Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

skull strip
by Tara Brah 29 Jul '10

29 Jul '10

I have a question regarding the skull stripping process. I ran my data through recon-all but still had much skull intact. I then followed the recommended process per the freesurfer wiki to change the watershed threshold levels on the recon process. I did so at the 20, 15, 10, 5, and 0 threshold with little improvement to the amount of skull removed. I know a similar question has been asked but in that scenario freesurfer was not including the skull as part of the cortical matter while in my scenario it is. Do you have any further suggestions as to how to remove the skull from my images? Thank you.

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recon-all error
by Watson, Christopher 29 Jul '10

29 Jul '10

I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010 make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1 The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was "recon-all -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", and saw the same error. It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz) The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Any ideas? Chris

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Script to get recon processing time
by Chris Watson 29 Jul '10

29 Jul '10

Hello, Do you guys have a script that parses recon-all.log and spits out the processing time for each step? Something that would be similar to this in recon-all --help: -<no>motioncor < 5 min -<no>nuintensitycor 3 min -<no>talairach 4 min -<no>normalization 3 min -<no>skullstrip 1 min -<no>gcareg 8 min -<no>canorm 1 min -<no>careg 10 hours and so on. Thanks, Chris

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ALICE overlay files conversion
by Gregory Dierksen 28 Jul '10

28 Jul '10

Hello, My lab group has some scans with overlays identifying hemorrhages that were made using ALICE (the files have a .oly extension) that we'd really like to be able to use with FreeSurfer Obviously mri_convert won't do anything with these files, but I was hoping that perhaps you have some old tools for converting these files...? Thanks a lot, Greg --

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Transforming aseg.mgz to DTI space
by liang wang 28 Jul '10

28 Jul '10

Hi, I wanted to transform mri/aseg.mgz (obtained by the command: make_average_subject) to a standard DTI space. I used the following command to get a register.data applied to the DTI data to obtain to a new DTI data in the Freesurfer conformed space. bbregister --mov mean_FA.nii.gz --dti --s average --init-fsl --reg register.dat and then using tkregister2 to adjust the mean_FA to align well with ?h.avg.white. The new register.dat was saved to replace the old one. I think that if I can inversely apply the register.dat to aseg.mgz, it would work. However, I don't know how to reversely apply this transformation file. I tried to use --apply_inverse_transform in mri_convert, but it doesn't work. Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Replacing talairach.xfm
by Lena Palaniyappan 28 Jul '10

28 Jul '10

Hi all, How do I replace talairach.xfm by an identity matrix to prevent reorienting of images when I make-average ? Cheers Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Correcting MRI distortions: NITRC and grad_unwarp problems.
by Matt Russell 28 Jul '10

28 Jul '10

Hello All, I’m working with some data that I would like to compare inter-site, and would like to correct the gradient distortion from the different scanners (Siemens Allegra and Trio). That being said, I have looked online at the documentation to do this and have not been able to get the correction working properly. I have gotten the .grad files from Siemens and tried to use them with the two solutions online (the NITRC files and the grad_unwarp command in FreeSurfer) to no avail. I appreciate any advice from those experienced in correcting distortions. The two problems that I am having now is: 1. While I have done all the steps listed online for the NITRC and do get an output, the files come out in what looks to be more distortion than before the correction. (The heads look very blocky after the correction and the surrounding box, which I believe should turn out square, now looks like Pacman went crazy and ate bites out of the sides.) 2. To use the grad_unwarp from freesurfer, I used the NITRC files to make the converted .gwv file for the distortion correction, but get this error (below). I assume this means I don’t have a table.mat file. Where do I get this? Also, grad_unwarp -help doesn’t really say much about how we’re supposed to setup the files/make the correction tables, any advice? Thanks for any help you have to offer! Matthew Russell >> Error Log: FreeSurfer/INDIV-2/grainab13530_WF_WNA/mri/orig 11% grad_unwarp -i 001.mgh -o allegra_uw.mgh -unwarp allegra -mydev …. convert_unwarp_resample(infile,seriesno,outfile,corfovflag,unwarpflag,jacflag,interp_method,unwarptype,QuitOnError); % 1 = run from script, for qoe INFO: using matlab installation matlab Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> GRADWARPPATH=/labs/deyounglab/FreeSurfer/grad_unwarp_tables TABLE=/labs/deyounglab/FreeSurfer/grad_unwarp_tables/table.mat QuitOnError=1 Interp method is cubic INFO: loading mgh-format infile 001.mgh INFO: loading mgh volume 001.mgh ??? Error using ==> load Unable to read file /labs/deyounglab/FreeSurfer/grad_unwarp_tables/table.mat: No such file or directory. Error in ==> convert_unwarp_resample>type2map at 331 load(TABLE); Error in ==> convert_unwarp_resample at 141 gradwarpfile = type2map(user_gradwarpfile); >> >> ERROR: output file not created

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Qcache error
by Robustelli, Briana (NIH/NIMH) [F] 27 Jul '10

27 Jul '10

Hello, I am new to Freesurfer and have recently encountered an error when trying to run a qcache on one of my subjects. Below is the error. I would appreciate any advise you can give. Thanks! Reading source surface reg /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg No such file or directory Linux thalamos 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 26 14:08:56 EDT 2010 Thank you, Briana

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Interpreting roisummary-sess
by Adam Nitenson 27 Jul '10

27 Jul '10

Hello, I am trying to use func2roi and roisummary to analyze activation of the left and right dACC. I used the following func2roi command to get the ROI data for our 1vFix condition: func2roi-sess -roidef dACC_fsaverage_left -analysis fmcsm5_functionals -anatlabel dACC_fsaverage-lh -maskcontrast Cond1vFix -maskthresh 1.3 -masktail pos -maskmap sig -sf /autofs/space/seymour_001/users/folate_subjects/Subject_files/10Pre10Post -d /autofs/space/seymour_001/users/folate_subjects I then used the following command to produce the data summary: roisummary-sess -roidef dACC_fsaverage_right -analysis fmcsm5_functionals -sf /autofs/space/seymour_001/users/folate_subjects/Subject_files/10Pre10Post -d /autofs/space/seymour_001/users/folate_subjects -sumfile /autofs/space/seymour_001/users/folate_subjects/dACC_fsaverage_right However, the resulting data sheet (see attached) appears to show 9 conditions with only 1 estimate for each. How do I generate multiple estimates for each condition, and, even better, how can I incorporate multiple conditions (3vFix, 5vFix, etc) into the same roisummary? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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qdec error
by aekairys＠umich.edu 26 Jul '10

26 Jul '10

Hello FS experts, I have attached a gimped image of an error I have encountered. it seems to only occur when I choose diagnosis as a discrete variable. however I made the appropriate levels file in the qdec folder. any advice would help! best, Anson K. University of Michigan

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Freesurfer July 2010