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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