Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

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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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

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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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Downsampling/decimating overlays (not surfaces)
by Nicola Toschi 24 Jan '13

24 Jan '13

Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around.

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mni152reg error (file permission denied)
by raij＠nmr.mgh.harvard.edu 23 Jan '13

23 Jan '13

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 --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Results Vary
by Varghese Chikku 23 Jan '13

23 Jan '13

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.

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Empty search space
by Jürgen Hänggi 23 Jan '13

23 Jan '13

Dear FS experts I run a longitudinal analysis, and all steps (cross, base, long) were run without errors. I used QA tools in order to look at the results and all recons are fine. However, when running glmfit with the --osgm option there is no error message, but there is also no results (sig=0, F=0). In the log I realized that the mask is empty (see below). Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to Cap_Thickness_LH.glmdir/mask.mgh Reshaping mriglm->mask... search space = 0.000000 What are the most plausible reasons for this empty mask? Should I try the pruning option? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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tracula bedpostx failure
by Cat Chong 22 Jan '13

22 Jan '13

Hello Experts, I am running bedpost x through fsl on the dmri directory (as advised in a previous post). I receive the fsl error message: “child process exited abnormally”. The command line error states: switching from /8000_tracula/8000_tracula_out/8005_DTI/dmri to /8000_tracula/8000_tracula_out/8005_DTI bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 /Applications/fsl/bin/bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 subjectdir is /8000_tracula/8000_tracula_out/8005_DTI/dmri /8000_tracula/8000_tracula_out/8005_DTI/dmri/data not found All the output files of the trac-all -prep stage are there, but could I have made a mistake on my configuration file? I have attached it. Thank you very much for your help, Cheers, Cat

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Freesurfer January 2013