Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

03 Mar '14

Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but I included the error below just in case). Should I just read in the thickness file in matlab/python and pull the data out from there (I assume it each frame is an input ordered respectively to the fsgd)? Thanks, Dan Is all of the data ingdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd Could not find XAxis tag in file. Using default one. �NggdfReadHeader: reading /autofs/cluster/neuromind/dwakeman/study/analysis_2/glm/g5_none.fsgd [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 marcie.nmr.mgh.harvard.edu by dwakeman Mon Mar 3 13:06:37 2014 [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

2 1

Freeview crashes xterm
by Venkataraman, Archana 03 Mar '14

03 Mar '14

Hi, I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the installation was successful and the paths are set correctly. However, my xterm crashes when I try to launch freeview. Strangely, the program works as expected when launched remotely via NX. Has anyone encountered this problem before? Thanks. - Archana

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Re: [Freesurfer] Problematic dilated ventricles
by Victor Kovac 03 Mar '14

03 Mar '14

Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz > > then run: > > recon-all -make all -s MPS1036-1 > > you should be all set > > Bruce > > > > On Mon, 9 Dec 2013, Victor Kovac wrote: > > I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you >> for looking into MPS2002-3 -- it is quite the brain. And somehow, with all >> those morphological abnormalities, this subject has an IQ of 130. Very >> strange. >> Thanks, >> Victor >> >> >> On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> which one? I'm still messing with MPS2002-3 in my spare time >> On Mon, 9 Dec 2013, Victor Kovac wrote: >> >> Hi Bruce, >> Is there a way for you to send the subject(s) you >> analyzed to me? I know >> it's too big for email, but could you possibly >> upload it to GoogleDrive? >> >> Thanks! >> Victor >> >> >> On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> p.s. the other thing I did was run the graph >> cut skull >> stripping, which removed a bunch of extraneous >> stuff >> On Wed, 4 Dec 2013, kovac081(a)umn.edu wrote: >> >> Hey! >> >> Victor Kovac (kovac081(a)umn.edu) has uploaded >> some files >> for you at the Martinos Center FileDrop: >> >> -> MPS2002-3.zip (292.12 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=55xjt9pflsi> >> -> MPS2017-1.zip (264.15 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=ak4v31bzu4p> >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here are the two subjects with ventriculomegaly that >> are causing >> the worst issues. The worst segmentation in >> MPS2002-3 is in the >> superior frontal (slices 150-180) and parietal >> (slices 50-95) >> cortical areas; this may be due to the numerous >> dilated >> Virchow-Robin spaces in his brain, which is another >> neuropathological feature of this disease. >> >> Thanks! >> Victor >> >> Please be aware, your upload will expire on December >> 31st. If >> you'd like to download these files, feel free to use >> the link >> below: >> >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep >> >> Cheers, >> The NMR Team >> >> >> >> >> >> 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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Fw: Re: error in mri_glmfit-sim when using --bg and doss
by charujing123 03 Mar '14

03 Mar '14

Hi doug and others, I am sorry for pasting files in my first contrast directory, if it can help me desolve the question: cache.th23.abs.pdf.dat mc-z.abs.2.sig.cluster.summary mc-z.neg.3.sig.cluster.summary mc-z.pos.3.sig.cluster.summary cache.th23.abs.sig.cluster.mgh mc-z.abs.2.sig.masked.mgh mc-z.neg.3.sig.masked.mgh mc-z.pos.3.sig.masked.mgh cache.th23.abs.sig.cluster.summary mc-z.abs.2.sig.ocn.annot mc-z.neg.3.sig.ocn.annot mc-z.pos.3.sig.ocn.annot cache.th23.abs.sig.masked.mgh mc-z.abs.2.sig.ocn.mgh mc-z.neg.3.sig.ocn.mgh mc-z.pos.3.sig.ocn.mgh cache.th23.abs.sig.ocn.annot mc-z.abs.2.sig.voxel.mgh mc-z.neg.3.sig.voxel.mgh mc-z.pos.3.sig.voxel.mgh cache.th23.abs.sig.ocn.mgh mc-z.abs.3.pdf.dat mc-z.neg.3.y.ocn.dat mc-z.pos.3.y.ocn.dat cache.th23.abs.sig.voxel.mgh mc-z.abs.3.sig.cluster.mgh mc-z.neg.pdf.dat mc-z.pos.pdf.dat C.dat mc-z.abs.3.sig.cluster.summary mc-z.neg.sig.cluster.mgh mc-z.pos.sig.cluster.mgh cnr.mgh mc-z.abs.3.sig.masked.mgh mc-z.neg.sig.cluster.summary mc-z.pos.sig.cluster.summary F.mgh mc-z.abs.3.sig.ocn.annot mc-z.neg.sig.masked.mgh mc-z.pos.sig.masked.mgh gamma.mgh mc-z.abs.3.sig.ocn.mgh mc-z.neg.sig.ocn.annot mc-z.pos.sig.ocn.annot gammavar.mgh mc-z.abs.3.sig.voxel.mgh mc-z.neg.sig.ocn.mgh mc-z.pos.sig.ocn.mgh maxvox.dat mc-z.abs.3.y.ocn.dat mc-z.neg.sig.voxel.mgh mc-z.pos.sig.voxel.mgh mc-z.abs.2.pdf.dat mc-z.neg.3.pdf.dat mc-z.pos.3.pdf.dat mc-z.pos.y.ocn.dat mc-z.abs.2.sig.cluster.mgh mc-z.neg.3.sig.cluster.mgh mc-z.pos.3.sig.cluster.mgh sig.mgh Thanks. All the best. Rujing Zha 2014-02-22 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-02-22 10:18 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDF…, I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-02-21 23:49 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 12

How to define a new label for aparc+aseg.mgz in FreeView
by Emad Ahmadi 03 Mar '14

03 Mar '14

Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

2 1

aligning/quality of CT
by Borzello, Mia 02 Mar '14

02 Mar '14

Hi Freesurfers, In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've done a coregistration and am looking at it in tkmedit and the quality of the image isn't so good. Thanks, Mia

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Re: [Freesurfer] longitudinal process
by Martin Reuter 02 Mar '14

02 Mar '14

Hi Anna, No, you can still use links. When rerunning the base, the cross are not changed. Once the base loiks good, you also have to rerun the longs of course. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson <ajonsson09(a)gmail.com> Date:03/02/2014 5:27 AM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal process Hi thank you for reply. May I ask other question; after editing the base it says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that all scans are located in the same directory? (Before i used symbolic links as scans are in different directories) but i am unsure whether after editing the abse anything further is actually done to the cross runs? Thank you for your help, Anna On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Anna, the linear mixed effects models can include subjects with a single time point and it would be a shame to drop that information. That is why we modified the longitudinal pipeline (use 5.3) to allow processing of subjects with a single time point. However, it is necessary that these images undergo the same processing steps as the rest of the data (to avoid bias). So you run it exactly as other subjects, with a cross sectional, -base and a -long step: recon-all -all -s <tp1id> -i path_to_tp1_dcm recon-all -base <templateid> -tp <tp1id> -all recon-all -long <tp1id> <templateid> -all Best, Martin On 02/18/2014 04:58 AM, Anna Jonsson wrote: Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.

1 0

longitudinal process
by Anna Jonsson 02 Mar '14

02 Mar '14

Dear Freesurfer experts, I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times? Thank you Kind Regards, Anna

2 2

Pb with a registration of diffusion images processed with tracula and anat images
by Celine Louapre 28 Feb '14

28 Feb '14

Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

3 4

Extracting only hippo campus volume
by Saurabh Thakur 28 Feb '14

28 Feb '14

Hello Freesurfer expert, I have done Hippo campus segmentation using Freesurfer. Can u tell me how to extract the only Hippo campus volume from nu.mgz Why only nu.mgz is used for the main volume--is there some specific reason to use? Thanks in advance , Saurabh Thakur,

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