Hi Antonella,
those regions should be compiled in the stats/aparc.annot.ctab file that should be easy to import into excel or other packages for analsys and plotting.
cheers Bruce
On Mon, 4 Jul 2011, Antonella Kis wrote:
Good morning Bruce,
I posted my message also to the list and I will appreciate any help I can get ASAP.
I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished the recon-all step and qcache -all. I was able to display the thickness map but I would like to get a quatitative measure of cortical thickenss for my subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, 5 lateral temporal, 11 frontal, etc) and display this data in a table where I want to include the number of vertices and the cortical tickness for different regions:
caudalanteriorcingulate, caudalmiddlefrontal, cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital Region R unknown bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital
I believe the thickness data is stored in lh. thickness and I should be able to read it in matlab but I am not very shure how. Also I want to estimate the cortical thickness for gyral based regions of in terest ROIs. The gyral-based ROIs should be derived from an automated labeling system tha t subdivides the cerebral cortex on volumetric MRI into 34 neuroanatomical regions per hemisphere. I don't know how to do this so would you advise/teach me please? Many thanks for your valuable help! Antonella
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Thank you very much Bruce!
The only files that I have in stats directory after running recon-all and qcache -al are the following:
lh.aparc.a2009s.stats lh.entorhinal_exvivo.stats rh.curv.stats lh.aparc.stats rh.aparc.a2009s.stats rh.entorhinal_exvivo.stats lh.BA.stats rh.aparc.stats wmparc.stats
As you can see there is no aparc.annot.ctab file but if I open rh.aparc.stats and rh.aparc.a2009s.stats I can find some information about cortical thickness. Is this data OK to be used for my cortical thickness measurements?
Thank you very much! Antonella
Hi Antonella,
those regions should be compiled in the stats/aparc.annot.ctab file that should be easy to import into excel or other packages for analsys and plotting.
cheers Bruce
On Mon, 4 Jul 2011, Antonella Kis wrote:
Good morning Bruce,
I posted my message also to the list and I will appreciate any help I can get ASAP.
I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished the recon-all step and qcache -all. I was able to display the thickness map but I would like to get a quatitative measure of cortical thickenss for my subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, 5 lateral temporal, 11 frontal, etc) and display this data in a table where I want to include the number of vertices and the cortical tickness for different regions:
caudalanteriorcingulate, caudalmiddlefrontal, cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital Region R unknown bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital
I believe the thickness data is stored in lh. thickness and I should be able to read it in matlab but I am not very shure how. Also I want to estimate the cortical thickness for gyral based regions of in terest ROIs. The gyral-based ROIs should be derived from an automated labeling system tha t subdivides the cerebral cortex on volumetric MRI into 34 neuroanatomical regions per hemisphere. I don't know how to do this so would you advise/teach me please? Many thanks for your valuable help! Antonella
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
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.
________________________________
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
Yes
On Jul 4, 2011, at 2:12 PM, Antonella Kis antonella.kis@sickkids.ca wrote:
Thank you very much Bruce!
The only files that I have in stats directory after running recon-all and qcache -al are the following:
lh.aparc.a2009s.stats lh.entorhinal_exvivo.stats rh.curv.stats lh.aparc.stats rh.aparc.a2009s.stats rh.entorhinal_exvivo.stats lh.BA.stats rh.aparc.stats wmparc.stats
As you can see there is no aparc.annot.ctab file but if I open rh.aparc.stats and rh.aparc.a2009s.stats I can find some information about cortical thickness. Is this data OK to be used for my cortical thickness measurements?
Thank you very much! Antonella
Hi Antonella,
those regions should be compiled in the stats/aparc.annot.ctab file that should be easy to import into excel or other packages for analsys and plotting.
cheers Bruce
On Mon, 4 Jul 2011, Antonella Kis wrote:
Good morning Bruce,
I posted my message also to the list and I will appreciate any help I can get ASAP.
I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished the recon-all step and qcache -all. I was able to display the thickness map but I would like to get a quatitative measure of cortical thickenss for my subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, 5 lateral temporal, 11 frontal, etc) and display this data in a table where I want to include the number of vertices and the cortical tickness for different regions:
caudalanteriorcingulate, caudalmiddlefrontal, cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital Region R unknown bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula
MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital
I believe the thickness data is stored in lh. thickness and I should be able to read it in matlab but I am not very shure how. Also I want to estimate the cortical thickness for gyral based regions of in terest ROIs. The gyral-based ROIs should be derived from an automated labeling system tha t subdivides the cerebral cortex on volumetric MRI into 34 neuroanatomical regions per hemisphere. I don't know how to do this so would you advise/teach me please? Many thanks for your valuable help! Antonella
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
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.
This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Bruce Fischl