Freesurfer

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30071 discussions

“ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
by Uquillas, Federico D'Oleire 21 Feb '17

21 Feb '17

Dear FreeSurfer experts, I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”. However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!” I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys. Thank you so much. Best, Fred

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Freeview X Error: BadValue
by Lebois, Lauren Ann Mcdonough 21 Feb '17

21 Feb '17

Hi FS gurus, I am remote logging in to nmr nexlin machines from my work iMAC and I am trying to view some freesurfer results with Freeview, but I am getting the following error: llebois@nexlin9:/eris/ressler/DD_FS_160222/150305_NTD015_FS/mri/assembly$ freeview -v nu.mgz left_discreteLabels.mgz X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) I have searched the archives and as far as I can tell, didn't find anything related to this error. Any ideas on how to troubleshoot this one? Thank you for your help and time. Sincerely, Lauren

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-no-isrunning flag question
by Joe Necus (PGR) 21 Feb '17

21 Feb '17

Hello, As I understand, adding the -no-isrunning flag will cause recon-all to ignore the 'isrunning.pial' file. I previously interrupted recon-all (while it was in the middle of a process) and I have now begun to re-run my subjects using this flag. I just wanted to check that any data which has previously been generated by freesurfer will now be overwritten. I.e. that there are no disadvantages to using this flag? Thanks , Joe

2 1

mri_normalize 5.4 vs v6
by Arman Eshaghi 21 Feb '17

21 Feb '17

Dear All, When I run mri_normalize on the same image using two freesurfer versions I get distorted results only on the V6. Can someone let me know how I can get the same results with V6? command: mri_normalize <input> <output> V5 output: voxel value range: 0 - 182 [image: Inline image 1] v6 output: voxel value range: 0-255 [image: Inline image 2] Thanks

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Comparability of FreeSurfer segmentations across different MRI acquisition specs
by Darko Sarovic 21 Feb '17

21 Feb '17

Hi, I’m doing volumetric analyses on MR structural data. The problem is that the scanning has been done on different MR machines, as well as with different sequences in some cases. This leads to different absolute values between subjects for volumes and thicknesses when being run through the FreeSurfer segmentation. My questions regarding this are: - Is there any way to standardize the results so that the segmentations with different acquisition specs (different MR sequences, MR machine developers) can be comparable? - I have used v5.3.0 for my segmentations; Is any part of v6.0.0 improved in this regard so that using that version would give more comparable results? Regards, Darko Sarovic Gothenburg University, Sahlgrenska Academy

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mri_cvs_register error : PETSC Error
by Bhavana Ganesh 21 Feb '17

21 Feb '17

Hi Developers, I'm receiving this error while I try to run mri_cvs_register. The same error was received when I reran the same even after increasing the memory allocated to my VB. Can anybody help me with the issue I am facing. Below are the details of my system and software configurations. PFA error log files. FreeSurfer version: freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c Platform: CentOS7 on VirtualBox Command Run: mri_cvs_register --mov bert2 0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648 <%28214%29%20748-3648> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 576224344! [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: surf2vol on a linux-gnu named localhost.localdomain by root Thu Feb 16 09:57:44 2017 [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: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in unknowndirectory/solver.h after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 Thank You *Regards,* *Bhavana* <https://www.linkedin.com/in/bhavanaganesh> <https://www.linkedin.com/in/bhavanaganesh> <https://www.linkedin.com/in/bhavanaganesh> <http://bhavanaganesh.weebly.com/>

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Nipype Workshop and Hackweek at MIT, March 27-31, 2017
by Satrajit Ghosh 21 Feb '17

21 Feb '17

The Nipype development team will be holding a workshop and hackweek at MIT, Cambridge, MA, USA, from March 27 - 31. For details and registration see: http://nipy.org/workshops/ 2017-03-boston/index.html cheers, satra

1 0

Output from mri_cvs_register
by Magnús Ingvi 20 Feb '17

20 Feb '17

Hi! I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ), the expected .m3z output file is called combined_tocvs_avg35_elreg_afteraseg-norm.m3z, but the output I get in the cvs folder is called final_CVSmorph_tocvs_avg35.m3z Is this the same file, or did I mess up somewhere? Best M.Ingvi

2 1

apply CVS morph to a list of coordinates
by Donos, Cristian 20 Feb '17

20 Feb '17

Hi, I have registered a patient’s MRI over the ColinN27 with mri_cvs_register and now i need convert an electrode (or voxel) coordinate from the subject’s space to the N27 space. I found an old post in the mailing list, but it did not work for me. The coords.txt file is just one line containing 10 10 10. What am i doing wrong? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39971.html Here are the commands i used and the results : > createMorph --out fullCSVmorph.tm3d --template /Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --subject /Volumes/Sector2/surfaces/TandonLang/TS076CD/mri/orig.mgz --in gcam /Volumes/Sector2/surfaces/TandonLang/TS076CD/TS076CD/csv/combined_toColin27_elreg_aseg.m3z atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.000 0.000 0.000 127.000; 0.000 0.000 1.000 -111.000; 0.000 -1.000 0.000 147.000; 0.000 0.000 0.000 1.000; ras 2 vox image = -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 138.000; -0.000 1.000 -0.000 143.000; 0.000 0.000 0.000 1.000; product = 1.000 0.000 0.000 1.000; 0.000 1.000 0.000 -9.000; 0.000 0.000 1.000 32.000; 0.000 0.000 0.000 1.000; transform at origin 1.000; -9.000; 32.000; 1.000; invalid voxel count = 9071323 saveTransform code writing transform size = 49918625 writing morph to file fullCSVmorph.tm3d > applyMorph --template /Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz --transform fullCVSmorph.tm3d point_list coords.txt transformed_coords.txt linear Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template Template name:/Volumes/Sector2/surfaces/TandonLang/TT_N27/mri/orig.mgz After loading template extension = tm3d Exception caught while loading transform VolumeMorph load - failed to open input stream Thank you, Cristian Donos, PhD Postdoctoral Research Fellow, Department of Neurosurgery 6431 Fannin Street | Suite G.550D | Houston, Texas 77030 Phone: 979-633-9208 Email: cristian.donos(a)uth.tmc.edu<mailto:cristian.donos@uth.tmc.edu>

2 1

Longitudinal proceesing for Pediatric data
by Dongnandi 20 Feb '17

20 Feb '17

Dear freesurfer exports, As it is mentioned in the documentation that 'pediatric data violates the fixed head size assumption' for the current longitudinal stream. Is there any solution for the issue now? Thanks Dong

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