Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

GLM in groups with unequal size
by Eelco van Duinkerken 14 Oct '16

14 Oct '16

Hi all, I am using FS with data from 2 different studies that were acquired on the same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the group sizes are not very balanced, with 31 controls, 16 obese and 32 diabetes patients. Is the GLM for thickness used in FS very sensitive to this unequal group size? Thanks for the help, Eelco

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issue with unpacksdcmdir
by Marco Loggia 14 Oct '16

14 Oct '16

Hello Doug and Freesurfers, We are having trouble unpacking DTI data collected in Bay7. Data are here: cd /autofs/eris/marco/tmp/seun The error I get is this one, which prevents the nii file from being created: ERROR: mri_convert child killed: segmentation violation It looks like the problem doesn’t occur for other data (E.g., BOLD, MPRAGE), so could it be only DTI-specific? More details are below, and the infodump.dat file is attached. Thanks! Marco ################## olaf:marco[195] cd /autofs/eris/marco/tmp/seun olaf:marco[196] unpacksdcmdir -src DTI_sevoEEG_006/ -targ . -generic -run 10 dti nii dti.nii -unpackerr $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /autofs/eris/marco/tmp/seun -src DTI_sevoEEG_006/ -targ . -generic -run 10 dti nii dti.nii -unpackerr Thu Oct 13 17:13:49 EDT 2016 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/13-21:13:49-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: marco Machine: olaf Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 olaf Linux olaf 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 13 17:13:49 EDT 2016 Log File is ./unpack.log INFO: Logfile is ./unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is ./dicomdir.sumfile INFO: status file is ./parse.status Scanning directory Thu Oct 13 17:13:49 EDT 2016 mri_parse_sdcmdir --sortbyrun --d DTI_sevoEEG_006/ --o ./dicomdir.sumfile --status ./parse.status 0 2 4 6 8 10 12 15 17 19 21 23 26 28 30 32 34 36 38 41 43 45 47 49 52 54 56 58 60 63 65 67 69 71 73 75 78 80 82 84 86 89 91 93 95 97 100 Done scanning Thu Oct 13 17:14:01 EDT 2016 ------------------------------------------ 10 ep2d_diff_mgh_30dir_b1000_2000_10b0_tensor err 128 128 64 70 MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899 unpacking config ------------------ {10 dti nii dti.nii} ----------------------------------- --------------------------------------------------------- Run 10 ----------------------------------------- Thu Oct 13 17:14:01 EDT 2016 10 dti nii dti.nii INFO: this run has an error, but trying anyway mri_convert DTI_sevoEEG_006//MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899 ./dti/dti.nii --sdcmlist ./dti/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation

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graphic board question
by Dix Meiberth 14 Oct '16

14 Oct '16

Dear all, I'm thinking about starting a cortical thickness analysis. Therefore I would like to buy a new machine, namely an Apple iMac 21,5" including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz); 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200 The Apple support told me that the graphic board may not be sufficient to perform FS analyses as the Intel Iris Pro Graphics 6200 card does not include an extern video memory. Does anyone of you has experience if the machine is in fact not sufficient? Thanks in advance and best regards, DM

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How to use -openmp flag/ Please help
by Farzaneh keyvanfard 14 Oct '16

14 Oct '16

Dear expert I'm beginner in using Freesurfer and I really need your help. However I've read all related responded questions about paralleling process. I found -openmp N flag to do that, but I don't understand its correct location in 'recon-all'. I used it as follows but it doesn't work. Also I want to use -qcache flag in addition to -openmp N. Would you please kindly let me know in which order, these flags should be used? I really appreciate your kind help. recon-all -i SerieMR-0002.dcm-subjid Results -all –openmp8 –qcache I'm looking forward to hearing from you. Best Regards F. Keyvanfard F.Keyvanfard

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Mac OS Support and Compatibility
by Mageshwar Selvakumar 13 Oct '16

13 Oct '16

Dear All, I am trying to get started with FreeSurfer. I would like to know if the Mac OS versions (Yosemite, Sierra) are compatible and can run the FreeSurfer, if not please let me know which is the latest Mac OS version that supports FreeSurfer. I tried installing it on Mac OS Sierra but it is not fully functional. I would like to know if the error is caused because of compatibility issues or if I have made a error with the installation. Looking forward for your response. Thanks in Advance, Kind Regards, Mageshwar Selvakumar

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recon-all exited with ERRORS
by Brad Matushewski 13 Oct '16

13 Oct '16

I just tried to run my first recon-all. What now? [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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FreeSurfer Atlas
by AKUDJEDU, THEOPHILUS 13 Oct '16

13 Oct '16

Hi All, Which default atlas does FreeSurfer 5.3 use for the segmentation of subcortical structures? Thanks Theo

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Gamma / Histogram
by Anders Hougaard 13 Oct '16

13 Oct '16

Dear Freesurfers, Please see the attached image. It shows inflated fsaverage surface with gamma.mgh overlaid. Gamma.mgh is from one contrast of a standard group analysis of cortical thickness (two groups A and B, two contrasts A>B and B>A). 1) Is it correct to interpret the gamma values as between-group difference of cortical thickness in mm? 2) I would like to reproduce the histogram in another software. Is it possible to extract the gamma values for each vertex for this purpose? All the best, Anders

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PET/MRI registration failed with bbregister or mri_coreg
by Matthieu Vanhoutte 12 Oct '16

12 Oct '16

Dear Freesurfer's experts, I would like to register PET image onto T1 anatomical. I used bbregister with the following command and it failed : *bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out Pet2T1.init.register.dof6.dat --o rPET.nii.gz * Having heard about mri_coreg solving some bbregister fails, I tested it with the following command : *mri_coreg --s SUBJID --mov PET.nii.gz --reg Pet2T1.register.dof6.mri_coreg.lta --regdat Pet2T1.register.dof6.mri_coreg.dat* But it failed in the same way than bbregister. Do you have any advice on this problem ? Best regards, Matthieu

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Remapping Volume
by Crawford, Anna 12 Oct '16

12 Oct '16

Hi, I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it into Matlab using load_mgh. In Matlab I remap the volume to different values. For example, all original values of 1022 will become 200 and all 1030 values will become 150. (This is just an example, not necessarily these numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same M and mr_parms that I got when I loaded in the original file. I'm not sure what these mean or if I need to change them. Then I use mri_vol2surf to create a new surface overlay onto the inflated hemisphere. When I do this, each region such as post central gyrus is 2 colors spotted together instead of a solid color like in the original. I have attached pictures as an example of what the original and remapped looked like. I didn't change the location of values, just simple gave each value a new one. Why is the one value speckled throughout? Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Freesurfer October 2016