Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay.
Thanks, Ali
On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote:
mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name
On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote: what is your surf2surf command?
On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas,Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas.
I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis.
Thanks, Ali
On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: I can't understand what you are asking. Can you elaborate?
On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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-- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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.
-- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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.
sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote:
Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay.
Thanks, Ali
On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks _N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote: what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis. Thanks, Ali On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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 -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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.-- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
Hi Bruce,
I have used the following command line:
mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
and got the following:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 15766121 15766121.0 Seg0000 2 2 182848 182848.0 Seg0002 3 3 215011 215011.0 Seg0003 4 4 6547 6547.0 Seg0004 5 5 572 572.0 Seg0005 6 7 14053 14053.0 Seg0007 7 8 47779 47779.0 Seg0008 8 10 7151 7151.0 Seg0010 9 11 4464 4464.0 Seg0011 10 12 5264 5264.0 Seg0012 11 13 1680 1680.0 Seg0013 12 14 889 889.0 Seg0014 13 15 1731 1731.0 Seg0015 14 16 17307 17307.0 Seg0016 15 17 3842 3842.0 Seg0017 16 18 1106 1106.0 Seg0018 17 24 1228 1228.0 Seg0024 18 26 656 656.0 Seg0026 19 28 3941 3941.0 Seg0028 20 30 26 26.0 Seg0030 21 31 1222 1222.0 Seg0031 22 41 191593 191593.0 Seg0041 23 42 200955 200955.0 Seg0042 24 43 6321 6321.0 Seg0043 25 44 295 295.0 Seg0044 26 46 16106 16106.0 Seg0046 27 47 46472 46472.0 Seg0047 28 49 6684 6684.0 Seg0049 29 50 4308 4308.0 Seg0050 30 51 5099 5099.0 Seg0051 31 52 1459 1459.0 Seg0052 32 53 4005 4005.0 Seg0053 33 54 988 988.0 Seg0054 34 58 633 633.0 Seg0058 35 60 3554 3554.0 Seg0060 36 62 36 36.0 Seg0062 37 63 1518 1518.0 Seg0063 38 72 18 18.0 Seg0072 39 77 1040 1040.0 Seg0077 40 80 22 22.0 Seg0080 41 85 124 124.0 Seg0085 42 251 721 721.0 Seg0251 43 252 403 403.0 Seg0252 44 253 322 322.0 Seg0253 45 254 360 360.0 Seg0254 46 255 742 742.0 Seg0255
However, I don't see the segmentation names (cortical parts). is my command true/ complete or not? These are 46 segmentations although I am using 17 networks cortical parcellation, is this true? Can I add anything to make the output more informative?. Also can I get any surface area ....etc?
Many thanks in advance. Ali
On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote:
Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay.
Thanks, Ali
On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks _N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote: what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis. Thanks, Ali On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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 -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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.-- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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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.
You should not use both --seg and --annot. What are you trying to accomplish?
On 10/2/15 3:34 AM, Ali Radaideh wrote:
Hi Bruce,
I have used the following command line:
mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
and got the following:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 15766121 15766121.0 Seg0000 2 2 182848 182848.0 Seg0002 3 3 215011 215011.0 Seg0003 4 4 6547 6547.0 Seg0004 5 5 572 572.0 Seg0005 6 7 14053 14053.0 Seg0007 7 8 47779 47779.0 Seg0008 8 10 7151 7151.0 Seg0010 9 11 4464 4464.0 Seg0011 10 12 5264 5264.0 Seg0012 11 13 1680 1680.0 Seg0013 12 14 889 889.0 Seg0014 13 15 1731 1731.0 Seg0015 14 16 17307 17307.0 Seg0016 15 17 3842 3842.0 Seg0017 16 18 1106 1106.0 Seg0018 17 24 1228 1228.0 Seg0024 18 26 656 656.0 Seg0026 19 28 3941 3941.0 Seg0028 20 30 26 26.0 Seg0030 21 31 1222 1222.0 Seg0031 22 41 191593 191593.0 Seg0041 23 42 200955 200955.0 Seg0042 24 43 6321 6321.0 Seg0043 25 44 295 295.0 Seg0044 26 46 16106 16106.0 Seg0046 27 47 46472 46472.0 Seg0047 28 49 6684 6684.0 Seg0049 29 50 4308 4308.0 Seg0050 30 51 5099 5099.0 Seg0051 31 52 1459 1459.0 Seg0052 32 53 4005 4005.0 Seg0053 33 54 988 988.0 Seg0054 34 58 633 633.0 Seg0058 35 60 3554 3554.0 Seg0060 36 62 36 36.0 Seg0062 37 63 1518 1518.0 Seg0063 38 72 18 18.0 Seg0072 39 77 1040 1040.0 Seg0077 40 80 22 22.0 Seg0080 41 85 124 124.0 Seg0085 42 251 721 721.0 Seg0251 43 252 403 403.0 Seg0252 44 253 322 322.0 Seg0253 45 254 360 360.0 Seg0254 46 255 742 742.0 Seg0255
However, I don't see the segmentation names (cortical parts). is my command true/ complete or not? These are 46 segmentations although I am using 17 networks cortical parcellation, is this true? Can I add anything to make the output more informative?. Also can I get any surface area ....etc?
Many thanks in advance. Ali
On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote: Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay. Thanks, Ali On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do? On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks _N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis. Thanks, Ali On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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I am trying to extract the cortical volume, thickness, and area based on these 17Networks cortical parcellation.
Thanks, Ali
On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You should not use both --seg and --annot. What are you trying to accomplish?
On 10/2/15 3:34 AM, Ali Radaideh wrote:
Hi Bruce,
I have used the following command line:
mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
and got the following:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 15766121 15766121.0 Seg0000 2 2 182848 182848.0 Seg0002 3 3 215011 215011.0 Seg0003 4 4 6547 6547.0 Seg0004 5 5 572 572.0 Seg0005 6 7 14053 14053.0 Seg0007 7 8 47779 47779.0 Seg0008 8 10 7151 7151.0 Seg0010 9 11 4464 4464.0 Seg0011 10 12 5264 5264.0 Seg0012 11 13 1680 1680.0 Seg0013 12 14 889 889.0 Seg0014 13 15 1731 1731.0 Seg0015 14 16 17307 17307.0 Seg0016 15 17 3842 3842.0 Seg0017 16 18 1106 1106.0 Seg0018 17 24 1228 1228.0 Seg0024 18 26 656 656.0 Seg0026 19 28 3941 3941.0 Seg0028 20 30 26 26.0 Seg0030 21 31 1222 1222.0 Seg0031 22 41 191593 191593.0 Seg0041 23 42 200955 200955.0 Seg0042 24 43 6321 6321.0 Seg0043 25 44 295 295.0 Seg0044 26 46 16106 16106.0 Seg0046 27 47 46472 46472.0 Seg0047 28 49 6684 6684.0 Seg0049 29 50 4308 4308.0 Seg0050 30 51 5099 5099.0 Seg0051 31 52 1459 1459.0 Seg0052 32 53 4005 4005.0 Seg0053 33 54 988 988.0 Seg0054 34 58 633 633.0 Seg0058 35 60 3554 3554.0 Seg0060 36 62 36 36.0 Seg0062 37 63 1518 1518.0 Seg0063 38 72 18 18.0 Seg0072 39 77 1040 1040.0 Seg0077 40 80 22 22.0 Seg0080 41 85 124 124.0 Seg0085 42 251 721 721.0 Seg0251 43 252 403 403.0 Seg0252 44 253 322 322.0 Seg0253 45 254 360 360.0 Seg0254 46 255 742 742.0 Seg0255
However, I don't see the segmentation names (cortical parts). is my command true/ complete or not? These are 46 segmentations although I am using 17 networks cortical parcellation, is this true? Can I add anything to make the output more informative?. Also can I get any surface area ....etc?
Many thanks in advance. Ali
On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote:
Can we get any stats from this type of parcellation? I only can see two
annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay.
Thanks, Ali
On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks _N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote: what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis. Thanks, Ali On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E > Outgoing: >
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >
_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo > / > /webpage:
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > 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 -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ 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.-- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
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*Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo ali.radaideh@hu.edu.jo * *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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.
Try
cd $SUBJECTS_DIR/subject/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.yeo.stats -b -a ../label/lh.yeo2011_17Networks_N1000.annot -c ../label/aparc.annot.ctab subject lh white
On 10/2/15 12:19 PM, Ali Radaideh wrote:
I am trying to extract the cortical volume, thickness, and area based on these 17Networks cortical parcellation.
Thanks, Ali
On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You should not use both --seg and --annot. What are you trying to accomplish? On 10/2/15 3:34 AM, Ali Radaideh wrote:Hi Bruce, I have used the following command line: mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum and got the following: # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 0 15766121 15766121.0 Seg0000 2 2 182848 182848.0 Seg0002 3 3 215011 215011.0 Seg0003 4 4 6547 6547.0 Seg0004 5 5 572 572.0 Seg0005 6 7 14053 14053.0 Seg0007 7 8 47779 47779.0 Seg0008 8 10 7151 7151.0 Seg0010 9 11 4464 4464.0 Seg0011 10 12 5264 5264.0 Seg0012 11 13 1680 1680.0 Seg0013 12 14 889 889.0 Seg0014 13 15 1731 1731.0 Seg0015 14 16 17307 17307.0 Seg0016 15 17 3842 3842.0 Seg0017 16 18 1106 1106.0 Seg0018 17 24 1228 1228.0 Seg0024 18 26 656 656.0 Seg0026 19 28 3941 3941.0 Seg0028 20 30 26 26.0 Seg0030 21 31 1222 1222.0 Seg0031 22 41 191593 191593.0 Seg0041 23 42 200955 200955.0 Seg0042 24 43 6321 6321.0 Seg0043 25 44 295 295.0 Seg0044 26 46 16106 16106.0 Seg0046 27 47 46472 46472.0 Seg0047 28 49 6684 6684.0 Seg0049 29 50 4308 4308.0 Seg0050 30 51 5099 5099.0 Seg0051 31 52 1459 1459.0 Seg0052 32 53 4005 4005.0 Seg0053 33 54 988 988.0 Seg0054 34 58 633 633.0 Seg0058 35 60 3554 3554.0 Seg0060 36 62 36 36.0 Seg0062 37 63 1518 1518.0 Seg0063 38 72 18 18.0 Seg0072 39 77 1040 1040.0 Seg0077 40 80 22 22.0 Seg0080 41 85 124 124.0 Seg0085 42 251 721 721.0 Seg0251 43 252 403 403.0 Seg0252 44 253 322 322.0 Seg0253 45 254 360 360.0 Seg0254 46 255 742 742.0 Seg0255 However, I don't see the segmentation names (cortical parts). is my command true/ complete or not? These are 46 segmentations although I am using 17 networks cortical parcellation, is this true? Can I add anything to make the output more informative?. Also can I get any surface area ....etc? Many thanks in advance. Ali On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: sure, you can use mri_segstats to get stats from it Bruce On Thu, 1 Oct 2015, Ali Radaideh wrote: Can we get any stats from this type of parcellation? I only can see two annotation files after running the mri_surf2surf command and these can be loaded tksurfer as an overlay. Thanks, Ali On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: that will generate a parcellation on the individual subject surface of Thomas Yeo's 17-network clustering. It won't do anything with the thickness though. What are you trying to do? On Tue, 29 Sep 2015, Ali Radaideh wrote: mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks _N1000.annot --tval $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot scz10 is my subject name On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is your surf2surf command? On 9/28/15 5:11 PM, Ali Radaideh wrote: Dear Douglas, Thanks for your email. I meant to say that after running the recon-all, i ran the sur2surf command to get the cortical parcellation using Thomas Yeo Atlas. I thought that the extracted cortical thickness after running the surf2surf command will be different from the one extracted before running the command. But, Bruce kindly replied to my email saying that it is the same if it is calculated on vertex-wise basis. Thanks, Ali On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I can't understand what you are asking. Can you elaborate? On 09/28/2015 01:51 PM, Ali Radaideh wrote: > Thanks alot Douglas, > > Yes it is there but after checking it many time I found it corrupted > for some subjects due to copying them many times between machines. > > But May I ask you some thing related. I have just posted a question > regarding getting the cortical thickness after running the surf2surf > command (17 networks cortical parcellation). Now I found the stats > file not updated after running this command only the annotation files > in label folder. [rh.Yeo2011_17Networks_N1000.annot]. We thought that > using Yeo Atlas will give slightly different cortical thickness, are > we correct? > > Thanks, > Ali > > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > does that file exist? > > On 09/28/2015 01:05 PM, Ali Radaideh wrote: > > Dear FreeSurfer experts, > > After finishing the recon-all, I am trying to extract the cortical > > thickness for each subject and group them into one table but > > unfortunately i keep getting the following error: > > > > rh.aparc.DKTatlas40.stats is not found or is too small to be a > valid > > statsfile > > Use --skip flag to automatically skip bad stats files > > > > i tried to change the stats file (e.g I used aparc.a2009s) but I got > > the same error. > > > > I tried each brain alone and also got the same error. > > > > Any ideas please > > Thanks, > > Ali > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> <mailto:ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo>> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo <mailto:ali.radaideh@hu.edu.jo> / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.-- /Ali M. Al-Radaideh. PhD Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 3903333 ext.5422, 5355, 5364 Email: ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
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