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. 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.
