Hi Annie, I am a little unsure why this might happen. Did you inspect if $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot is correct?
Cheers, Thomas On Mon, May 18, 2015 at 1:52 PM, 陳昱潔 <poohann1...@gmail.com> wrote: > Hi Dr. Yeo : > > Thank you very much for helping us a lot! > I ran the command this below: > mri_surf2surf --srcsubject fsaverage5 --trgsubject 5204 --hemi lh \ > --sval-annot > $SUBJECTS_DIR/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot \ > --tval $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot > and after I ran this command: > mris_anatomical_stats -a > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot -b 5202 rh > All turned out > MRISreadAnnotationIntoArray: vertex index out of range: 892219914 > i=352E320A, in_array_size=153173 > annot file: > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot > MRISreadAnnotationIntoArray: vertex index out of range: 892219914 > i=352E320A, in_array_size=153173 > annot file: > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot > MRISreadAnnotationIntoArray: vertex index out of range: 892219914 > i=352E320A, in_array_size=153173 > annot file: > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot > MRISreadAnnotationIntoArray: vertex index out of range: 892219914 > i=352E320A, in_array_size=153173 > annot file: > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot > MRISreadAnnotationIntoArray: vertex index out of range: 892219914 > i=352E320A, in_array_size=153173 > > Best wishes, > Annie > > 2015-05-15 8:15 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: > >> Hi Annie, >> >> Can you tell us the exact mri_surf2surf command you use? >> >> Cheers, >> Thomas >> >> On Fri, May 15, 2015 at 5:24 PM, 陳昱潔 <poohann1...@gmail.com> wrote: >> > Hi Dr. Yeo, >> > >> > Thank you very much for your help! It is the exactly we need! >> > Only a little question that when we ran mris_surf2surf >> > Something seems wrong , but I can't figure out. >> > annot file: >> > >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 152420 >> > i=00A4F8DC, >> > in_array_size=10242 >> > annot file: >> > >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 152421 >> > i=00A4F8DC, >> > in_array_size=10242 >> > annot file: >> > >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot >> > MRISreadAnnotationIntoArray: vertex index out of range: 152422 >> > i=00010101, >> > in_array_size=10242 >> > annot file: >> > >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\ >> > reading colortable from annotation file... >> > colortable with 18 entries read (originally MyColorLUT) >> > Reading target surface reg >> > /home/annie/test_run_allindex/5204/surf/lh.sphere.reg >> > Done >> > Mapping Source Volume onto Source Subject Surface >> > surf2surf_nnfr: building source hash (res=16). >> > Surf2Surf: Forward Loop (160564) >> > >> > Surf2Surf: Dividing by number of hits (160564) >> > INFO: nSrcLost = 0 >> > nTrg121 = 160564, nTrgMulti = 0, MnTrgMultiHits = 0 >> > nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits = >> > 15.677 >> > Saving target data >> > Converting to target annot >> > Saving to target annot >> > >> > /home/annie/test_run_allindex/5204/label/lh.Yeo2011_17Networks_N1000.annot >> > >> > >> > Sorry for giving such long code. But it seems the vertex number didn't >> > match. >> > Or just something goes wrong while I proceed. >> > >> > Best, >> > Annie >> > >> > 2015-05-14 4:54 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: >> > >> >> Hi Annie, >> >> >> >> I have previously extracted individual regions from the 7 and 17 >> >> networks. You can download them here >> >> >> >> >> >> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0). >> >> Please see the README in the folder for more explanations. There >> >> should be a precuneus DMN region. >> >> >> >> The 17 networks consist of 114 regions that have been previously >> >> published: >> >> >> >> 1) Krienen et al., Reconfigurable state-dependent functional coupling >> >> modes cluster around a core functional architecture. Philosophical >> >> Transactions of the Royal Society B, 369:20130526, 2014 >> >> >> >> 2) Yeo et al., Functional connectivity during rested wakefulness >> >> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158, >> >> 2015 >> >> >> >> Hope this helps. >> >> >> >> Cheers, >> >> Thomas >> >> >> >> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 <poohann1...@gmail.com> wrote: >> >> > Hello Dr. Yeo, >> >> > >> >> > Thank you for your previous help and reply. We've worked out the way >> >> > to >> >> > switch the resolution of parcellation and successfully extracted the >> >> > anatomical information using your mask derived from iFC work. >> >> > >> >> > However, we came across a new problem to apply the cortical mask and >> >> > need >> >> > your kind help again. We aim to conduct a seed-based analysis to >> >> > investigate >> >> > structural covariance based on the network defined by iFC, and find >> >> > your >> >> > work of cortical parcellation conceptually perfectly suit our >> >> > research >> >> > question. Based on the current approach, however, it seemed that we >> >> > could >> >> > only extract the anatomical information from the whole well-defined >> >> > network, >> >> > but not the specific hub within the network (e.g., the anatomical >> >> > information of the precuneus from the DMN). We wonder if you have any >> >> > suggestion to resolve our problem, ie, to be specific, is there any >> >> > way >> >> > to >> >> > only extract the discrete hub information rather than the whole >> >> > network? >> >> > >> >> > We really appreciate your generous help. Thank you very much. >> >> > >> >> > p.s. This email would also forward to my senior colleague, Dr. >> >> > Hsiang-Yuan >> >> > Lin, who is a child and adolescent psychiatrist doing imaging >> >> > research >> >> > in >> >> > Taiwan. >> >> > >> >> > >> >> > 2015-05-13 19:15 GMT+08:00 陳昱潔 <poohann1...@gmail.com>: >> >> >> >> >> >> Hi Professor Yeo : >> >> >> >> >> >> Thank you for helping us so much! >> >> >> After mris_anatomical_stat I tried aparcstats2table to extract the >> >> >> table. >> >> >> But I failed with generating the table. >> >> >> >> >> >> >> >> >> Best wishes, >> >> >> Annie >> >> >> >> >> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: >> >> >> >> >> >>> Hi Annie, >> >> >>> >> >> >>> I assume this means 5202 is your subject ID? Maybe you should check >> >> >>> if >> >> >>> >> >> >>> >> >> >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot >> >> >>> exist? >> >> >>> >> >> >>> If so, you can run mris_anatomical_stats to generate statistics for >> >> >>> the parcellation. >> >> >>> >> >> >>> Cheers, >> >> >>> Thomas >> >> >>> >> >> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 <poohann1...@gmail.com> wrote: >> >> >>> > Hi Professor Yeo : >> >> >>> > After I rechecked the directory and run again mri_surf2surf >> >> >>> > I got the result: >> >> >>> > "Saving target data >> >> >>> > Converting to target annot >> >> >>> > Saving to target annot >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot" >> >> >>> > The file of 5202/label didn't come out with >> >> >>> > lh.Yeo2011_7Networks_N1000.annot >> >> >>> > But it seems succeed, right? >> >> >>> > How can I get the stat of this parcellation ? >> >> >>> > >> >> >>> > Thank you very much! >> >> >>> > >> >> >>> > Best wishes, >> >> >>> > Annie >> >> >>> > >> >> >>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: >> >> >>> > >> >> >>> >> Hi Annie, >> >> >>> >> >> >> >>> >> mri_surf2surf is complaining that it cannot write out the >> >> >>> >> annotation. >> >> >>> >> >> >> >>> >> Just to clarify, is your subject called test_run_allindex? In >> >> >>> >> other >> >> >>> >> words, is the variable s equal to test_run_allindex? >> >> >>> >> >> >> >>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? >> >> >>> >> If >> >> >>> >> not, then you first need to create the directory first, and then >> >> >>> >> mri_surf2surf can write the resulting annotation file into the >> >> >>> >> directory. >> >> >>> >> >> >> >>> >> Cheers, >> >> >>> >> Thomas >> >> >>> >> >> >> >>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 <poohann1...@gmail.com> >> >> >>> >> wrote: >> >> >>> >> > Hi Professor Yeo : >> >> >>> >> > >> >> >>> >> > We tried the code >> >> >>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi >> >> >>> >> >>> lh >> >> >>> >> >>> --sval-annot >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> >> >> >>> >> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot >> >> >>> >> >>> --tval >> >> >>> >> >>> $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot >> >> >>> >> > However there came an error of "could not write annot file >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot >> >> >>> >> > No such file or directory" >> >> >>> >> > And we checked our individual subject's label there isn't >> >> >>> >> > lh.Yeo2011_7Networks_N1000.annot >> >> >>> >> > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot >> >> >>> >> > into >> >> >>> >> > our >> >> >>> >> > subjects/label first? >> >> >>> >> > What can we do ? >> >> >>> >> > Thank you very much! >> >> >>> >> > >> >> >>> >> > Best wishes, >> >> >>> >> > Annie >> >> >>> >> > >> >> >>> >> > >> >> >>> >> > 2015-05-05 8:36 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>: >> >> >>> >> > >> >> >>> >> >> Hi Annie, >> >> >>> >> >> >> >> >>> >> >> Please cc the freesurfer list when you reply because there >> >> >>> >> >> might >> >> >>> >> >> be >> >> >>> >> >> other people more qualified to answer your question. >> >> >>> >> >> >> >> >>> >> >> Based on what you are saying, I think you can first use >> >> >>> >> >> mri_surf2surf >> >> >>> >> >> (with the "sval-annot" flag) to transform the 2011 functional >> >> >>> >> >> networks >> >> >>> >> >> .annot file from fsaverage space to the subject's native >> >> >>> >> >> surface >> >> >>> >> >> space. Type "mri_surf2surf --help" to see examples. >> >> >>> >> >> >> >> >>> >> >> You can then use mris_anatomical_stats to compute thickness >> >> >>> >> >> statistics. >> >> >>> >> >> >> >> >>> >> >> Cheers, >> >> >>> >> >> Thomas >> >> >>> >> >> >> >> >>> >> >> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 <poohann1...@gmail.com> >> >> >>> >> >> wrote: >> >> >>> >> >> > Dear Pro. Yeo: >> >> >>> >> >> > >> >> >>> >> >> > Very appreciate for your reply ! >> >> >>> >> >> > >> >> >>> >> >> > We are trying to use your definition of the functional >> >> >>> >> >> > network >> >> >>> >> >> > regions >> >> >>> >> >> > to >> >> >>> >> >> > re-parcellate our images >> >> >>> >> >> > and get the regions of volume or cortical thickness for our >> >> >>> >> >> > study >> >> >>> >> >> > interest >> >> >>> >> >> > of structural network. >> >> >>> >> >> > However, we did not want to re-run the first recon-all >> >> >>> >> >> > again >> >> >>> >> >> > due >> >> >>> >> >> > to >> >> >>> >> >> > it's >> >> >>> >> >> > spending to much time. >> >> >>> >> >> > And we are still can't find the way to solve this problem. >> >> >>> >> >> > Thank you very much for helping us! >> >> >>> >> >> > >> >> >>> >> >> > Best wishes, >> >> >>> >> >> > Annie Chen >> >> >>> >> >> > >> >> >>> >> >> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo >> >> >>> >> >> > <ytho...@csail.mit.edu>: >> >> >>> >> >> >> >> >> >>> >> >> >> Hi Yu-Chieh, >> >> >>> >> >> >> >> >> >>> >> >> >> I am cc-ing the freesurfer list who may help you with your >> >> >>> >> >> >> issues. >> >> >>> >> >> >> >> >> >>> >> >> >> Can you explain what exactly you are trying do? The >> >> >>> >> >> >> parcellation >> >> >>> >> >> >> is >> >> >>> >> >> >> released in different resolutions including fsaverage5. >> >> >>> >> >> >> Why >> >> >>> >> >> >> can't >> >> >>> >> >> >> you >> >> >>> >> >> >> just use the fsaverage5 parcellation? >> >> >>> >> >> >> >> >> >>> >> >> >> Cheers, >> >> >>> >> >> >> Thomas >> >> >>> >> >> >> >> >> >>> >> >> >> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 >> >> >>> >> >> >> <poohann1...@gmail.com> >> >> >>> >> >> >> wrote: >> >> >>> >> >> >> > Dear professor Yeo : >> >> >>> >> >> >> > >> >> >>> >> >> >> > My name is Yu-chieh Chen , I am a graduated student >> >> >>> >> >> >> > from >> >> >>> >> >> >> > National >> >> >>> >> >> >> > Taiwan >> >> >>> >> >> >> > University of medical school, and my supervisor is >> >> >>> >> >> >> > professor >> >> >>> >> >> >> > Susan >> >> >>> >> >> >> > Shur-Fen >> >> >>> >> >> >> > Gau from department of psychiatry, National Taiwan >> >> >>> >> >> >> > University >> >> >>> >> >> >> > Hospital & >> >> >>> >> >> >> > College of Medicine. We are very interesting about your >> >> >>> >> >> >> > paper >> >> >>> >> >> >> > published >> >> >>> >> >> >> > in >> >> >>> >> >> >> > 2011 which using resting MRI to separate brain regions >> >> >>> >> >> >> > to >> >> >>> >> >> >> > functional >> >> >>> >> >> >> > networks. We'd like to use your percellation to >> >> >>> >> >> >> > re-separate >> >> >>> >> >> >> > the >> >> >>> >> >> >> > brain >> >> >>> >> >> >> > regions based on your released data in Freesurfer( >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). >> >> >>> >> >> >> > And >> >> >>> >> >> >> > use >> >> >>> >> >> >> > these volume of brain regions for our study, however, >> >> >>> >> >> >> > there >> >> >>> >> >> >> > comes >> >> >>> >> >> >> > the >> >> >>> >> >> >> > problem that we assumed that we can change the fsaverage >> >> >>> >> >> >> > into >> >> >>> >> >> >> > fsaverage5, >> >> >>> >> >> >> > thus we may get the new volume of the parcellation_Yeo. >> >> >>> >> >> >> > But >> >> >>> >> >> >> > it >> >> >>> >> >> >> > is >> >> >>> >> >> >> > not >> >> >>> >> >> >> > work. >> >> >>> >> >> >> > So I send this email for help. Last , I am very >> >> >>> >> >> >> > appreciate >> >> >>> >> >> >> > your >> >> >>> >> >> >> > kindness >> >> >>> >> >> >> > and >> >> >>> >> >> >> > very sorry for my inappropriate and rough. >> >> >>> >> >> >> > Thank you very much for read this email and sorry for >> >> >>> >> >> >> > occupied >> >> >>> >> >> >> > your >> >> >>> >> >> >> > time. >> >> >>> >> >> >> > >> >> >>> >> >> >> > Best wishes, >> >> >>> >> >> >> > Yu-chieh Chen >> >> >>> >> >> >> > >> >> >>> >> >> > >> >> >>> >> >> > >> >> >>> >> > >> >> >>> >> > >> >> >>> > >> >> >>> > >> >> >> >> >> >> >> >> > >> > >> > > > _______________________________________________ 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. 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