Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks, Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Thu, 27 Mar 2014 11:31:13 +0000 De: _andreia_@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, vinke@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 vinke@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, _andreia_@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
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 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
----- Fim de mensagem reenviada -----
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 greve@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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----- Fim de mensagem reenviada -----
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks, Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Thu, 27 Mar 2014 11:31:13 +0000 De: _andreia_@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, vinke@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 vinke@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, _andreia_@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
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 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
----- Fim de mensagem reenviada -----
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 greve@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
----- Fim de mensagem reenviada -----
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The values of the example are correct.
Thanks!
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks, Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Thu, 27 Mar 2014 11:31:13 +0000 De: _andreia_@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, vinke@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 vinke@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, _andreia_@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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and what do the surfaces look like in those regions? For the wm surface are to be larger it probably needs to be a lot less smooth
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The values of the example are correct.
Thanks!
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks, Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Thu, 27 Mar 2014 11:31:13 +0000 De: _andreia_@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, vinke@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 vinke@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, _andreia_@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 > > > _______________________________________________ > 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 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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How do I overlay aparc labels in tkmedit? I can load Brodmann area labels, but not aparc.
Thanks! Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
and what do the surfaces look like in those regions? For the wm surface are to be larger it probably needs to be a lot less smooth
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The values of the example are correct.
Thanks!
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote:
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks, Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Thu, 27 Mar 2014 11:31:13 +0000 De: _andreia_@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, vinke@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 vinke@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, _andreia_@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 >> >> >> _______________________________________________ >> 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 > 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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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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the easiest way is to just use the aparc+aseg.mgz
cheers Bruce On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
How do I overlay aparc labels in tkmedit? I can load Brodmann area labels, but not aparc.
Thanks! Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
and what do the surfaces look like in those regions? For the wm surface are to be larger it probably needs to be a lot less smooth
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The values of the example are correct.
Thanks!
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote: > Hello all, > > How do I get aparc stats (area) using the pial surface, please? > > Thanks, > Andreia > > > > ----- Mensagem encaminhada de _andreia_@sapo.pt ----- > Data: Thu, 27 Mar 2014 11:31:13 +0000 > De: _andreia_@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, > vinke@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 vinke@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, _andreia_@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 >>> >>> >>> _______________________________________________ >>> 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 >> 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 > > ----- Fim de mensagem reenviada ----- > > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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I cannot properly access my desktop PC today, tomorrow I'll give you feedback, However, with a corase inspection the surfaces look ok.
Thank you Bruce!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
the easiest way is to just use the aparc+aseg.mgz
cheers Bruce On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
How do I overlay aparc labels in tkmedit? I can load Brodmann area labels, but not aparc.
Thanks! Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
and what do the surfaces look like in those regions? For the wm surface are to be larger it probably needs to be a lot less smooth
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The values of the example are correct.
Thanks!
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be) and in your second you said white matter
cheers Bruce
On Sun, 30 Mar 2014, _andreia_@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels?
Thank you! Andreia
----- Mensagem encaminhada de _andreia_@sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_@sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer@nmr.mgh.harvard.edu
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
This only happens in these 3 labels and in both hemispheres. Is this expected?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
> try this > mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f > ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c > ../label/aparc.annot.ctab vrfp-oct11-anat lh pial > > > On 03/28/2014 06:31 AM, _andreia_@sapo.pt wrote: >> Hello all, >> >> How do I get aparc stats (area) using the pial surface, please? >> >> Thanks, >> Andreia >> >> >> >> ----- Mensagem encaminhada de _andreia_@sapo.pt ----- >> Data: Thu, 27 Mar 2014 11:31:13 +0000 >> De: _andreia_@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, >> vinke@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 vinke@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, _andreia_@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 >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> 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 >> >> ----- Fim de mensagem reenviada ----- >> >> _______________________________________________ >> 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 > greve@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
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