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 <gr...@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 <fis...@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 < >>> fis...@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 >>> <gr...@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 >>> <gr...@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 >>> > <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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.radai...@hu.edu.jo >>> <mailto:ali.radai...@hu.edu.jo> >>> > <mailto:ali.radai...@hu.edu.jo >>> <mailto:ali.radai...@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 >>> > gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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.radai...@hu.edu.jo >>> <mailto:ali.radai...@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 >>> gr...@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.radai...@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.radai...@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.radai...@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.radai...@hu.edu.jo <ali.radai...@hu.edu.jo> * > *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>* > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radai...@hu.edu.jo <ali.radai...@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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