Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

surface DTI group contrast
by Robert Levy 20 Aug '07

20 Aug '07

Hello, I have been attempting to run a between group DTI contrast using glmfit, and it could not determine how to produce the data that is given to mri_glmfit as its input. My approach below may be wrong, so if you can recommend a better way of doing it please advise. Assuming this method is a valid approach, here is my technical problem: the resampling step shown below seems to work, but glmfit reports that there is an incorrect number of rows, so I guess something goes wrong. The first thing I do is resample from volume to surface onto average7 for each of the subjects: cat Subject_Lists/bw-group-error-dti-5 | while read sub ; do mri_vol2surf \ --src "$sub"/dti/unwarp/maps/sreg/fa.bhdr \ --srcreg "$sub"/bold/register.dat \ --trgsubject average7 \ --out DTI_HCvASD_mriglfmit/surface/"$sub"_fa.mgh \ --hemi lh done And then I create a final output to give to mri_glmfit: mri_concat DTI_HCvASD_mriglfmit/surface/mano*_fa.mgh --o DTI_HCvASD_mriglfmit/all_fa.mgh The process I'm attempting above is similar to what mris_preproc uses surf2surf to do, but I think I need to use vol2surf instead of surf2surf. As far as I can tell mris_preproc would not work, because in what I am doing I need to go from the volume to the surface. This vol2surf method "works" in that it doesn't have any errors when running (though some warnings about registration file being different from source file), and it generates the resampled surface that I concatenate at the end. So far so good but when I run mri_glmfit, I get an error message (see below). mri_glmfit \ --really-use-average7 \ --y DTI_HCvASD_mriglfmit/all_fa.mgh \ --fsgd fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd \ --glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir \ --C fsgd_and_contrast_files/BwGroupErrorDTI5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir DoFFx 0 Creating output directory DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir Loading y from /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh Matrix condition is 1 Pruning voxels by frame. Found 155495 voxels in mask Saving mask to DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir/mask.mgh search space = 155495 *ERROR: dimension mismatch between y and X. y has 23 inputs, X has 24 rows. * My .fsgd file matches the exact set of subjects that went into the aggregate .mgh file, so that isn't the reason. What do you think might be the cause of this error? Thanks, Rob Also, here is some information on the environment I ran these commands in: -------- freesurfer-Linux-centos4_x86_64-dev-20070819 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) pwd /space/ventzl/1/users/SUBJECTS_DIR -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Validation for surfaces
by Goldman, Aaron (NIH/NIMH) [C] 20 Aug '07

20 Aug '07

Hi, regarding validation of freesurfer's surface reconstructions, I was just wondering which papers you would most recommend citing. Thanks, -Aaron-

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Re: [Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13-add gray matter
by Wang, Xin 20 Aug '07

20 Aug '07

Thank great helps from the group. I have a related issue. In my images some gray matters at the top of medial wall is lass than 60, so that these small areas are not included in gray matter. This may be due to the shadow of RF coil. Can I fix it by either decrease the threshold of gray matter or manually include these small areas? Thank you again, Xin Bruce Fischl Mon, 09 Jul 2007 15:08:20 -0700 usually it's because the bias field brings the gm too low, so if you find nearby white matter (that is *not* partial volumed) that is below 110, putting some control points there will also move the pial surface out a bit. Or the skull strip could have removed it. Or the topology fixer might have done something strange. This can be checked by looking at the ?h.orig.nofix surface and seeing if it is more accurate than the ?h.orig. If this is the case you'll need to identify and correct the topological defect in the wm.mgz volume. cheers, Bruce On Mon, 9 Jul 2007, Sebastian Moeller wrote: Hi, not being an expert, please take my rambling with a grain of salt. But I am somewhat curious to learn better ways ;) On Jul 9, 2007, at 11:03 PM, [EMAIL PROTECTED] wrote: Message: 9 Date: Mon, 9 Jul 2007 17:01:42 -0400 From: "Wang, Xin" <[EMAIL PROTECTED]> Subject: [Freesurfer] add the gray matter To: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? 1) If you have nothing where gray matter should be, then check brainmask.mgz, if this is missing gray matter, around where your problems occur edit the bainmask.mgz volume and pick up your reconstruction from there. (IIRC there is something in the tutorial about this) 2) If there is white matter where gray matter should be, be sure to to check nu.mgz and brainmask.mgz at the critical parts for too high intensity in the supposed gray matter. Either control points might helo (unlikely) or redoing the intensity correction (and then starting again from that point). At least for my data, acquired with surface coils, sub-optimal intensity correction is really annoying. ahoi & good luck Sebastian Thank you in advance. Xin

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tksurfer: "window type not found"
by Stefan Vollmar 19 Aug '07

19 Aug '07

Hi, we are running the current version of freesurfer on a number of SunFire X2200 servers (Fedora Core 7). Everything works fine when we run tksurfer remotely from some Linux and MacOS X boxes on the X2200 servers. However, when using a SunFire T2000 server (Solaris 10) as a front end, we experience the following problem when trying to run tksurfer on the X2200 systems: "window type not found" and tksurfer's graphics window remains blank. Solaris 10 on that machine uses the Xorg server with Mesa, so, in theory, GLX extensions should not be the problem here (tkmedit, infact, does work). This is an important issue for us, as we could use freesurfer on our SunRay thin clients if we get it to work on the T2000 (I am aware that, in an ideal world, we would want to run all of freesurfer on some local system using hardware acceleration, however, our server/ thin client-setup - although not ideal for freesurfer - does make a lot of sense for other applications). Many thanks in advance, Stefan -- Dr. Stefan Vollmar, Dipl.-Phys. Max-Planck-Institut für neurologische Forschung Gleuelerstr. 50, 50931 Köln, Germany Tel.: +49-221-4726-213 FAX +49-221-4726-298 Tel.: +49-221-478-5713 Mobile: 0173-5340707 Email: vollmar(a)nf.mpg.de http://www.nf.mpg.de

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qdec for old ?
by Kirk, Gregory 17 Aug '07

17 Aug '07

Hi , I would imaging we would need to be running the most recent freesurfer version to use qdec We just finished a study with V3.0 and are doing the analysis. Mainly interested to see if we could do some analysis with subcortical structures. thanks Greg.

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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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Freesurfer