Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

RE: [Freesurfer] remote batch job?
by Don Hagler 17 Aug '07

17 Aug '07

There is a renderoffscreen flag that can be used from a tcl script. Unfortunately, this feature was broken when a particular section of the tksurfer code was commented out. The problem was that the tclscriptflag used to determine whether to open a window was not getting set to true. Look for this: /* rkt: commented this part out. i'm not sure how it was accepting any other command line options with it active. */ I think I emailed Kevin Teich about this some time ago. Since then, I've made a modified version of tksurfer where this problem is fixed. The solution is to actually replace tclscriptflag with the newer scriptok variable when it comes time to open a window only if not running from a script. I can send that code to the mgh guys if desired, but as I said, the fix is easy (assuming you can compile the source code). So anyway, this modified version can render offscreen (like the prehistoric versions of tksurfer). This is very useful to me and probably to others who want to render in batches (e.g. making movies). The only remaining problem, however, is that you still need a valid display. So for example, you can't run these batch render jobs on a cluster. I haven't yet tried to get tksurfer to render without any display, but I fear that it won't be possible for some OpenGL reason. But if anyone can figure that one out, I would be very grateful. Don >From: "Darren Weber" <dweber(a)radmail.radiology.ucsf.edu> >Reply-To: Darren.Weber(a)radiology.ucsf.edu >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >Subject: [Freesurfer] remote batch job? >Date: Thu, 16 Aug 2007 16:12:01 -0700 > >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > > >Hi Bruce et al., > >I want to run a batch job that will use tksurfer to display an inflated >surface, load some patches, and rotate and save images. I have a .tcl >script to control the process in tksurfer and I have a shell script to >start the whole process off for a number of subjects. My question now >is how to handle the case where I am working remotely and it is too slow >to have the display piped to the remote display, so I want to have >either (a) no visible display or (b) a display on the host machine. If >I try the usual trick of setting DISPLAY env for the host machine, I'm >failing to open the display for any commands sent from the remote xterm. > >Do you have a solution for this situation? > >Take care, Darren > >- -- > >Darren L. Weber, Ph.D. >Postdoctoral Scholar > >Dynamic Neuroimaging Laboratory, >UCSF Department of Radiology, >185 Berry Street, Suite 350, Box 0946, >San Francisco, CA 94107, USA. > >Tel: +1 415 353-9444 >Fax: +1 415 353-9421 >www: http://dnl.ucsf.edu/users/dweber >pgp: http://dnl.ucsf.edu/users/dweber/dweber_pgp.html > >"To explicate the uses of the brain seems as difficult >a task as to paint the soul, of which it is commonly >said, that it understands all things but itself." > Thomas Willis (The Anatomy of the Brain and Nerves, 1664) > >"Fourteen billion nerve cells responding in complex ways >with multitudinous connections to each other give little >likelihood of providing a rational solution that would >allow prediction of mental process." > Michael Posner (Chronometric Explorations of Mind, 1978) >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.4.6 (GNU/Linux) >Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > >iD8DBQFGxNnBxaCYN7qs0v4RAiOOAJ48XbFN1UzICRYbe8yho2UIcMbm3ACfcp6Y >5GyJeS0o6a5L43pz74jeMyI= >=G5Ph >-----END PGP SIGNATURE----- >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Learn.Laugh.Share. Reallivemoms is right place! http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us

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remote batch job?
by Darren Weber 16 Aug '07

16 Aug '07

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Bruce et al., I want to run a batch job that will use tksurfer to display an inflated surface, load some patches, and rotate and save images. I have a .tcl script to control the process in tksurfer and I have a shell script to start the whole process off for a number of subjects. My question now is how to handle the case where I am working remotely and it is too slow to have the display piped to the remote display, so I want to have either (a) no visible display or (b) a display on the host machine. If I try the usual trick of setting DISPLAY env for the host machine, I'm failing to open the display for any commands sent from the remote xterm. Do you have a solution for this situation? Take care, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber pgp: http://dnl.ucsf.edu/users/dweber/dweber_pgp.html "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) "Fourteen billion nerve cells responding in complex ways with multitudinous connections to each other give little likelihood of providing a rational solution that would allow prediction of mental process." Michael Posner (Chronometric Explorations of Mind, 1978) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGxNnBxaCYN7qs0v4RAiOOAJ48XbFN1UzICRYbe8yho2UIcMbm3ACfcp6Y 5GyJeS0o6a5L43pz74jeMyI= =G5Ph -----END PGP SIGNATURE-----

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mris_volmask + mris_volume
by Leila BH 16 Aug '07

16 Aug '07

Hi again, I need the command mris_volmask that I found in the website but I don't have it I my freesurfer (stable3), someone can help me? And how to use mris_volume? I wrote:mris_volume in the surf folder, after small time I can see like an output this number 333731, but I can not find any new volume, do you know if his function works? Thanks Leila

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better looking structural for function display
by Avram Holmes 16 Aug '07

16 Aug '07

All, I have a quick question. I would like to present some volume data on a detailed Talairach structural (the fsaverage talairach template is quite blurry). In SPM I can use the high resolution Collins brain. Does anyone know if that structural is available somewhere in the FreeSurfer system? If not could anyone tell me how to generate such an image. Thanks, Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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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How to extract beta weights, by condition, for whole-brain regression analysis
by Dan Dillon 16 Aug '07

16 Aug '07

Dear FreeSurfers, I have completed individual and group level functional analyses using FS-FAST, and would like to correlate individual differences in self-report measures against the betas for several of my 13 conditions (I used -gammafit in mkanalysis). My questions are: 1) Where are the beta weights located? and 2) How do I extract beta weights for each condition for each participant? I suspect that the solution involves the h files, but I'm not sure. Note that I'm trying to do a whole-brain analysis here-I know how to extract betas from functionally and structurally defined ROIs, but I don't know how to do this for the whole brain. Any help will be greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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images use different protocols
by Wang, Xin 16 Aug '07

16 Aug '07

Hello, Group I have two set of images acquired with different imaging protocols (e.g., TRs and bandwidth are different). Can I poll them together for the analysis? I saw in the email list that some groups reported problems in generating the average of images with different TR for the group analysis. I do not seem have problem to make average include all the images. But is the result acceptable if the images acquired with multiple protocols? Thank you

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procedural question about FDR correction
by Dara Manoach 16 Aug '07

16 Aug '07

Hi, FDR correction for multiple comparisons gives you different p-values for the left and right hemispheres. It seems really weird to report in a paper: a) that you've corrected for the right and left hemispheres separately and b) that the p-value that gave rise to a corrected probability of .05 was different for each. How do people deal with this issue? Take the most stringent p-value and use it for both hemispheres? Just report that FDR adjusted the p- value to .05? Also, correcting for right and left hemispheres separately assumes that they are independent observations. Unless you're studying callosotomy patients (and maybe even if you are) this doesn't seem justified. Are we supposed to be adjusting p-values accordingly? Thanks, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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mri_surf2vol
by Leila BH 16 Aug '07

16 Aug '07

Hello, I need to convert the white matte surface to a volume :binary volume with 1 in white matter and 0 outside. I am using the mri_surf2vol command (on both hemisphere), and fill it using matlab. Do you know if it is possible to obtain the volume from the surface already filled ? Thanks a lot. Here is the command I use : Mri_surf2vol --mkmask --hemi lh --template /my_image.img --volregidentity mysubject --outvol outputvol_lh.img

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Assertion failed at line 827 in file templates/CachedArray.cc
by Richard Frye 15 Aug '07

15 Aug '07

While running freesurfer I obtain the following error message Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)ERROR: nu_correct The mri looks okay. I cannot find anything in the wiki Any ideas appreciated. -- Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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qdec / qcache
by Claus Reinsberger 14 Aug '07

14 Aug '07

Hi everybody, I tried to run the qdec-tool in the dev-env, but experienced some problems with my last subject. This is the environment, I'm working in: FREESURFER_HOME: /usr/local/freesurfer/dev Build stamp: freesurfer-Linux-centos4-dev-20070811 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: tkmeg SUBJECTS_DIR: /space/megraid/83/MEG-MRI/seder/freesurfer/ PWD: /space/megraid/83/MEG-MRI/seder/freesurfer ... and here's the error I get when I start the group analysis in qdec, subj nmr00199 is the one I added (after I ran -qcache): ERROR: dimension mismatch between /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nm r00188_a/surf/lh.thickness.fwhm10.fsaverage.mgh and /autofs/space/megraid_083/MEG-MRI/s eder/freesurfer/nmr00199/surf/lh.thickness.fwhm10.fsaverage.mgh Error in Analyze: command failed: mri_concat /autofs/space/megraid_083/MEG-MRI/seder/fr eesurfer/nmr00188_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/ME G-MRI/seder/freesurfer/nmr00172_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/ megraid_083/MEG-MRI/seder/freesurfer/nmr00035/surf/ lh.thickness.fwhm10.fsaverage.mgh /a utofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00039_a/surf/ lh.thickness.fwhm10.fs average.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00046/surf/ lh.thickne ss.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00127/sur f/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/ nmr00156/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder /freesurfer/nmr00158/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/M EG-MRI/seder/freesurfer/nmr00159/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/m egraid_083/MEG-MRI/seder/freesurfer/nmr00180_a/surf/ lh.thickness.fwhm10.fsaverage.mgh / autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00189_a/surf/ lh.thickness.fwhm10.f saverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00034/surf/ lh.thickn ess.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00031_a/ surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurf er/nmr00070/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/se der/freesurfer/nmr00098/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_08 3/MEG-MRI/seder/freesurfer/nmr00013/surf/ lh.thickness.fwhm10.fsaverage.mgh /autofs/spac e/megraid_083/MEG-MRI/seder/freesurfer/nmr00182_a/surf/ lh.thickness.fwhm10.fsaverage.mg h /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00052/surf/ lh.thickness.fwhm10. fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00123/surf/ lh.thick ness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00076/s urf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfe r/nmr00183_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/s eder/freesurfer/nmr00184_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid _083/MEG-MRI/seder/freesurfer/nmr00181_a/surf/ lh.thickness.fwhm10.fsaverage.mgh /autofs /space/megraid_083/MEG-MRI/seder/freesurfer/nmr00068/surf/ lh.thickness.fwhm10.fsaverage .mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00073/surf/ lh.thickness.fwhm 10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00199/surf/lh.th ickness.fwhm10.fsaverage.mgh --o /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/qde c/Untitled/y.mgh Could this be due to the dev-env of the qcache-command (the log says everything went fine)? Autorecon-3 also seems to have run fine in this patient. Thanks a lot for your help, Claus

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