Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011
by Parker, Richard 14 Dec '15

14 Dec '15

Hi Prof, Thanks for the speedy reply, When you specify fsaverage5 as -srcsubject and your own subject as -trgsubject, the code executes but the resulting .annot file looks like a mess. Your proposed two-step call to mri_surf2surf seems more promising. If I run the following: mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh --sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval ./lh.YeoUpsample.annot I end up with a .annot file in the same space as fsaverage, but there seem to be large gaps between the labels. Here's a screenshot of what I mean: http://imgur.com/VvqYEWx Do you have any suggestions on how to account for this? Is there some unresolved mismatch between the number of vertices following upsampling, perhaps? Best wishes, Richard Hi Richard, Sorry. My original reply was rejected by the list. Resending. In the mri_surf2surf command, Instead of the srcsubject being fsaverage, can you try using the srcsubject as fsaverage5 instead? Alternatively, you can try running mri_surf2surf twice. Once to upsample the fsaverage5 annot to fsaverage and then run the mri_surf2surf command from your email. (This might actually work better). Thanks, Thomas On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard <richard.r.par...(a)kcl.ac.uk> wrote: > Hi Professor Yeo, > > > > Thanks for providing a link to your split region MNI space files. > > > > Could you please advise on how to get these labels into subject native > space? > > > > If using the standard version of the network labels that comes packaged with > Freesurfer 5.3.0, I can get the annotation file into native space quite > easily with the following command: > > > > > > mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh > --sval-annot > $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot > --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot > > > > However, in the dropbox link you posted, it doesn't seem that there is a > .annot file compatible with fsaverage. The fsaverage5 version is present, > but if I try slotting the fsaverage5 .annot file into the above call to > mri_surf2surf, I get disastrous results. > > > > Do you perhaps have a .annot file for the upsampled (and split) network > labels? Or perhaps there's an easier way to achieve what I'm after. I notice > that you have provided a .nii file for the network ROIs that is in the same > space as fsaverage, perhaps this file can be warped to native space somehow? > > > > Best wishes, > > > > Richard Parker > > King's College London > > > > > > > > > > > > > > > > Hi Erica, > > > > You can try this link: > > https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Sp… > > > > Regards, > > Thomas > > > > On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung <orange...(a)gmail.com> > wrote: > >> Dear Prof. Yeo, > >> > >> I would like to extract the brain regions of the functional canonical > >> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you >> have > >> provided the split regions of 7&17 Network in previous discussion string. > >> >> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html > >> ) > >> > >> However, the dropbox download link you offered has expired. > >> Would you mind uploading it again? > >> > >> Thank you very much. > >> > >> Erica

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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011
by Parker, Richard 14 Dec '15

14 Dec '15

Hi Professor Yeo, Thanks for providing a link to your split region MNI space files. Could you please advise on how to get these labels into subject native space? If using the standard version of the network labels that comes packaged with Freesurfer 5.3.0, I can get the annotation file into native space quite easily with the following command: mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot However, in the dropbox link you posted, it doesn't seem that there is a .annot file compatible with fsaverage. The fsaverage5 version is present, but if I try slotting the fsaverage5 .annot file into the above call to mri_surf2surf, I get disastrous results. Do you perhaps have a .annot file for the upsampled (and split) network labels? Or perhaps there's an easier way to achieve what I'm after. I notice that you have provided a .nii file for the network ROIs that is in the same space as fsaverage, perhaps this file can be warped to native space somehow? Best wishes, Richard Parker King's College London Hi Erica, You can try this link: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Sp… Regards, Thomas On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung <orange...(a)gmail.com> wrote: > Dear Prof. Yeo, > > I would like to extract the brain regions of the functional canonical > network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have > provided the split regions of 7&17 Network in previous discussion string. > (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html > ) > > However, the dropbox download link you offered has expired. > Would you mind uploading it again? > > Thank you very much. > > Erica

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T1 to FS
by Reza Farimani 13 Dec '15

13 Dec '15

Hi everybody, I am new to freesurfer so sorry for my naive questions. I am trying to export raw DICOM files to freesurfer. The CD I have apparently have all T1,T2, and other MR image types. How should I filter only T1 for freesurfer? Thanks Reza

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Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs
by Slater David 13 Dec '15

13 Dec '15

Hi, I have the same problem with tksurfer in Ubuntu. The keyboard entry doesn't work for the tksurfer input boxes - I can't set any values in the overlay configuration window, edit label info, configure phase encoded data display etc. All of the text / numeric entry boxes have this issue. Any suggestions on how to fix this? My freesurfer verion is freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same problem before updating to v6-beta. Thanks, David -----Message d'origine----- De : freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs Hi Lars can you give more details? What prevents you from entering values? Do you get any errors when tksurfer loads? cheers Bruce On Sat, 15 Aug 2015, Lars M. Rimol wrote: > > Hi all, > > I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am > unable to set threshold values in the edit boxes in the "configure > overlay" display in tksurfer. Does anybody know how to fix this (without specifying the threshold on the command line each time)? > > Thank you! > > > > > > yours, > Lars M. Rimol, PhD > Department of Medicine > John A. Burns School of Medicine > University of Hawai'i > 1356 Lusitana Street, University Tower Honolulu, HI 96813 > > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Freesurfer Problem Report
by Timothy Hendrickson 11 Dec '15

11 Dec '15

Freesurfer experts and/or developers, I ran a recon-all on a particular subject. When I attempted to open the subject in freeview I received an error, which is below. Here is the information requested when submitting a freesurfer problem report: FREESURFER_HOME: /opt/local/freesurfer-5.3/x86_64 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.7 (Santiago) Kernel info: Linux 2.6.32-504.1.3.el6.x86_64 x86_64 1) subject name: *47266_SE003* 2) the entire command-line executed: *manualEdits 47266_SE003* (included the script manualEdits.sh as an attachment) 3) the error message generated: *freeview.bin: ../../src/mesa/tnl/t_vertex.c:423: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed.Abort (core dumped)* 4) optionally include the subject's /script/recon-all.log Please let me know if you require additional information. -Tim -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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questions about summary of Monte Carlo simulation‏
by Karl Liu 11 Dec '15

11 Dec '15

Dear Freesurfer experts, I repost my question from yesterday since it is not answered. Thanks in advance for any help. After running Monte Carlo simulation from the command line, I noticed two cluster summary files are produced for each contrast: cache.th20.neg.sig.cluster.summary and mc-z.neg.th20.sig.cluster.summary. They are quite similar, with different number of surviving clusters in some cases. I am wondering which is the one to report final results. Will you explain a bit more about the differences between them? Also, after reading the summary file, we still have to visualize the results. If the MC simulation is done in QDEC GUI, then the QDEC automatically presents the outcome from mc-z.neg.th20.sig.cluster.mgh, but I am not sure if this is the right file. I am using FS version 5.3 without tksurferfv. I found the tksurfer is running quite slow and unresponsive. Any other suggestions? Thank you very much! Karl

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R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 11 Dec '15

11 Dec '15

Thanks, in which folder I should put this file? Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 7-dic-2015 19.23 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FDR in FS-FAST > > > >On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >> Hi list, >> I have two concerns, please: >> 1) It is possible to apply FDR correction on rs-fMRI seed based >> analysis by FS-FAST? If yes, I can I do it? >try this binary >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr >> 2) I have apply the FS guidelines and I have used Montecarlo >> correction with threshold at 1.3 but in the within group analysis the >> clusters are very large. In the guide I read examples with a threshold >> at 3. Is there a specific reason? >There is not a hard-and-fast criteria for the voxel-wise threshold. 3 is >fine as is 1.3 >> Thanks >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)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. > >

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average cortical thickness measure?
by Maria Kharitonova 11 Dec '15

11 Dec '15

I know that the aseg atlas provides a number of voume measures (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a variable for an average cortical thickness? I'd like to see if thickness in some of the regions is associated with a variable of interest over and above an overall main effect, so would like to control for the average thickness, but can't figure out a good way to do that. Thanks! Maria - Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.kharitonova(a)northwestern.edu<mailto:maria.kharitonova@northwestern.edu>

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Freeview PETSC Error
by Udunna Anazodo 11 Dec '15

11 Dec '15

Hi, I downloaded and installed Freesurfer stable release 5.3 distribution linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes with a PETSC error. I read the freesurfer archives and followed the instructions found on https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-November/041243.…. I downloaded the most recent version of freeview.bin using wget as suggested but I still get the same error message. Any ideas how to work around this. Thanks [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named udunna-work by udunna Thu Dec 10 17:42:30 2015 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 -- Udunna

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Convert TAL coordinates to surface RAS coordinates
by Inês Violante 11 Dec '15

11 Dec '15

Dear experts, I have a set of Talairach coordinates that I want to convert to the individual subject surf RAS coordinates. How can I do this? Thank you very much. Ines

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Freesurfer December 2015