Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Configuring freesurfer developer's environment on Ubuntu
by Kim, Daniel 03 Oct '12

03 Oct '12

Hello freesurfer users! I've got a brand new PC with Ubuntu 12.04 64-bit running and following the freesurfer developer's guide to set up a developer environment, I'm getting numerous "undeclared function / undefined type" errors during make. Seeing that the undeclared functions or variable types are actually defined in .h files that are being declared correctly, I'm suspecting there's configuration problem and was wondering has anyone had success in building freesurfer on Ubuntu 12.04 64-bit or building freesurfer on any previous Ubuntu release? The steps I took to get as far as getting undeclared function/undefined type errors are: - Pre-built 3rd party libraries were downloaded and put into /usr/pubsw/packages/ During configuration, I've made modification to bypass errors: - changed configure script so that script will not end when libvtkfreetype, libBLT is "not found" by the script, although, I have the .so files in the correct library - disabled -Werror flag - copied /usr/bin/libtool into ~/dev/ in order to avoid libtool version mismatch error - In Makefile for ~/utils/ commented out any rules for unwarpGradientNonLinearity since this file is no where to be seen Thank you for any advice and pointers! Danny Kim BC Children's Hospital Danny Kim Children's Brain Mapping Centre BC Children's Hospital

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Skullstrip error issue
by Rashmi Singh 03 Oct '12

03 Oct '12

Hello experts, I am getting skull strip issues with FreeSurfer recon-all runs in every data. I ran recon-all on my T1-data and noticed that the skullstrip is not so good. Almost in every subjects there were dura included, so I tried the suggestion of using the flags -skullstrip and -Clean–bm and –gcut in my recon-all command line for one subject. Forexmaple: I ran reconall using the following command lin: recon-all –skullstrip first -clean–bm –gcut –s AA***.T* -all -use–mritotal The run was complete and I looked at the brainmask.mgz file of the output. But I didn't see any correction. I am attaching the jpg image of the sagittal view of brainmask.nii ( I converted the mgz file to nii to view tham in afni) SubjFS: is the image from recon-all run SubjFS: is the image from recon-all that was run with Skullstrip/clean-bm/gcut options included. Did I do anything wrong? Your guidance and suggestion needed. Thanks, Rashmi.

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mri_glmfit and --mask
by Brain Apprentice 02 Oct '12

02 Oct '12

Hello everyone, I am trying to incorporate a binary FMRI mask into mri_glmfit. The problem is that it does not matter what I put in for the mask file I get the same results. This is the command I am using: mri_glmfit \ --y /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/y.mgh \ --fsgd /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/qdec.fsgd dods \ --glmdir /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2-msk6 \ --surf fsaverage lh \ --mask /shared/subjects/4-aut-v510/a-aut-v510/3-long/<Files listed below>\ --label /shared/subjects/4-aut-v510/a-aut-v510/3-long/fsaverage/label/lh.aparc.label \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Avg-Intercept-thickness.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Avg-thickness-TOMAL_COMPOSITE_MEMORY_INDEX-Cor.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Diff-Control-ASD-Intercept-thickness.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Diff-Control-ASD-Cor-thickness-TOMAL_COMPOSITE_MEMORY_INDEX.mat Here are the files that are getting inserted: DMN-b.mgz - Is a binary version of FMRI activation. DMN2-b.mgz - Is a binary file with nothing but zeros. DMN3-b.mgz - Is a binary file with nothing but ones.. I should also point out that the glmdir directory is changing with each new run of mri_glmfit. There is one other thing I should mention, and that is the above command other than the --mask part I got from qdec including the contrast1.mat part. I am sure it is me and I am doing something wrong. If someone can suggest an alternative I would be most grateful. Thanks

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CUDA error on mac os x, freesurfer 5.1.0
by Chris Adamson 02 Oct '12

02 Oct '12

I get a CUDA error: MRISCcomputeVertexDistances: invalid device function . during mris_sphere_cuda with a Quadro FX 5600, see the log below, any advice?: \n mris_sphere_cuda -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov_11_15:26:50_PST_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 5.0 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: Quadro FX 5600 doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.56 (0.00-->7.32) (max @ vno 74508 --> 74520) face area 0.02 +- 0.03 (-0.24-->0.53) CUDA error: MRISCcomputeVertexDistances: invalid device function . scaling brain by 0.300... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.911, avgs=0 005/300: dt: 0.9000, rms radial error=176.653, avgs=0 010/300: dt: 0.9000, rms radial error=176.099, avgs=0 015/300: dt: 0.9000, rms radial error=175.369, avgs=0 020/300: dt: 0.9000, rms radial error=174.537, avgs=0 025/300: dt: 0.9000, rms radial error=173.647, avgs=0 030/300: dt: 0.9000, rms radial error=172.725, avgs=0 035/300: dt: 0.9000, rms radial error=171.787, avgs=0 040/300: dt: 0.9000, rms radial error=170.841, avgs=0 045/300: dt: 0.9000, rms radial error=169.892, avgs=0 050/300: dt: 0.9000, rms radial error=168.943, avgs=0 055/300: dt: 0.9000, rms radial error=167.997, avgs=0 060/300: dt: 0.9000, rms radial error=167.054, avgs=0 065/300: dt: 0.9000, rms radial error=166.115, avgs=0 070/300: dt: 0.9000, rms radial error=165.182, avgs=0 075/300: dt: 0.9000, rms radial error=164.252, avgs=0 080/300: dt: 0.9000, rms radial error=163.328, avgs=0 085/300: dt: 0.9000, rms radial error=162.408, avgs=0 090/300: dt: 0.9000, rms radial error=161.493, avgs=0 095/300: dt: 0.9000, rms radial error=160.583, avgs=0 100/300: dt: 0.9000, rms radial error=159.677, avgs=0 105/300: dt: 0.9000, rms radial error=158.777, avgs=0 110/300: dt: 0.9000, rms radial error=157.882, avgs=0 115/300: dt: 0.9000, rms radial error=156.991, avgs=0 120/300: dt: 0.9000, rms radial error=156.104, avgs=0 125/300: dt: 0.9000, rms radial error=155.222, avgs=0 130/300: dt: 0.9000, rms radial error=154.345, avgs=0 135/300: dt: 0.9000, rms radial error=153.472, avgs=0 140/300: dt: 0.9000, rms radial error=152.604, avgs=0 145/300: dt: 0.9000, rms radial error=151.742, avgs=0 150/300: dt: 0.9000, rms radial error=150.884, avgs=0 155/300: dt: 0.9000, rms radial error=150.031, avgs=0 160/300: dt: 0.9000, rms radial error=149.182, avgs=0 165/300: dt: 0.9000, rms radial error=148.340, avgs=0 170/300: dt: 0.9000, rms radial error=147.503, avgs=0 175/300: dt: 0.9000, rms radial error=146.670, avgs=0 180/300: dt: 0.9000, rms radial error=145.842, avgs=0 185/300: dt: 0.9000, rms radial error=145.019, avgs=0 190/300: dt: 0.9000, rms radial error=144.200, avgs=0 195/300: dt: 0.9000, rms radial error=143.386, avgs=0 200/300: dt: 0.9000, rms radial error=142.576, avgs=0 205/300: dt: 0.9000, rms radial error=141.770, avgs=0 210/300: dt: 0.9000, rms radial error=140.969, avgs=0 215/300: dt: 0.9000, rms radial error=140.173, avgs=0 220/300: dt: 0.9000, rms radial error=139.381, avgs=0 225/300: dt: 0.9000, rms radial error=138.594, avgs=0 230/300: dt: 0.9000, rms radial error=137.810, avgs=0 235/300: dt: 0.9000, rms radial error=137.032, avgs=0 240/300: dt: 0.9000, rms radial error=136.257, avgs=0 245/300: dt: 0.9000, rms radial error=135.488, avgs=0 250/300: dt: 0.9000, rms radial error=134.722, avgs=0 255/300: dt: 0.9000, rms radial error=133.961, avgs=0 260/300: dt: 0.9000, rms radial error=133.204, avgs=0 265/300: dt: 0.9000, rms radial error=132.451, avgs=0 270/300: dt: 0.9000, rms radial error=131.703, avgs=0 275/300: dt: 0.9000, rms radial error=130.959, avgs=0 280/300: dt: 0.9000, rms radial error=130.219, avgs=0 285/300: dt: 0.9000, rms radial error=129.484, avgs=0 290/300: dt: 0.9000, rms radial error=128.753, avgs=0 295/300: dt: 0.9000, rms radial error=128.025, avgs=0 300/300: dt: 0.9000, rms radial error=127.302, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17578.61 Darwin XXX 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s test exited with ERRORS at Wed Oct 3 10:49:05 EST 2012 For more details, see the log file /data/addo/nsclp/connectivity/freesurfer/test/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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mri_vol2vol
by Andrew Bock 02 Oct '12

02 Oct '12

Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew

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error in mri_segstats, important
by Knut J Bjuland 02 Oct '12

02 Oct '12

I have download the latest verion of mri_segstats from the release notes. But it does not generate asegstats. 4 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012 /home/knutjb/freesurfer/20_ucsd_automatic_version2/004 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004 ERROR: Option --sum unknown #------------------------------------------ recon-all -s 004 finished without error at Tue Oct 2 07:36:17 CEST 2012 done knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats USAGE: mri_label2vol Possible inputs: --label labelid <--label labelid> --annot annotfile : surface annotation file --seg segpath : segmentation --aparc+aseg : use aparc+aseg.mgz in subjectdir as seg --temp tempvolid : output template volume --reg regmat : VolXYZ = R*LabelXYZ --regheader volid : label template volume (needed with --label or --annot) for --seg, use the segmentation volume --identity : set R=I --invertmtx : Invert the registration matrix --fillthresh thresh : between 0 and 1 (def 0) --labvoxvol voxvol : volume of each label point (def 1mm3) --proj type start stop delta --subject subjectid : needed with --proj or --annot --hemi hemi : needed with --proj or --annot --surf surface : use surface instead of white --o volid : output volume --hits hitvolid : each frame is nhits for a label --label-stat statvol : map the label stats field into the vol --stat-thresh thresh : only use label point where stat > thresh --offset k : add k to segmentation numbers (good when 0 should not be ignored) --native-vox2ras : use native vox2ras xform instead of tkregister-style --version : print version and exit --help $Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $ knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum ERROR: Option --sum unknown Knut J

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Re: [Freesurfer] correcting rippled image
by Deirdre O Shea 02 Oct '12

02 Oct '12

Sorry, I thought I had attached the image. Here it is anyway. cheers, On Tue, Oct 2, 2012 at 3:08 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I don't know since I don't know what went wrong. Send us an image and cc > the list and we'll take a look. > > > cheers > Bruce > On Tue, 2 Oct 2012, Deirdre O Shea wrote: > > Hi Bruce, >> >> That's what I meant so I take it that there's nothing i can do to improve >> the image with FreeSurfer then? >> >> Thanks, >> Deirdre >> >> >> >> On Tue, Oct 2, 2012 at 3:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Deirdre >> >> I'm not sure exactly what you mean, but probably what you are >> seeing (the circular patterns) are the effects of >> motion >> >> cheers >> Bruce >> On Tue, 2 Oct 2012, Deirdre O Shea wrote: >> >> Hey everyone, >> >> I was wondering if anyone knew how to correct for a ripple >> like effect in >> the image. I have adjusted the talairach and it still looks >> the same. Any >> suggestions would be great. see image attached. >> >> Thanks, >> Deirdre >> >> >> >> >> 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<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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correcting rippled image
by Deirdre O Shea 02 Oct '12

02 Oct '12

Hey everyone, I was wondering if anyone knew how to correct for a ripple like effect in the image. I have adjusted the talairach and it still looks the same. Any suggestions would be great. see image attached. Thanks, Deirdre

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Appropriate Segmentation Sequence?
by Sullivan, Patrick M. 02 Oct '12

02 Oct '12

Hello, I have a set of archival data (so I was unfortunately not able to specify the acquisition sequences and include the recommended MPRAGE sequence). I am asking which sequence (if any) would be most conducive to volumetric/regional analysis using FreeSurfer. A Philips Achieva 3.0T was used for all acquisitions. All patients all have a the following sequences: FLAIR (TE 140ms, TR 10ms, Flip 90) T2W_FFE (TE 16ms, TR 1.5s Flip 18) Spin Echo (TE 16ms, TR 600ms Flip 90) DUAL_TSE CLEAR (TE 13ms, TR 3.4s, Flip 90) Would any of these be appropriate for segmentation and volumetric analysis? Thank you very much. -Patrick

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processing scans on more than one computer
by pietro de rossi 02 Oct '12

02 Oct '12

Dear FreeSurfer experts, I'm processing scans on three different computers and I would like to know if it is possible to collect all the processed scans together in order to analyze data on just one computer. I realized that even moving the processed subjects folders to another folder within the same computer (even if I set the new folder as the SUBJECTS_DIR) I'm not able to run tksurfer and tkmedit for those subjects....am I doing anything wrong? is it just that once you've processed the scans the proc_folders cannot be moved? thanks, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Freesurfer October 2012