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freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Mismatching hippocampal output
by Dean, Sophie 08 Aug '18

08 Aug '18

External Email - Use Caution Dear FreeSurfer developers, As I understand it is recommended data is processed using the same OS. However, it also states on the FreeSurfer webpage that there is an exception for some post-processing tools. Recon-all was first done with: FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Darwin Kernel Version 17.4.0 Post-processing for hippocampal segmentation was done separately on two different machines with different operating systems: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux Version 2.6.32-696.23.1.el6.x86_64 2) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Darwin Kernel Version 17.7.0 Both have slightly different volume outputs. Is this difference due to software/OS differences? Which output would you recommend using? I have attached recon-all logs in case they are of use for my inquest. With thanks and kind regards, Sophie

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paradigm file for functional block design
by Desch, Simon 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer experts, I have a mapping paradigm with block design. Each off-block has a jittered length of 12-14s. Each on-block belongs to 1 out of 5 conditions (in this case stimulation sites). When creating the paradigm-file (like here: https://surfer.nmr.mgh.harvard.edu/fswiki/SensMotOddEvenPar) is it necessary to include each off-block as a separate line? Or is it sufficient to include only on-blocks and silently assume all the rest of the sequence to be of kind „NULL event“ coded with 0 (i.e. similar to what FSL does)? Thank you in advance! Sincerely, Simon Desch Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _____________________________________________ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone: +49 (0) 621 1703 6304

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structure of project directory for longitudinal functional analysis
by Desch, Simon 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer experts, I’m very new to Freesurfer and I’m struggling to setup my project directory for a functional analysis. I’m running a study with each subject doing two MRI sessions, i.e. before and after they perform a perceptional training at home for three month. In each session (i.e. before and after training) they do a sensory mapping task and I want to compare mapping pre- and post-training. If possible I’d like to run this analysis contrasting two groups (who performed different kinds of training). I’m about to setup the project directory structure as depicted here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV4.5. The first issue I stumbled across is if to put data of all pre-training measurements of all subjects in a different „Session“ ( it says "All the data collected in one functional session (or visit) are placed under the folder (the "session directory").). As far as I can see the tutorial does neither cover longitudinal within subject comparisons nor between group comparisons (using mri_glmfit). Thus, any help is highly appreciated! Thank you! Sincerely, Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _____________________________________________ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone: +49 (0) 621 1703 6304

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Postdoctoral Fellowship in Neuroimaging (MRI & DWI)
by Meaghan Perdue 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer Community, Please consider the job opportunity below and pass along to colleagues who may be interested. *POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)* The LandiLab (PI: Nicole Landi, PhD *https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>*) at Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/>* (which is closely affiliated with Yale and the University of Connecticut) is seeking to hire a postdoctoral research fellow. This postdoc will join a project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (structural and diffusion imaging data). This position is part of a multi-site project (Haskins Laboratories, University of Houston, Baylor College of Medicine) that is aggregating and analyzing neuroimaging and genotyping data from multiple locations to explore gene-brain-behavior relationships. Applicants must have a background conducting research using MRI. The ideal candidate will also have experience with diffusion weighted imaging (DWI) and experience with advanced statistical analysis of imaging data (e.g. imaging-genetic analyses, Bayesian methods, machine learning). *For details regarding required qualifications and application procedure, please visit: https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti <https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti>* Best regards, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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surface arithmetic?
by Rockers, Elijah D. 07 Aug '18

07 Aug '18

External Email - Use Caution Hello, I have a subject with two MRIs and surface reconstructions, several years apart. I would like to directly compare these surfaces if possible, for instance, to subtract (new - old) to see a "difference surface" or something similar. Is there a way to A) Get the surfaces into the same space so they can be combined mathematically, and B) performs operations with the surfaces, a la fslmaths? Many thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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WM segmentation
by Ben M 07 Aug '18

07 Aug '18

External Email - Use Caution Hi, I would like to create a mask of the WM for fMRI analysis. I read a previous post in which it was suggested to get the wm segmentation and erode it, since the result will be exclusively WM. My question is why is this so? Why can I assume that getting the WM mask from the aseg file will almost certainly get me high probability WM, >0.9 for example? In most segmentation algorithms we get posterior probabilities at each voxel, so that we can then select voxels with posterior probabilities >0.90 for example. Why is freesurfer's WM segmentation so accurate that we do not need posterior probabilities? Are these very high probabilities somehow already coded in freesurfer's segmentation algorithm? Thanks, Ben

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mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels
by Lalonde, Francois (NIH/NIMH) [E] 07 Aug '18

07 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run the hippocampal and amygdala subfield segmentation and take advantage of the .6mm resolution of the scan. I was able to run recon-all successfully on the scan without the -cm option. I get the following error: ------------------------------ SUBJECT nomove_xpace_06mm_tr3bcm DATE Fri Aug 3 11:58:33 EDT 2018 USER flalonde HOST cn0638 PROCESSOR x86_64 OS Linux Linux cn0638 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /data/flalonde/freesurfer_dev/bin/recon-all PWD /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/scripts CMD mris_register -curv -rusage /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /data/flalonde/freesurfer_dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg I’ve attached a copy of the recon-all.log 1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev-20180723-7bf4760 2) Platform: CentOS Linux release 7.5.1804 (Core) 3) uname -a: Linux felix.nimh.nih.gov 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached The list mentions running a post-hoc surface deformation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47309.html) using mris_make_surfaces as a workaround but I’m not sure if this is applies in my case or what the full command might be (e.g. mris_make_surfaces subjectname lh). Thanks, François M. Lalonde, Ph.D. DNU / HGB / DIRP / NIMH 10 Center Drive, Room 4N244 Bethesda, MD 20892-1600

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Getting error while extracting hippocampus volume in dev version of freesurfer
by Yubraj Gupta 07 Aug '18

07 Aug '18

External Email - Use Caution Hello Freesurfer Developers, While extracting the Hippocampus volume from the subject folder, I'm getting the following error. This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch @#@FSTIME 2018:08:08:01:27:03 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 868.58 S 607.16 U 8388.47 P 1035% M 3765176 F 0 R 23295004 W 0 c 1773466 w 3380046 I 0 O 847496 L 19.31 35.64 36.84 @#@FSLOADPOST 2018:08:08:01:41:31 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 28.36 47.98 45.74 Linux tars 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Aug 8 01:41:31 KST 2018 I've searched the list and no similar errors have been reported. Does anyone have any thought on how to troubleshoot this one? Also, I've attached the Hippo_T1.log in case it's of any use. 1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev- 20180725-1793f7a 2) platform: centos-release 7centos 3) unmae -a: Linux tars 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) Hippo_T1.log: see attached

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XL Defect Detected
by Rockhill, Alexander P. 07 Aug '18

07 Aug '18

Hi all, I am running recon-all and the command is stuck on the output CORRECTING DEFECT 31 (vertices=8161, convex hull=3290, v0=29848) XL defect detected... It has been on that step overnight. Is there some way to ignore the defect or correct it without taking so long? This is using freesurfer 6. Thanks, Alex Rockhill Translational NeuroEngineering Laboratory Division of Neurotherapeutics, Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charlestown #2301, Boston, MA 02129

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wm.mgz values
by Aaron Tanenbaum 07 Aug '18

07 Aug '18

External Email - Use Caution Hello Freesurfers. I was wondering of for the purposes of editing wm.mgz if changing voxel values to anything but 255 and 1 will be useful in anyway. If so I was wondering if you can explain to me what the following values mean and how do I use them. #define THICKEN_FILL 200 #define NBHD_FILL 210 #define VENTRICLE_FILL 220 #define DIAGONAL_FILL 230 #define DEGENERATE_FILL 240 #define OFFSET_FILTER_FILL 245 #define AUTO_FILL 250 #define PRETESS_FILL 215 #define WM_EDITED_ON_VAL 255 #define WM_EDITED_OFF_VAL 1

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