Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30095 discussions

problem with qdec in full install of 5.2 beta
by Carl Anderson 26 Jan '13

26 Jan '13

Dear Freesurfer, When trying to start qdec I get the following error: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap Any suggestions for a work around? Thanks, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

2 1

mean cluster surface area in mri_glmfit
by xiangbo_2010 25 Jan '13

25 Jan '13

Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found using command line (mri_glmfit). I used mri_glmfit for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (using FDR corrected, is not Clusterwise Correction for Multiple Comparisons). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? thanks! Bo Xiang

2 1

Two questions: autocorrelation correction and vertex distance
by Alex Kell 25 Jan '13

25 Jan '13

Hi Freesurfers, I have two unrelated questions. 1. I want to pre-whiten some functional data without running a GLM on them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and mailing archives, but I can't find how to pre-whiten the data without running a GLM. Is there a straightforward way? If not, I guess we could just do it in matlab. 2. Separately, we're bringing some volume masks to the surface and are preprocessing them with dilation and erosion to clean them up. We're trying to get a sense of how much is a reasonable amount to dilate and erode by, and it would be helpful to know about how far apart the adjacent surface vertices are. Roughly, what's the mean distance between adjacent vertices? Thanks in advance. Best, Alex

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Problems calling Free Surfer...
by Rosalia Dacosta Aguayo 25 Jan '13

25 Jan '13

Dear Free Surfer experts, I am having problems with my FS installation. I am working with Linux/Ubuntu version 11.10...I have followed the indications of the FS wiki and it seems that it is installed but it does not work...it does not run in the terminal and I do not know why and how can I do: osi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/FREE_SURFER/ freesurferrosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ export FREESURFER_HOME=/home/rosi/FREE_SURFER/freesurfer rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/rosi/FREE_SURFER/freesurfer FSFAST_HOME /home/rosi/FREE_SURFER/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/rosi/FREE_SURFER/freesurfer/subjects MNI_DIR /home/rosi/FREE_SURFER/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/FREE_SURFER/freesurfer$ freesurfer FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at: https://surfer.nmr.mgh.harvard.edu Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text. Direct comments and questions to: freesurfer(a)nmr.mgh.harvard.edu *You are running this version of FreeSurfer: freesurfer-Linux-centos4-**stable-pub-v5.1.0 rosi@rosi-HP-Pavilion-dv9700-* *Notebook-PC:~/FREE_SURFER/**freesurfer$ How can I call FreeSurfer?? *Thanks in advance, Rosalia.

3 3

xhemi problem
by Gabriel Gonzalez Escamilla 25 Jan '13

25 Jan '13

2 1

gcut problem
by Isabelle Deschamps 25 Jan '13

25 Jan '13

Good morning, I tried to run the following command: recon-all -skullstrip -clean-bm -gcut -subjid S01 to remove the skull and remaining dura mater. However, for some subjects, I get the following error: ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead! I tried adjusting the wsthresh, as suggested in previous posts, but without success. Is there something else, I can try? Thank you in advance for your help, Isabelle

1 0

Testing new beta v5.2.0: Error in mri_segstats --euler
by Johnson, Hans J 24 Jan '13

24 Jan '13

In mri_segstats command line generated from autorecon, I get an error that the option "--euler" is unknown. ==================================================== == /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all 3667 if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix ) ) then 3668 set cmd = ($cmd --euler) 3669 endif ==================================================== Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 RedHat release: CentOS release 5.8 (Final) Kernel info: Linux 2.6.18-308.16.1.el5 x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 1)Subject Name = 12126_12126_20091110_30 2) We are running on a shared cluster of computers, so we wanted to break it into 3 sections to make it more robust to failing jobs. #!/bin/bash export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon1 status=$? exit $status #!/bin/bash export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon2 status=$? exit $status #!/bin/bash export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer export SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug -subjid 12126_12126_20091110_30 -make autorecon3 status=$? exit $status 3) #-------------------------------------------- #@# ASeg Stats Thu Jan 24 20:57:29 CST 2013 /nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS/12126_12126_20091110_30 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/ASegStatsLUT.txt --subject 12126_12126_20091110_30 ERROR: Option --euler unknown Linux helium-login-0-0.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 12126_12126_20091110_30 exited with ERRORS at Thu Jan 24 20:57:30 CST 2013 ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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thickness=0, what that means?
by jm 24 Jan '13

24 Jan '13

Dears Freesurfer: We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we can see some vertexes with thickness value equal to 0 (thickness=0 mm). Could you tell me when that value is reported by Freesurfer? what do (thickness=0) means? Thanks in advance !!!

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Re: [Freesurfer] Results Vary
by Nick Schmansky 24 Jan '13

24 Jan '13

Derin, the results vary only a tiny bit because of differences in the talairach_with_skull.lta file, which was created twice, the second time with aseg info, which would cause the brainmask to vary slightly if run a second time. the result differences are well below what you would find with randomness enabled. Nick > Hi Nick, > > Could you clarify this? So if we re-run a subject in 5.1 (say after doing > some edits), we would then need to run it again a third time in order to > maintain consistency? Thanks. > > -Derin > > > On Jan 22, 2013, at 2:17 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > wrote: > >> also there is an issue in v5.1 where the second run of recon-all on a >> given platform will produce different results from the first (but >> subsequent runs should produce identical results). this issue has been >> fixed in the upcoming v5.2 release. >> >> nick >> >> >> On Tue, 2013-01-22 at 10:18 -0500, Douglas N Greve wrote: >>> Hi Chikku, while we try to resolve these differences, you are not >>> guaranteed to get identical results when you use different platforms. >>> This is an issue with using different computes and applies to all >>> software, not just FS.It is caused by the use of different math >>> libraries and different binary operations. The difference you show is >>> only 0.3% which should not be enough to cause false results. >>> doug >>> >>> >>> >>> On 01/22/2013 08:13 AM, Varghese Chikku wrote: >>>> >>>> Dear FS team, >>>> I processed two set of MRI data for a single patient,Thats BL scan >>>> and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual >>>> machine installed. >>>> Though I was expecting the same segstats,the results vary from >>>> Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for >>>> the same images in VM the results are 177432.Does it happened to >>>> any one before....Whats the reson its happening and how can I >>>> remedy,validate the results. >>>> Much appreciate your advice,... >>>> In Thanks >>>> Chikku. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >> _______________________________________________ >> 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. >> > > > >

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ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!
by Garikoitz Lerma-Usabiaga 24 Jan '13

24 Jan '13

Hi FS experts, I read that the current dev version for recon-all is going to be the same to the 5.2 version, so I started a new project with the dev version (in CentOS 4). I have this very strange error that I am unable to interpret, when running mpr2mni305 in one case the target is specified as 711-2C_as_mni_average_305, but in the dev version the target is 3T18yoSchwartzReactN32_as_orig, this file does not exist... What should I try now? (just in case, this is the command I launch: recon-all --i xxxxx -s xxxxxxx -qcache -hippo-subfields -all (This is the talairach_avi.log) ERROR WITH DEV VERSION -------------------------------------------- /home/glerma/FS/52/freesurfer/subjects/TNT/S_08/mri /home/glerma/FS/52/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.10 2012/07/16 15:54:03 nicks Exp $ Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 24 00:26:09 CET 2013 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.202 2012/10/17 19:23:56 greve Exp $ reading from orig_nu.mgz... TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00 i_ras = (-1, -3.03407e-09, 2.32831e-10) j_ras = (1.16415e-10, 0, -1) k_ras = (3.03407e-09, 1, 3.72529e-09) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 132.933; -0.000 0.000 1.000 -105.037; 0.000 -1.000 0.000 161.057; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Thu Jan 24 00:26:10 CET 2013 /home/glerma/FS/52/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=3T18yoSchwartzReactN32_as_orig ERROR: /home/glerma/FS/52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist! SAME SUBJECT, SAME HARD and OS, 5.0 VERSION --------------------------------------------------------------------------------- /home/BCBL/glerma/freesurfer/subjects/TNT/S_08/mri /usr/local/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Sat Aug 25 06:44:15 CEST 2012 mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from nu.mgz... TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00 i_ras = (-1, 0, 5.55112e-17) j_ras = (5.55112e-17, 3.72529e-09, -1) k_ras = (4.44089e-16, 1, -1.05964e-18) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 132.933; 0.000 0.000 1.000 -105.037; 0.000 -1.000 -0.000 161.057; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Sat Aug 25 06:44:16 CEST 2012 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 -------------------------------- continues....---------------------- and this is the setup output: -------- freesurfer-Linux-centos4_x86_64-dev-20121127 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/glerma/FS/52/freesurfer FSFAST_HOME /home/glerma/glerma/software/freesurfer/fsfast >> older version location FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/glerma/FS/52/freesurfer/subjects/TNT MNI_DIR /home/glerma/FS/52/freesurfer/mni FSL_DIR /usr/local/fsl many thanks! Gari

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