Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

glibc
by skenny＠uchicago.edu 18 Dec '06

18 Dec '06

hi all, i'm trying to do a freesurfer install on a cluster that is using glibc-2.2.5 and the latest freesurfer requires glibc- 2.3 libraries. i'm wondering if the source is available so that i can compile for use with glibc-2.2.5, or alternatively if someone might suggest another workaround for this (?) thanks sarah

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Scan quality & FS
by Derin Cobia 14 Dec '06

14 Dec '06

Some of the scans I work with are of the same subject, but differ only in the length of time they were in the scanner. Obviously the scans of longer length (everything else being equal) will yield better quality; however, I'm interested in a kind of "bang-for-your-buck" approach. Is there a point where some amount of diminishing returns occurs with respect to FS processing and scan quality? Therefore, my main question: 1) Is there anything in the FS processing stream that would be a reasonable heuristic for determining if one scan processes better than another (all things being equal beside length of time being scanned)? For example, # of topological defects to correct, length of processing, amount of manual correction, or just visual quality? I understand some of this is related to what structure(s) I'm interested in measuring, but was wondering about it in a general fashion. This may come in handy down the road for us because many of our subjects are individuals with schizophrenia, and being in an enclosed space (let alone the time it takes to yield a high-quality scan) is traumatic enough for them. Thanks for any input. -Derin

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spherical smoothing
by Cameron Ellis 14 Dec '06

14 Dec '06

Hi, I am trying to smooth fucntional data on the spherical surface and I see that there are a few options for how this can be done and was wondering if anyone has any suggestions for an optimum smoothing technique. I see one option is implementing smoothing as a tag in mri_vol2surf but I also see sphsmooth-sess as another option. Does mri_vol2surf call sphsmooth-sess and work off the same algorithm? If not, when would I use sphsmooth? I also see that func2sph offers the option of smoothing before resampling. When would this be a good idea? Thanks, Cameron

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error message during autorecon1: Can't find the talairach xform
by Bum Seok Jeong 14 Dec '06

14 Dec '06

During autorecon1, I find error message below during autorecon1, eventhough recon-all-status.log said 'recon-all finished without error ' Is it not considerable error message or important thing? Thank you bsjeong --------------------- Can't find the talairach xform 'spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /spgr_nifti/N3/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /spgr_nifti/N3/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.26912/nu0.mnc... ........... #@# Talairach Thu Dec 14 14:00:02 EST 2006 /spgr_nifti/N3/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /spgr_nifti/N3/mri /freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.4 2006/04/18 23:05:05 nicks Exp $ Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 14 14:00:03 EST 2006 tmpdir is transforms/tmp.talairach.27507 /spgr_nifti/N3/mri mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc mri_convert nu.mgz transforms/tmp.talairach.27507/src.mnc Can't find the talairach xform '/spgr_nifti/N3/mri/transforms/talairach.xfm' Transform is not loaded into mri

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RE: [Freesurfer] Freesurfer and Grid computing
by Andries van der Leij 14 Dec '06

14 Dec '06

Hi Darren, Nick and freesurfers, Thanks very much for your replies! I've discussed this and have a couple of questions. I would be very glad if you could help me out. I'm currently talking with my group to decide where to go. Like I said, we will get a research-only 3T scanner, which (if used as much as we hope) will deliver about 20 GB of raw data each week. We need to think of a solid processing and storage pipeline in order to be able to do something with the data ;) We discussed this and are trying to come up with a good solution, both storage and analyses-wise. One solution for the enhancement of the analyses would be to buy a couple of solid workstations. The other would be a grid solution. The main problem isn't as much finance as it is manpower. No current member of the faculty has the time to invest in setting up and maintaining a grid if that will be a very difficult task to do. Hopefully we will get the money to hire an ICT person to do this. However, this is not certain. So I have a question concerning the difficulty of setting up the grid like proposed by Nick: semi-parallel in the sense that different commands of a batch are distributed to different nodes. We are wondering just how difficult this is. I address this question to both of you. Darren: you have SUN grid and Nick you have something like SUN grid. Nick, you state: <snip> You are on-track with the first scenario. If you have the technical skills and time to install the Sun Grid Engine, or PBS (which does nearly the same thing), then the batch interface will be easy for others to submit as many 'recon-all' instances as they want and will handle balancing. Once a batch system is setup, you can expect to have to spend some time maintaining the system (help-line, monitoring for stalled jobs, failed nodes, or failed disks, etc). You could also write your own scripts implementing a simple batch system, if you don't mind semi-manually tracking the resources, and if you will oversee it or use it yourself, and keep it small-scale. </snip> The issue of course is this: 1. Just how much technical skills and time does the installation and maintenance of a Grid cost? It is my impression that the implementation of the SUN grid is not that hard. But I'm always an optimist if it comes to computers, although at times this has proven to be a great overestimation of my own knowledge and skills. 2. How 'intuitive' is the usage of a batch system like SUN grid and how stable is it? That is: given that we write guidelines, howtos, and set up a Wiki, how difficult will drag&drop type users will be able to work with such a system? The final maintenance issues that Nick addresses concerns failure. 3. Hardware failure: freezing nodes and disk failures I expect to cost as much time as it will cost when we buy individual workstations, Maybe even less? 4. Software failure. Maybe I'm way off here, but it's my impression that the host running the batch system uploads the input data from a central server to a node, which analyses the data and then downloads the resulting output again, deleting the data on the node. If this is correct and if a single job fails, do you have to manually delete working data on a node? I hope you can help me out with this. Thank you! Andries

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3.0.3 for Debian (RedHat 9)
by Christopher L. Hamilton 14 Dec '06

14 Dec '06

We are looking at deploying a debian install to all of our linux machines but need the 3.0.3 version of freesurfer until we can test 3.0.4. Where can we download older versions? Chris Hamilton

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problem in runnign tkmedit on linux...
by Shahabuddin Ansari 14 Dec '06

14 Dec '06

Hi I am getting the following error when I run tkmedit or tksurfer: Couldn't create output file .xdebug_tkmeditfreeglut (tkmedit): OpenGL GLX extension not supported by display ':0.0' It seems X11 server configuration is not set properly to run OpenGL applications. Any ideas? Thanks Shahab ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com

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compatability between 32 and 64 bit versions
by Glenn Lawyer 13 Dec '06

13 Dec '06

Hi, Is there any problem mixing subjects processed with the 32 bit version and the 64 bit version, using FS 3.? How about between the RH9 build and the Centos build? I would be very surprised if this did present a problem, but my supervisor wants me to check. Yes, I did see Nick's email (28 mar 2006) on the slight differences in the floating point optimizations, which he felt were minor. +glenn -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 661 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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combining conditions
by Cameron Ellis 13 Dec '06

13 Dec '06

Hi, I have three conditions specified in my paradigm files that I have been comparing to one another. Two conditions I would like to combine and compare to the third in one contrast and was wondering if this would require modifying my paradigm files to refer to these two conditions with the same number or if I can just positively weight the two I want to combine in mkcontrast-sess and negatively weight the other. That's all. Thanks, Cameron

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GLM analysis question
by Avram Holmes 13 Dec '06

13 Dec '06

FSFast support folks, I am looking for some support running an analysis in FSFast. As far as we can tell we have successfully run every step in a random effects analysis but we are having trouble viewing/interpreting the results. I was hoping that I would be able to post my processing stream and see if anyone would give us feedback on what we have or havent done correctly (see below). My understanding is that after I run mkanalysis-sess.new, selxavg-sess, mkcontrast-sess, stxgrinder-sess, and isxavg-re-sess, I have fit a model to the data and I am testing the fit of the model across our contrasts. However, Im not seeing the expected effects and I am wondering if I am missing a step or if my stream is not optimized. I have spent a considerable amount of time searching the wiki page and I havent been able to track down a detailed description of how to conduct and interpret a complete GLM analysis in FSFast so I am a little unsure if I have everything correct. Any help would be greatly appreciated, Avram #! /bin/csh -f Step1 set mypath = . set sub = $1 mc-sess -fstem f -fmcstem fmc -s ${sub} -d ${mypath} stc-sess -i fmc -o fmcstc -so siemens -s ${sub} -d ${mypath} spatialsmooth-sess -i fmcstc -o fmcstcsm5 -fwhm 5 -d ${mypath} -s ${sub} mkbrainmask-sess -s ${sub} -d ${mypath} Step2 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm moneygame.par -designtype event-related -timewindow 30 -funcstem fmcstcsm5 -nconditions 5 -polyfit 1 -mcextreg -taumax 20 -mask brain foreach s ($subj) selxavg-sess -s ${s} -d . -analysis ${analysis} end mkcontrast-sess -analysis ${analysis} -contrast omnibus -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 -nosumconds mkcontrast-sess -analysis ${analysis} -contrast pun_v_noinc -a 1 -c 2 mkcontrast-sess -analysis ${analysis} -contrast rew_v_noinc -a 3 -c 2 mkcontrast-sess -analysis ${analysis} -contrast pun_v_rew -a 1 -c 3 mkcontrast-sess -analysis ${analysis} -contrast rew_v_pun -a 3 -c 1 foreach s ($subj) autoreg-sess -d . -s ${s} -fsd bold end Step3 set mypath = . set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' foreach s ($subj) stxgrinder-sess -contrast omnibus -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_rew -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_pun -analysis ${analysis} -s ${s} -d ${mypath} end Step4 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' set glist = 'GROUPLIST' set group = 'Controls' set contrasts = 'omnibus pun_v_noinc rew_v_noinc pun_v_rew rew_v_pun' foreach s ($subj) foreach anal ($analysis) func2tal-sess -res 4 -analysis ${anal} -d . -s ${s} foreach hemi (lh rh) func2sph-sess -analysis ${anal} -hemi ${hemi} -projfrac .3 -d . -s ${s} sphsmooth-sess -smoothsteps 10 -analysis ${anal} -insphdir sph -outsphdir sphsm10 -hemi ${hemi} -d . -s ${s} end end end foreach c ($contrasts) isxavg-re-sess -analysis ${analysis} -group ${group} -space tal -d . -sf ${glist} -contrast ${c} foreach hemi (lh rh) isxavg-re-sess -analysis ${analysis} -group ${group} -space sph -hemi ${hemi} -d . -sf ${glist} -contrast ${c} end end ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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