Hi,
Yes, sorry! I copied the error message from terminal, but copied the command
from my script so I copied the error message for the wrong hemisphere. I
apologise for the confusion.
I've attached the terminal output (I've put ##### at the lines above the error
message) and the script I use in this email.
Thank you for all your help!
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Thursday, November 5, 2020 9:44 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file
Is that the right error msg? It says it can't find the RH, but you are running
it with LH. Can you post the entire terminal output?
On 11/3/2020 2:00 PM, Chan, Shi Yu wrote:
Hi FreeSurfer Developers,
I'm trying to calculate cortical thickness statistics from the Yeo 17 Network
cortical parcellation and have used mri_surf2surf to get the .annot files for
each subject.
However, when I run mris_anatomical_stats, I get an error:
ERROR: stating file
subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot
It seems like the "sub-001/label" portion is repeated.
The command I use for mris_anatomical_stats is:
mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f
sub-001/stats/lh.Yeo_17Networks.stats -b -a
sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white
The command still runs despite the error, and outputs the stats files
accordingly, so I'm not sure how important this error is, but I can't figure
out how to fix it.
This is a similar issue to:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html but
I've checked $SUBJECTS_DIR, and it is correct. If I run ls
$SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri
stats labels etc)
Any help would be much appreciated! Thank you!
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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PHS009090:freesurfer pnlmcleaneeg$ bash extractYeo17.sh
/Volumes/SY_MRI/freesurfer/recon_unedited
sub-001_ses-01
Setting mapmethod to nnf
7.1.1
setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh
--sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
sysname Darwin
hostname PHS009090
machine x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-01
trgval =
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.sphere.reg
Loading source data
Reading surface file
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.orig
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Reading target surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (134953)
Surf2Surf: Dividing by number of hits (134953)
INFO: nSrcLost = 0
nTrg121 = 134953, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 1, nSrcLost = 0, nSrcMulti = 10241, MnSrcMultiHits = 13.1776
Saving target data
Converting to target annot
Saving to target annot
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
Setting mapmethod to nnf
7.1.1
setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi lh
--sval-annot
fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
sysname Darwin
hostname PHS009090
machine x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-01
trgval =
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.sphere.reg
Loading source data
Reading surface file
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/lh.orig
reading colortable from annotation file...
colortable with 115 entries read (originally MyColorLUT)
Reading target surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (134953)
Surf2Surf: Dividing by number of hits (134953)
INFO: nSrcLost = 0
nTrg121 = 134953, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 1, nSrcLost = 0, nSrcMulti = 10241, MnSrcMultiHits = 13.1776
Saving target data
Converting to target annot
Saving to target annot
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using sub-001_ses-01/label/lh.cortex.label as mask to calc cortex
NumVert, SurfArea and MeanThickness.
computing statistics for each annotation in
sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot.
reading volume
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/mri/wm.mgz...
reading input surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 252202
Total vertex volume 248594 (mask=0)
reading input pial surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.pial...
reading input white surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.white...
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Saving annotation colortable sub-001_ses-01/label/lh.Yeo_17Networks.annot.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
#############
ERROR: stating file
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/sub-001_ses-01/label/lh.Yeo2011_17Networks_N1000.annot
atlas_icv (eTIV) = 1636252 mm^3 (det: 1.190590 )
computing (and caching) brain volume statistics
ComputeBrainVolumeStats using version with fixed volume (VoxelVol=1)
lhCtxGM: 247833.745 (247410.000) diff= 423.7 pctdiff= 0.171
rhCtxGM: 243244.171 (243051.000) diff= 193.2 pctdiff= 0.079
lhCtxWM: 254127.207 (253936.000) diff= 191.2 pctdiff= 0.075
rhCtxWM: 249922.704 (250917.000) diff= -994.3 pctdiff=-0.398
SubCortGMVol 61111.000
SupraTentVol: 1071693.828 (1069672.000) diff= 2021.8 pctdiff= 0.189
SupraTentVolNotVent: 1058485.828 (1056464.000) diff= 2021.8 pctdiff= 0.191
BrainSegVol: 1219407.000 (1216197.000) diff= 3210.0 pctdiff= 0.263
BrainSegVolNotVent: 1201816.000 (1201470.828) diff= 345.2 pctdiff= 0.029
CerebellumVol 145193.000
VentChorVol 13208.000
3rd4th5thCSF 4383.000
CSFVol 1173.000, OptChiasmVol 159.000
MaskVol 1773782.000
9440 6045 2467 0.949 1.492 0.083 0.027 88 9.4
FreeSurfer_Defined_Medial_Wall
11310 7462 17648 2.204 0.644 0.143 0.034 147 15.4
17Networks_1
8736 5818 11613 1.934 0.606 0.134 0.033 108 11.5
17Networks_2
10838 6888 16562 2.248 0.600 0.117 0.028 97 12.4
17Networks_3
8219 5446 14130 2.494 0.664 0.115 0.027 75 8.6
17Networks_4
7349 5012 12280 2.289 0.570 0.121 0.026 75 7.6
17Networks_5
7534 5051 13018 2.407 0.536 0.122 0.029 78 9.3
17Networks_6
7926 5470 16062 2.768 0.673 0.117 0.029 74 9.4
17Networks_7
5838 4066 12508 2.686 0.719 0.130 0.035 69 8.6
17Networks_8
5452 3872 16795 3.330 0.835 0.139 0.038 82 8.3
17Networks_9
5034 3520 12406 3.024 0.784 0.142 0.039 78 8.4
17Networks_10
2742 1857 4363 2.144 0.696 0.132 0.031 38 3.5
17Networks_11
8425 5703 15407 2.480 0.616 0.128 0.030 103 9.9
17Networks_12
6454 4488 13775 2.656 0.703 0.133 0.035 80 8.8
17Networks_13
3469 2415 8452 2.921 0.675 0.126 0.031 39 4.6
17Networks_14
2570 1729 5634 2.937 0.730 0.117 0.033 28 3.3
17Networks_15
10351 7215 22887 2.755 0.752 0.137 0.034 148 14.8
17Networks_16
13266 9192 32586 2.902 0.702 0.135 0.035 181 19.0
17Networks_17
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using sub-001_ses-01/label/lh.cortex.label as mask to calc cortex
NumVert, SurfArea and MeanThickness.
computing statistics for each annotation in
sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot.
reading volume
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/mri/wm.mgz...
reading input surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 252202
Total vertex volume 248594 (mask=0)
reading input pial surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.pial...
reading input white surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/lh.white...
reading colortable from annotation file...
colortable with 115 entries read (originally MyColorLUT)
Saving annotation colortable
sub-001_ses-01/label/lh.Yeo_17Networks_split.annot.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
###########
ERROR: stating file
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/sub-001_ses-01/label/lh.Yeo2011_17Networks_split.annot
atlas_icv (eTIV) = 1636252 mm^3 (det: 1.190590 )
52559 35397 90083 2.312 1.126 0.122 0.032 619 66.1
Background+FreeSurfer_Defined_Medial_Wall
705 467 782 1.671 0.346 0.131 0.037 7 1.0
17Networks_LH_VisCent_Striate
7843 5151 12546 2.274 0.654 0.140 0.033 100 10.2
17Networks_LH_VisCent_ExStr
1551 1075 1708 1.658 0.513 0.118 0.026 13 1.6
17Networks_LH_VisPeri_Striate
1710 1169 2568 2.161 0.636 0.141 0.035 26 2.4
17Networks_LH_VisPeri_ExStrInf
2652 1719 3542 1.953 0.506 0.133 0.030 31 3.0
17Networks_LH_VisPeri_ExStrSup
9161 5745 13875 2.224 0.595 0.119 0.030 87 11.0
17Networks_LH_SomMotA
1967 1265 2754 2.125 0.637 0.100 0.019 14 1.6
17Networks_LH_SomMotB_Cent
1462 1003 2859 2.799 0.690 0.137 0.039 16 2.2
17Networks_LH_SomMotB_S2
71 54 146 2.957 0.356 0.089 0.011 0 0.0
17Networks_LH_SomMotB_Ins
2003 1318 3220 2.399 0.483 0.102 0.021 15 1.5
17Networks_LH_SomMotB_Aud
1572 1051 2638 2.475 0.562 0.130 0.032 17 2.1
17Networks_LH_DorsAttnA_TempOcc
708 507 1352 2.369 0.622 0.124 0.024 7 0.8
17Networks_LH_DorsAttnA_ParOcc
2019 1375 3087 2.029 0.464 0.105 0.021 16 1.5
17Networks_LH_DorsAttnA_SPL
133 108 280 2.275 0.558 0.137 0.031 2 0.2
17Networks_LH_DorsAttnB_TempOcc
3214 2097 5463 2.414 0.517 0.124 0.029 35 3.8
17Networks_LH_DorsAttnB_PostC
1071 774 1729 2.445 0.432 0.113 0.023 7 1.1
17Networks_LH_DorsAttnB_FEF
78 51 171 2.614 0.387 0.101 0.024 1 0.1
17Networks_LH_DorsAttnB_PrCv
1556 1080 3432 2.628 0.619 0.133 0.034 19 2.2
17Networks_LH_SalVentAttnA_ParOper
606 420 1340 2.617 0.584 0.096 0.024 5 0.6
17Networks_LH_SalVentAttnA_PrCv
978 657 2207 3.226 0.877 0.096 0.030 7 1.2
17Networks_LH_SalVentAttnA_Ins
798 539 1083 2.583 0.541 0.119 0.027 5 0.9
17Networks_LH_SalVentAttnA_ParMed
879 623 1996 2.979 0.482 0.139 0.031 12 1.1
17Networks_LH_SalVentAttnA_FrMed
245 170 305 2.340 0.483 0.099 0.023 1 0.2
17Networks_LH_SalVentAttnB_IPL
29 21 123 3.598 0.523 0.183 0.042 1 0.0
17Networks_LH_SalVentAttnB_PFCd
1628 1172 3424 2.516 0.710 0.144 0.037 22 2.7
17Networks_LH_SalVentAttnB_PFCl
556 400 1149 2.629 0.647 0.116 0.023 5 0.6
17Networks_LH_SalVentAttnB_PFCv
98 65 277 3.121 0.511 0.139 0.049 1 0.2
17Networks_LH_SalVentAttnB_OFC
578 394 1195 2.926 0.696 0.115 0.030 4 0.7
17Networks_LH_SalVentAttnB_PFCmp
4359 3083 13349 3.346 0.831 0.138 0.037 64 6.6
17Networks_LH_Limbic_TempPole
3936 2741 9612 2.983 0.773 0.142 0.040 63 6.9
17Networks_LH_Limbic_OFC
464 330 875 2.411 0.587 0.147 0.034 8 0.8
17Networks_LH_ContA_Temp
1844 1232 3234 2.295 0.543 0.135 0.030 24 2.3
17Networks_LH_ContA_IPS
182 132 305 2.478 0.440 0.116 0.037 1 0.2
17Networks_LH_ContA_PFCd
1553 1051 2308 2.439 0.482 0.110 0.021 14 1.5
17Networks_LH_ContA_PFCl
477 322 924 2.510 0.648 0.127 0.031 6 0.5
17Networks_LH_ContA_PFClv
61 34 63 2.558 0.351 0.144 0.021 1 0.0
17Networks_LH_ContA_Cinga
280 221 870 2.984 0.582 0.170 0.039 5 0.4
17Networks_LH_ContB_Temp
689 475 1127 2.366 0.498 0.104 0.024 5 0.6
17Networks_LH_ContB_IPL
105 61 340 3.495 0.578 0.159 0.063 2 0.2
17Networks_LH_ContB_PFCd
501 355 969 2.399 0.545 0.120 0.034 6 0.6
17Networks_LH_ContB_PFCl
1341 928 2660 2.477 0.708 0.141 0.034 17 1.9
17Networks_LH_ContB_PFClv
75 59 206 3.140 0.221 0.137 0.031 0 0.1
17Networks_LH_ContB_PFCmp
1035 689 1583 2.092 0.550 0.130 0.034 13 1.6
17Networks_LH_ContC_pCun
438 257 390 1.691 0.519 0.170 0.037 12 0.6
17Networks_LH_ContC_Cingp
883 578 1558 2.365 0.738 0.127 0.027 11 1.0
17Networks_LH_DefaultA_IPL
1352 930 2250 2.470 0.498 0.108 0.022 11 1.2
17Networks_LH_DefaultA_PFCd
2095 1487 4659 2.829 0.713 0.137 0.032 27 2.8
17Networks_LH_DefaultA_PCC
2632 1898 6505 2.888 0.810 0.150 0.042 44 5.1
17Networks_LH_DefaultA_PFCm
3628 2530 8925 2.982 0.760 0.128 0.034 46 4.8
17Networks_LH_DefaultB_Temp
808 535 1536 2.607 0.619 0.114 0.025 8 0.7
17Networks_LH_DefaultB_IPL
2561 1783 6710 3.040 0.694 0.149 0.042 41 4.7
17Networks_LH_DefaultB_PFCd
543 371 1157 2.755 0.456 0.141 0.036 6 0.8
17Networks_LH_DefaultB_PFCl
1662 1183 4465 2.786 0.618 0.149 0.039 30 2.5
17Networks_LH_DefaultB_PFCv
81 52 158 2.533 0.804 0.080 0.019 1 0.1
17Networks_LH_DefaultC_IPL
305 217 512 2.813 0.454 0.120 0.039 3 0.5
17Networks_LH_DefaultC_Rsp
797 531 1761 3.041 0.715 0.105 0.025 6 0.9
17Networks_LH_DefaultC_PHC
1836 1317 4246 2.841 0.656 0.118 0.029 16 2.2
17Networks_LH_TempPar
Setting mapmethod to nnf
7.1.1
setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi rh
--sval-annot fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_N1000.annot
sysname Darwin
hostname PHS009090
machine x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-01
trgval =
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_N1000.annot
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
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/rh.sphere.reg
Loading source data
Reading surface file
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/rh.orig
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Reading target surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/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 (134397)
Surf2Surf: Dividing by number of hits (134397)
INFO: nSrcLost = 0
nTrg121 = 134397, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits = 13.1221
Saving target data
Converting to target annot
Saving to target annot
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_N1000.annot
Setting mapmethod to nnf
7.1.1
setenv SUBJECTS_DIR /Volumes/SY_MRI/freesurfer/recon_unedited
cd /Volumes/SY_MRI/freesurfer/recon_unedited
mri_surf2surf --srcsubject fsaverage5 --trgsubject sub-001_ses-01 --hemi rh
--sval-annot
fsaverage5/label/rh.Yeo2011_17Networks_N1000.split_components.annot --tval
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_split.annot
sysname Darwin
hostname PHS009090
machine x86_64
user pnlmcleaneeg
srcsubject = fsaverage5
srcval = (null)
srctype =
trgsubject = sub-001_ses-01
trgval =
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_split.annot
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
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/rh.sphere.reg
Loading source data
Reading surface file
/Volumes/SY_MRI/freesurfer/recon_unedited/fsaverage5/surf/rh.orig
reading colortable from annotation file...
colortable with 115 entries read (originally MyColorLUT)
Reading target surface reg
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/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 (134397)
Surf2Surf: Dividing by number of hits (134397)
INFO: nSrcLost = 0
nTrg121 = 134397, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits = 13.1221
Saving target data
Converting to target annot
Saving to target annot
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/rh.Yeo2011_17Networks_split.annot
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using sub-001_ses-01/label/rh.cortex.label as mask to calc cortex
NumVert, SurfArea and MeanThickness.
computing statistics for each annotation in
sub-001_ses-01/label/rh.Yeo2011_17Networks_N1000.annot.
reading volume
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/mri/wm.mgz...
reading input surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 246563
Total vertex volume 243804 (mask=0)
reading input pial surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.pial...
reading input white surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.white...
reading colortable from annotation file...
colortable with 18 entries read (originally MyColorLUT)
Saving annotation colortable sub-001_ses-01/label/rh.Yeo_17Networks.annot.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
#############
ERROR: stating file
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/sub-001_ses-01/label/rh.Yeo2011_17Networks_N1000.annot
atlas_icv (eTIV) = 1636252 mm^3 (det: 1.190590 )
9471 6078 2493 0.882 1.444 0.083 0.028 100 9.3
FreeSurfer_Defined_Medial_Wall
12896 8430 20043 2.230 0.632 0.137 0.032 152 16.8
17Networks_1
8466 5587 12040 2.083 0.612 0.129 0.033 91 11.2
17Networks_2
9327 5772 13576 2.180 0.634 0.108 0.026 74 9.6
17Networks_3
6921 4571 12139 2.522 0.680 0.113 0.027 60 7.5
17Networks_4
9984 6800 17622 2.363 0.633 0.127 0.030 110 12.0
17Networks_5
6263 4217 10468 2.278 0.602 0.117 0.026 60 6.4
17Networks_6
7902 5410 16219 2.678 0.686 0.120 0.031 79 9.6
17Networks_7
7980 5441 16747 2.644 0.723 0.130 0.032 94 10.4
17Networks_8
5740 3923 16117 3.279 0.805 0.133 0.038 77 8.4
17Networks_9
4318 2960 10541 2.886 0.851 0.134 0.038 65 7.3
17Networks_10
3264 2146 5332 2.212 0.654 0.138 0.036 47 4.7
17Networks_11
7347 4968 13311 2.456 0.665 0.126 0.029 86 8.9
17Networks_12
10382 7223 23208 2.655 0.738 0.133 0.034 133 13.8
17Networks_13
4575 3118 9511 2.774 0.672 0.120 0.029 49 5.5
17Networks_14
2445 1633 4814 2.598 0.691 0.112 0.027 24 2.5
17Networks_15
11130 7663 24354 2.662 0.789 0.133 0.034 156 14.6
17Networks_16
5986 4070 15268 2.949 0.737 0.133 0.035 84 8.0
17Networks_17
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using sub-001_ses-01/label/rh.cortex.label as mask to calc cortex
NumVert, SurfArea and MeanThickness.
computing statistics for each annotation in
sub-001_ses-01/label/rh.Yeo2011_17Networks_split.annot.
reading volume
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/mri/wm.mgz...
reading input surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 246563
Total vertex volume 243804 (mask=0)
reading input pial surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.pial...
reading input white surface
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/surf/rh.white...
reading colortable from annotation file...
colortable with 115 entries read (originally MyColorLUT)
Saving annotation colortable
sub-001_ses-01/label/rh.Yeo_17Networks_split.annot.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
##############
ERROR: stating file
/Volumes/SY_MRI/freesurfer/recon_unedited/sub-001_ses-01/label/sub-001_ses-01/label/rh.Yeo2011_17Networks_split.annot
atlas_icv (eTIV) = 1636252 mm^3 (det: 1.190590 )
52621 35186 90396 2.278 1.139 0.119 0.031 607 63.3
Background+FreeSurfer_Defined_Medial_Wall
814 487 953 1.888 0.461 0.138 0.041 10 1.3
17Networks_RH_VisCent_Striate
9107 5996 14417 2.276 0.630 0.137 0.031 108 11.3
17Networks_RH_VisCent_ExStr
1349 906 1370 1.771 0.470 0.114 0.028 10 1.6
17Networks_RH_VisPeri_Striate
1632 1051 2639 2.352 0.630 0.134 0.038 21 2.6
17Networks_RH_VisPeri_ExStrInf
2896 1899 4636 2.251 0.552 0.138 0.031 34 3.7
17Networks_RH_VisPeri_ExStrSup
7818 4776 11181 2.147 0.628 0.108 0.026 64 8.2
17Networks_RH_SomMotA
1604 1073 2009 1.908 0.530 0.102 0.022 10 1.5
17Networks_RH_SomMotB_Cent
1367 931 2593 2.784 0.552 0.124 0.035 14 2.0
17Networks_RH_SomMotB_S2
94 70 165 2.649 0.344 0.109 0.017 0 0.1
17Networks_RH_SomMotB_Ins
1548 978 2950 2.705 0.492 0.109 0.023 14 1.3
17Networks_RH_SomMotB_Aud
1791 1251 3306 2.602 0.538 0.142 0.038 20 3.0
17Networks_RH_DorsAttnA_TempOcc
1259 830 2514 2.541 0.614 0.138 0.032 19 1.5
17Networks_RH_DorsAttnA_ParOcc
3082 2078 4563 1.999 0.486 0.120 0.026 30 3.4
17Networks_RH_DorsAttnA_SPL
97 67 135 2.309 0.506 0.079 0.014 1 0.0
17Networks_RH_DorsAttnB_TempOcc
2634 1769 4212 2.210 0.649 0.123 0.026 27 2.9
17Networks_RH_DorsAttnB_PostC
758 525 1091 2.167 0.416 0.110 0.025 6 0.7
17Networks_RH_DorsAttnB_FEF
135 94 331 2.744 0.275 0.120 0.026 2 0.2
17Networks_RH_DorsAttnB_PrCv
1313 867 2343 2.478 0.561 0.120 0.027 15 1.4
17Networks_RH_SalVentAttnA_ParOper
142 85 290 2.762 0.405 0.192 0.131 3 0.9
17Networks_RH_SalVentAttnA_PrC
603 409 1441 2.692 0.579 0.121 0.028 8 0.6
17Networks_RH_SalVentAttnA_PrCv
963 690 2103 3.140 0.727 0.110 0.031 9 1.1
17Networks_RH_SalVentAttnA_Ins
712 493 851 2.189 0.512 0.108 0.018 4 0.6
17Networks_RH_SalVentAttnA_ParMed
1084 757 2309 2.677 0.579 0.135 0.035 11 1.6
17Networks_RH_SalVentAttnA_FrMed
295 220 699 2.912 0.585 0.142 0.033 4 0.3
17Networks_RH_SalVentAttnB_IPL
125 92 280 2.693 0.444 0.144 0.030 1 0.1
17Networks_RH_SalVentAttnB_PFCd
1855 1255 3586 2.486 0.603 0.133 0.036 23 2.6
17Networks_RH_SalVentAttnB_PFCl
246 162 570 2.477 0.583 0.177 0.058 6 0.5
17Networks_RH_SalVentAttnB_PFClv
1082 744 2137 2.825 0.783 0.118 0.025 9 1.1
17Networks_RH_SalVentAttnB_PFCv
783 540 1728 2.755 0.704 0.126 0.031 10 1.0
17Networks_RH_SalVentAttnB_PFCmp
61 33 63 1.944 0.521 0.176 0.024 2 0.1
17Networks_RH_SalVentAttnB_Cinga
4600 3170 13247 3.299 0.797 0.135 0.037 60 6.7
17Networks_RH_Limbic_TempPole
3157 2171 7629 2.819 0.831 0.131 0.039 48 5.4
17Networks_RH_Limbic_OFC
243 177 507 2.450 0.584 0.135 0.021 3 0.2
17Networks_RH_ContA_Temp
1601 1048 2515 2.276 0.649 0.115 0.020 16 1.3
17Networks_RH_ContA_IPS
138 88 318 2.691 0.442 0.157 0.043 3 0.2
17Networks_RH_ContA_PFCd
1805 1236 2914 2.458 0.475 0.113 0.025 15 1.8
17Networks_RH_ContA_PFCl
39 24 21 1.366 0.265 0.147 0.039 1 0.1
17Networks_RH_ContA_Cinga
748 559 1613 2.984 0.584 0.120 0.026 5 0.7
17Networks_RH_ContB_Temp
1193 814 2562 2.503 0.629 0.118 0.027 12 1.3
17Networks_RH_ContB_IPL
1551 1089 3544 2.670 0.669 0.137 0.036 18 2.4
17Networks_RH_ContB_PFCld
2610 1813 5431 2.370 0.687 0.146 0.037 43 4.1
17Networks_RH_ContB_PFClv
223 154 676 3.476 0.435 0.106 0.021 2 0.2
17Networks_RH_ContB_PFCmp
1308 891 2215 2.245 0.547 0.133 0.030 16 1.9
17Networks_RH_ContC_pCun
385 236 313 1.719 0.434 0.170 0.043 9 0.5
17Networks_RH_ContC_Cingp
364 247 906 2.662 0.541 0.136 0.047 6 0.8
17Networks_RH_DefaultA_Temp
1132 787 2178 2.531 0.598 0.131 0.040 15 1.6
17Networks_RH_DefaultA_IPL
1133 767 2357 2.851 0.533 0.114 0.026 11 1.2
17Networks_RH_DefaultA_PFCd
1658 1161 3217 2.545 0.776 0.124 0.024 18 1.6
17Networks_RH_DefaultA_PCC
3289 2253 7150 2.508 0.891 0.136 0.038 51 5.2
17Networks_RH_DefaultA_PFCm
324 249 739 2.628 0.451 0.097 0.017 2 0.2
17Networks_RH_DefaultB_Temp
706 484 1692 2.911 0.762 0.111 0.024 6 0.8
17Networks_RH_DefaultB_AntTemp
1367 881 3803 3.144 0.751 0.137 0.037 20 2.0
17Networks_RH_DefaultB_PFCd
726 493 2065 3.037 0.675 0.165 0.054 17 1.6
17Networks_RH_DefaultB_PFCv
173 127 430 2.416 0.588 0.134 0.023 2 0.1
17Networks_RH_DefaultC_IPL
341 242 687 2.904 0.479 0.109 0.030 3 0.3
17Networks_RH_DefaultC_Rsp
478 323 939 2.634 0.675 0.098 0.025 4 0.4
17Networks_RH_DefaultC_PHC
3235 2210 6275 2.724 0.638 0.120 0.029 33 3.9
17Networks_RH_TempPar#### Annotation File
#lh.Yeo2011_17Networks_N1000.annot
## Set up freesurfer
set -e
root=/Volumes/SY_MRI/freesurfer/ ### change this to real root
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
## Change to correct folder
cd $root/recon_unedited/ #### change this
export SUBJECTS_DIR=`pwd`
echo $SUBJECTS_DIR
####
## left hemisphere
for sub in sub-3??_*; do
#for sub in sub-001_ses-01; do
echo $sub
for hemi in lh rh; do
mri_surf2surf --srcsubject fsaverage5 --trgsubject $sub --hemi $hemi \
--sval-annot fsaverage5/label/$hemi.Yeo2011_17Networks_N1000.annot \
--tval $SUBJECTS_DIR/$sub/label/$hemi.Yeo2011_17Networks_N1000.annot
mri_surf2surf --srcsubject fsaverage5 --trgsubject $sub --hemi $hemi \
--sval-annot fsaverage5/label/$hemi.Yeo2011_17Networks_N1000.split_components.annot \
--tval $SUBJECTS_DIR/$sub/label/$hemi.Yeo2011_17Networks_split.annot
#mris_anatomical_stats -th3 -mgz -a $sub/label/$hemi.Yeo2011_17Networks_N1000.annot -f $sub/stats/$hemi.Yeo_17Networks2.stats -b -c $sub/label/$hemi.Yeo_17Networks.annot.ctab $sub $hemi
mris_anatomical_stats -th3 -mgz -cortex $sub/label/$hemi.cortex.label -a $sub/label/$hemi.Yeo2011_17Networks_N1000.annot -f $sub/stats/$hemi.Yeo_17Networks.stats -b -c $sub/label/$hemi.Yeo_17Networks.annot.ctab $sub $hemi white
mris_anatomical_stats -th3 -mgz -cortex $sub/label/$hemi.cortex.label -a $sub/label/$hemi.Yeo2011_17Networks_split.annot -f $sub/stats/$hemi.Yeo_17Networks_split.stats -b -c $sub/label/$hemi.Yeo_17Networks_split.annot.ctab $sub $hemi white
done
done
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