Freesurfer August 2005

freesurfer@nmr.mgh.harvard.edu

42 participants
72 discussions

fsl_rigid_register
by Steve Stufflebeam 29 Aug '05

29 Aug '05

fsl_rigid_register is not as it has in the past. It seems the script isn't writing the correct outvol.* format in the /tmp directory. My command line and output are below. Thanks, --Steve lucy [flash] fsl_rigid_register -r orig.mgh -i flash5.mgh -o flash5_fsl.mgh $Id: fsl_rigid_register,v 1.7 2003/08/21 23:28:03 ebeth Exp $ Mon Aug 29 09:31:13 EDT 2005 flash5_fsl.mgh -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img reading from orig.mgh... TR=2000.00, TE=3.37, TI=950.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img... Analyze Output Matrix -1.000 -0.000 -0.000 129.806; -0.000 0.000 1.000 -58.312; 0.000 -1.000 -0.000 126.746; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 'coronal flipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.imgmri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img reading from flash5.mgh... TR=20.00, TE=1.80, TI=1.80, flip angle=5.00 i_ras = (0.0729938, -0.963132, 0.258938) j_ras = (0.0105586, -0.25887, -0.965855) k_ras = (-0.997276, -0.0732354, 0.00872654) writing to /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img... Analyze Output Matrix 0.073 0.011 -1.326 76.077; -0.963 -0.259 -0.097 234.646; 0.259 -0.966 0.012 88.186; 0.000 0.000 0.000 1.000; -------------------- No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash/flash5.mgh are: x_r = 0.0730, y_r = 0.0106, z_r = -0.9973, c_r = 0.6410 x_a = -0.9631, y_a = -0.2589, z_a = -0.0732, c_a = 70.6763 x_s = 0.2589, y_s = -0.9659, z_s = 0.0087, c_s = -2.2521 INFO: set hdr.hist.orient to 'transverse unflipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash tkregister2 --targ orig.mgh --mov flash5.mgh --reg /tmp/fsl_rigid_register.6917/tkregister.dat --fslregout /tmp/fsl_rigid_register.6917/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume orig.mgh movable volume flash5.mgh reg file /tmp/fsl_rigid_register.6917/tkregister.dat LoadVol 0 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgh Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable flash5.mgh Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.330 -85.120; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; register: file /tmp/fsl_rigid_register.6917/tkregister.dat written Init FSL Mat based on geometry ------------------- -0.07299379 -0.01055863 0.99727648 53.97108841 -0.25893784 0.96585459 -0.00872653 38.25601959 -0.96313190 -0.25886959 -0.07323541 290.63790894 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash flirt -in /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.6917/initxfm.fslmat -omat /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh reading from /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img... ERROR: analyzeRead(): cannot find any files for /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img

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encounter error during fill
by Yuan-Fen Kuo 29 Aug '05

29 Aug '05

Hi. I am ( again) trying out the stage1 work flow. I have been encountering the following error during the fill step which terminates the work flow. mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005 how may I go about solving this? The complete output is at the end of the message. Thank you for help, Eric Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison --------------------------------------------- Fill Mon Aug 29 14:01:26 CDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm wm filled /Users/Shared/freesurfer/subjects/005CO/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Volume /tmp/mritotal_20452/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.078 -0.013 -0.035 -5.822; 0.018 1.076 0.141 -29.222; 0.032 -0.136 1.035 16.018; 0.000 0.000 0.000 1.000; mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 12102 (min = 350, max = 1400), aspect = 0.79 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status recon-all exited with errors at Mon Aug 29 14:02:23 CDT 2005

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Cannonical Registration
by Yuan-Fen Kuo 26 Aug '05

26 Aug '05

Hi: I am trying out the recon-all command with the -stage1 workflow. The Cannonical Registration ( mri_ca_register) runs for many many hours. I have not found much reference regarding this step. It is not mentioned in the help in the -stage1 section, nor is it mentioned under step-wise directives. Is this a necessary step if I'd just like to have basic segmentation and being able to proceed to the manual editing procedure? Thank you, Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

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Distributions: which? ; Archives -- forbidden
by Graham Wideman 26 Aug '05

26 Aug '05

Folks: I would like to get up-to-date on our FreeSurfer installation. Are there some notes which describe the various snapshots at: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ ? In particular, some of these downloads are much huger than others, which makes one wonder what's included in each. I also tried to see if there were some email messages covering this in the archives, but the archive seems to be broken currently: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ ... returns "Forbidden" -- ie: permissions problem. Regards, Graham

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parcellation of frontal lobe
by marc ruiz 26 Aug '05

26 Aug '05

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autorecon1 difficulty
by Elizabeth Fenstermacher 25 Aug '05

25 Aug '05

Hello, I was trying to test the autorecon tools that we're planning to use to process some of our newer data. In order to do so I sourced source /usr/local/freesurfer/nmr-dev-env Then after setting my subject directory [/space/thigpen/1/users/efenster/example] typed: recon-all -subjid 002 -autorecon1 It failed during the intensity normalization I believe yielding the following error message ----------------------------------------------------------------------------------- BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct recon-all exited with errors at Thu Aug 25 14:23:21 EDT 2005 ----------------------------------------------------------------------------------- When viewing the file it sites as being problematic it seems to be the initialization of one of the MNI tools, specifically the following line use MNI::Startup qw(nocputimes); Is there a problem in how I initialized FreeSurfer that created this error and if so how would it be recommended to initialize FreeSurfer in order to use the autorecon tools? Thank You Eliz

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ERROR:nu_correct
by Margaret Duff 25 Aug '05

25 Aug '05

Hello, I am running the command: recon-all -subjid SM2S12_autoreconall -autorecon1 -notalairach on troy and getting the following error message: --------------------------------------------- Nu Intensity Correction Thu Aug 25 12:11:42 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, -1.01845e-10, -1.20596e-09) j_ras = (-1.65567e-09, 6.42749e-09, -1) k_ras = (-2.65927e-10, 1, 9.43205e-09) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mduff@troy:/autofs/space/troy_001/users/FREESURFER/SM2S12_autoreconall/mri/] [2005-08-25 12:11:52] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_27529/ nu0.mnc nu1.imp /usr/pubsw/packages/mni/current/bin/volume_stats: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct recon-all exited with errors at Thu Aug 25 12:11:53 EDT 2005 This command was working yesterday, so I am not sure what has changed over night. Thanks for your help, Margaret

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COR to BRIK
by Michele Perry 25 Aug '05

25 Aug '05

Hi, Is there a way to view an aseg with colors in afni once it has been converted to .img? Michele

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Re: [Freesurfer] Tiger and MNI Linear Register
by Nick Schmansky 24 Aug '05

24 Aug '05

Eric, Hi. The MNI Linear Register option is code that is found in the MINC toolkit, and it is that code that is generating the message about not being implemented. So I am afraid you are out of luck in that respect, in that we do not maintain the MINC toolkit. I think our default registration tools do a good job though. Also, we advocate usage of the command-line tools over csurf, which is a gui that we no longer support. The reason is that it is easier to perform a work-flow from the command-line, and more importantly, it is easier to copy-and-paste any error messages that may appear in a failed run. You should have a look at the script recon-all. Type: recon-all --help This will talk about the processing stages, and is the main 'front-end' to the freesurfer tools. We will be releasing an online tutorial soon that will fully describe a workflow using recon-all. Per the message about perl found in your email, freesurfer does use the perl executable installed on the machine, and the MNI tools puts there perl scripts in the path found in the PERL5LIB that freesurfer prints out. That path looks like the /System path I think only because it makes clear which perl version MNI is using. Nick On Wed, 2005-08-24 at 14:45 -0500, Yuan-Fen Kuo wrote: > Hi Nick: > Thanks for your reply and sorry for my late reply. > > I have checked the "MNI Linear Register" option in the expert > Preference. > When I run "Convert/Average" in "Setup Structural Scan > Parameters" I am prompted with the following message "MNI align not > yet implemented." in a popped up window. I do all these in the GUI. > I did check the log window, and no messages were printed out in > there. I have installed the full package ( freesurfer-Darwin-tiger- > full.dmg ) with no customization. > > In the previous message I have mentioned my changes to the > SetUpFreeSurfer.csh script. I have figured out why I did not need to > make the modificaitons, however, if you are still interested, I do > explain why I made the changes below. > > > Thank you, > Eric > > ********************************* > > > > > 1) I used to un-comment the following lines in > SetUpFreeSurfer.csh attempting to use the MINC tools ( as modifying > the script is usually the first step any tutorial instructs. ) > > #setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > #setenv MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > I realized that these directories do not exist so I changed them to > > MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin > MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib > > then I finally realized that if I do not un-comment the two > lines in SetUpFreesurfer.csh, the two variables will anyway be set to > > MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin > MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib > > so I have no problem with these two variables now. However, > perhaps it should be modified in the > SetUpFreeSurfer.csh script to avoid confusion? > > > 2) PERL5LIB is set to > > /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6 > > while this package is a tiger package, perhaps we can use the > Perl that comes with Tiger in > > /System/Library/Perl/5.8.6 > > I realize in FreeSurferEnv.csh, Tiger's Perl is checked, but it > is nevertheless set back to > > /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6 > > > > > On Aug 22, 2005, at 3:39 PM, Nick Schmansky wrote: > > > Yuan-Fen, > > > > Hello, I think I need more information before I can diagnose the > > problem. What is being run when the error message appears? If you > > could copy and paste the command-line output, that would be helpful. > > > > Also, I am not sure what was changed in the SetUpFreeSurfer.csh > > script, > > as the MINC_BIN_DIR and MINC_LIB_DIR vars are correct (and are the > > default). What were they set to prior? > > > > Thanks, > > > > Nick > > > > > > On Mon, 2005-08-22 at 14:50 -0500, Yuan-Fen Kuo wrote: > > > >> Hi. > >> > >> > >> I have installed the > >> freesurfer-Darwin-tiger-full.dmg > >> > >> > >> and I would like to use the MNI Linear Register option. > >> > >> > >> I have been prompted that "MNI has not been align not yet > >> implemented." > >> > >> > >> Because of this message, I have changed my SetUpFreeSurfer.csh script > >> so that the following directories are pointed to the corresponding > >> path instead of the default that came with the package. > >> > >> > >> MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin > >> MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib > >> PERL5LIB /System/Library/Perl/5.8.6 > >> > >> > >> > >> > >> However, I still get the same message. > >> > >> > >> Is there something I am missing? > >> > >> > >> Thanks in advance. > >> Eric > >> _______________________________________________ > >> 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 > > > >

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paradigm ill-conditioned
by Hans Op de Beeck 24 Aug '05

24 Aug '05

Hi all, When I run selxavg-sess, I sometimes get the following error message at the beginning of the algorithm (right after I get the Residual Error Estimation): ERROR: paradigm is ill-conditioned (1.17293e+07) Check your paradigm file for file for periodicities My paradigm is fairly simple. It is a block-design, I use -gammafit, and there are 3 conditions that I present in 3 different orders across runs (e.g., in one run it might be 0 1 2 3 0 3 2 1 0). I always use the same paradigm-files, and this error message doesn't appear always. In general I include the motion-correction parameters as covariates (flag -mcextreg in mkanalysis-sess.new). The problem is easily solved by not including the motion-correction parameters in the analysis. Can this error message be caused by a strong correlation between 2 of my mc-parameters ? What is the best solution in that case ? Maybe to compute a lower number of principal components whenever the problem occurs ? Thank you for your help, Hans P. Op de Beeck Kanwisher lab

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Freesurfer August 2005