Freesurfer

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xhemi problem
by Gabriel Gonzalez Escamilla 25 Jan '13

25 Jan '13

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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

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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

2 1

Memory problem
by Borzello, Mia 24 Jan '13

24 Jan '13

Hey Freesurfers, I received a "Cannot allocate memory" error while running a recon overnight. I think there should be enough space on the machine to store the data so I'm suspicious that it's a different memory problem. I attached the recon-all.log file. Thanks for your help! m

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Re: [Freesurfer] How to generate Cohen´s d Maps in Freesurfer
by Douglas N Greve 24 Jan '13

24 Jan '13

Hi Javier, you don't want to use the gammarvar for Cohen's D. Gammavar is like the standard error (square of the std error). Instead, use rstd.mgh located in the main glmfit folder. Otherwise, I think your equation is right. I don't think you can do this with one call to fscalc. I think you'd need at least two. doug ps. Please post questions to the list and not directly to me. Thanks! On 01/24/2013 07:55 AM, Javier Navas wrote: > Hi Doug, > > I´m very new in Freesurfer and I cannot obtain a Cohen´s d Map as a > Effect Size measure. Is it possible to generate surface maps for the > Cohen´s d in cortical thickness between 2 groups within with Freesurfer. > I have the mean thickness for each group; after obtained these > gamma.mgh I tried with fscalc but I do not know how to do it: | > MeanGroup1 sub MeanGroup2 | /sqrt((Std12add Std22)/2) ... it is right??? > > Is the gammavar.mgh the Standard Deviation (Std) ??? > > Thank you in advance > > -- > /**********************************************************\ > Francisco Javier Navas Sánchez > Laboratorio de Imagen Médica U.M.C.E. > Hospital General Universitario Gregorio Marañón > Dr Esquerdo 46, 28007 Madrid, Spain > Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 > e-mail:jnavas@hggm.es <mailto:e-mail%3Ajnavas@hggm.es> > http://image.hggm.es -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Problem with glmfit: matrix is ill-conditioned
by Ed Gronenschild 24 Jan '13

24 Jan '13

Hi, Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following error message: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh -- fsgd ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ fsgd_sib_con_cann_aangepast3.fsgd dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf fsaverage lh -- C ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ group_thickness_gender_scan_age_educ_hand_cann.mtx 2. The FSGD file (if using one) 3. And the design matrix above Please find attached the requested files. I noticed that rows 68 and 147 of the matrix Xg.dat are identical, and most probably caused the error. In the fsgd file I see that the correspondig cases indeed have identical values, although they are referring to different data. How to proceed? Cheers, Ed

2 1

Re: [Freesurfer] mni152reg error (file permission denied)
by Chris McNorgan 24 Jan '13

24 Jan '13

Hi Tommi, The mkdir error suggests to me that there is some system-level permissions thing going on. If it can't make the directory, then there is no directory into which fsl can write the refvol.fslregister.nii files, hence the final 2 errors. From the command line, are you able to navigate to directory: /usr/pubsw/packages/fsl/current/data/standard/ And within that directory, execute: mkdir <somedirectoryname> My guess is that you will get a permission denied error. You can try using chmod to make the directory writable: chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/ and see if you can now do a mkdir in that directory (you might have to be a superuser to do this) Dear Surfers, mni152reg --$SUBJECT exits with the error: mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402': Permission denied Thereafter, a couple consequential errors follow ... niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii ... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii This is on FS 5.1.0 stable. The error seems linux box independent. Please let me know if you need further info. Thanks! Bests, Tommi -- Chris McNorgan Postdoctoral Researcher Developmental Cognitive Neuroscience Laboratory Northwestern University, Evanston, IL DCNL Lab: http://tinyurl.com/9q35abd Frontiers Profile: http://tinyurl.com/aut488k

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