surface, please?

Thanks,
Andreia



----- Mensagem encaminhada de _andre...@sapo.pt -----
           Data: Thu, 27 Mar 2014 11:31:13 +0000
             De: _andre...@sapo.pt
Responder Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
        Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and  
aparcstats2table
           Para: freesurfer@nmr.mgh.harvard.edu, vi...@nmr.mgh.harvard.edu

Hi Louis,

It didn't work either. This is what shows up in the terminal after
running mris_anatomical_stats:

mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.aparc.annot.
reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
reading input surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input pial surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input white surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ./aparc.ctab

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

   1272    793   2092  2.485 0.342     0.141     0.042       24     2.4
   bankssts
   1184    957   2200  2.419 0.757     0.226     0.187      248    11.5
   caudalanteriorcingulate
   3222   2408   5307  2.324 0.512     0.136     0.040       58     4.8
   caudalmiddlefrontal
   2468   1735   2917  1.798 0.388     0.150     0.064       54     5.2  cuneus
    504    582   1801  3.807 0.663     0.256     0.084       24     2.0
   entorhinal
   4892   3757   9658  2.696 0.715     0.183     0.073      167    15.0
   fusiform
   8153   6383  13887  2.315 0.543     0.160     0.049      179    16.6
   inferiorparietal
   4885   3695  10298  2.929 0.668     0.171     0.069      187    14.8
   inferiortemporal
   1470   1045   2169  2.137 0.673     0.200     0.129      154     8.8
   isthmuscingulate
   6612   4848  10068  2.208 0.530     0.161     0.058      217    15.6
   lateraloccipital
   3665   2871   6467  2.380 0.684     0.186     0.067      123    11.1
   lateralorbitofrontal
   4593   3224   5598  1.811 0.528     0.170     0.072      165     
13.4  lingual
   2623   2020   4262  2.290 0.776     0.191     0.072      179     8.1
   medialorbitofrontal
   4570   3991  10068  2.785 0.605     0.169     0.052      154    10.0
   middletemporal
   1041    802   1923  2.621 0.705     0.161     0.058       20     2.4
   parahippocampal
   2067   1415   2808  2.156 0.580     0.115     0.024       20     2.1
   paracentral
   1534   1130   2779  2.551 0.445     0.149     0.042       29     2.5
   parsopercularis
   1366   1265   2718  2.458 0.607     0.184     0.049       23     2.9
   parsorbitalis
   2166   1826   3699  2.258 0.484     0.166     0.048       34     4.8
   parstriangularis
   2637   1647   2528  1.563 0.436     0.137     0.043       47     4.7
   pericalcarine
   6180   4524   7746  1.879 0.596     0.122     0.030       62     7.3
   postcentral
   1694   1270   2783  2.265 0.721     0.188     0.088       64     7.6
   posteriorcingulate
   7118   5162  11283  2.336 0.590     0.115     0.027       67     8.4
   precentral
   5554   4071   8657  2.206 0.527     0.149     0.051      108    12.8
   precuneus
    975    856   2003  2.660 0.591     0.167     0.063       27     2.8
   rostralanteriorcingulate
   8524   6942  13736  2.121 0.581     0.163     0.047      168    16.2
   rostralmiddlefrontal
   9820   7927  17866  2.426 0.605     0.150     0.043      144    16.4
   superiorfrontal
   8910   6920  12666  1.952 0.561     0.134     0.033      102    11.5
   superiorparietal
   5164   4064   9880  2.602 0.579     0.141     0.041      129     8.5
   superiortemporal
   4538   3307   6832  2.129 0.591     0.140     0.035       63     6.4
   supramarginal
    395    426    864  2.488 0.541     0.199     0.057        6     0.9
   frontalpole
    612    699   2018  3.610 0.559     0.213     0.073       17     2.2
   temporalpole
    479    330    680  2.330 0.353     0.110     0.024        3     0.5
   transversetemporal
   3442   1950   6183  2.886 0.890     0.376     1.131      154   291.0  insula
[user@localhost label]$ aparcstats2table --hemi rh --subjects
FERNANDORODRIGUES --parc aparcpial --meas area -t
rh_FERNANDORODRIGUES.aparc.surface.pial.txt
Number of subjects : 1
Building the table..
ERROR: cannot find
/home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/rh.aparcpial.stats
Use --skip flag if you want to continue in such cases


Maybe is the mris_anatomical_stats that has something wrong? I've been
using the command for Brodmann Areas and just tried to adapt it to
aparc. For BA I've also had to run label2label and had to create a new
BA.annot but that was because I had to get the thresholded BA values,
I think this doesn't apply to aparc. From aparc I only want to get
surface area based on the pial surface.

Thank you,
Andreia


Quoting Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>:

> Hi Andreia,
> If you remove the underscore from aparc_pial for the --parc flag in the
> aparcstats2table command, that should do the trick.
> -Louis
>
> On Wed, 26 Mar 2014, _andre...@sapo.pt wrote:
>
>> Hello list,
>>
>> I'm trying to get aparc surface area from the pial surface in a table
>> using aparcstats2table but I'm not being able to...
>>
>> I've already created the file aparc_pial.stats inside the stats dir
>> running the following command line from the subjects's label dir:
>>
>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
>> ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial
>>
>> And if I open the aparc_pial.stats file the surfaces are bigger then
>> in aparc (white matter).
>>
>> But when I try to get the table using:
>>
>> aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial
>> --meas area -t rh_aparc_surface_pial.txt
>>
>> I get the message:
>>
>> Number of subjects : 1
>> Building the table..
>> ERROR: cannot find
>> /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats
>> Use --skip flag if you want to continue in such cases
>>
>> What's wrong?
>>
>> Thank you,
>> Andreia
>>
>>
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>>
>>
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