Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

?h.aparc.a2005s.stats and ?h.aparc.a2009s.stats
by Guang Zeng 30 Sep '09

30 Sep '09

Hi, there, What is the difference between ?h.aparc.a2005s.stats (from ver 4.4) and ?h.aparc.a2009s.stats (from ver 4.5) in the stats folder? ?h.aparc.a2009s.stats is still based on Christophe's atlas, right? Thanks a lot! Guang _________________________________________________________________ Microsoft brings you a new way to search the web. Try Bing™ now http://www.bing.com?form=MFEHPG&publ=WLHMTAG&crea=TEXT_MFEHPG_Core_tagline_… bing_1x1

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autorecon1 changes orientation
by Angela Y. Wang 30 Sep '09

30 Sep '09

Hi, When I use autorecon1 it changes the orientation of my original image. My 001.mgz is in LAI. After autorecon1, I get rawavg.mgz is in LAI, however, orig.mgz, T1.mgz and brainmask.mgz are now in LIA. I checked the orientations using tkmedit. How do I prevent this change in orientation? Thanks for any advice, Angela

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CEPHES ERROR: fdtrc domain error
by Jürgen Hänggi 30 Sep '09

30 Sep '09

Dear FS experts I have run a group analysis on thickness and area maps and everything worked fine. When running the same analysis on cortical volume maps, the following error occurred (figures are attached): *** CEPHES ERROR: fdtrc domain error *** *** CEPHES ERROR: fdtrc domain error *** *** CEPHES ERROR: fdtrc domain error *** *** CEPHES ERROR: fdtrc domain error *** Fit completed in 0.453067 minutes Computing spatial AR1 on surface INFO: fwhmFromAR1: Fixing group surface area Residual: ar1mn=0.998253, ar1std=0.002494, gstd=10.000979, fwhm=23.550507 Writing results sad_Design maxvox sig=-1e+10 F=-18.96 at index 0 0 0 seed=1254498771 Computing kurtosis of residuals mri_glmfit done Neuromorphometer:/usr/local/freesurfer/subjects/average/stats/glm> Any idea what is wrong? I used FS 4.3.0 centos4 distribution on Ubuntu Linux and applied dods. When using doss and the DeMeanFlag = 1, the error did not occurred. Thanks in advance Regard Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] Freesurfer Digest, Vol 67, Issue 72
by Sebastian Moeller 30 Sep '09

30 Sep '09

Aloha, tksurfer is extremely picky about the underlaying opengl libraries, many do not work at all. People had dofferent degrees of success updating the graphic drivers on their computers to the most recent versions their hardware maker saupplies (if I recall correctlt especially with nvidia cards). One thing that worked for me was to force the use of redhat server 4 opengl libraries on a system that only runs with software opengl (mesa I presume), or alternatively use virtualbox (virtual boxes opengl drivers play nicely with tksurfer). Thanks to Pedro Paulo Oliveira you can even download a virtualbox image that should work right away (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/VirtualBoxFS45-… but see http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/VirtualBoxFS45-… first ). The virtualbox image can be used from windows macosx and linux... Good luck Sebastian On Sep 30, 2009, at 6:16 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Wed, 30 Sep 2009 10:31:27 +0200 > From: "Ahmed, F, Me <fahmed(a)sun.ac.za>" <fahmed(a)sun.ac.za> > Subject: [Freesurfer] tksurfer > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <5B91A2407B81E042A12EBA1B8CCFED4831A3182B01(a)TYGEVS02.tyg.sun.ac.za> > Content-Type: text/plain; charset="us-ascii" > > Hello, > > I'm trying to view and check the smoothing and inflation surfaces, > the white and pial surfaces for "bert" using tksurfer as I'm trying > to get used to using Freesurfer, but I'm a little confused to what > I'm seeing. When I type in: "tksurfer bert lh inflated" for example, > I only see a very small section at the very end of the image...is > this correct? When I view the curv files, I do see a green pattern > overlaid on the inflated surface, however it's still so small. When > I view the pial and white surfaces, again, the section displayed is > very small, I don't know if this is correct or if this is what I am > supposed to be seeing? Also, when I type in: "tksurfer bert lh > sphere", I see nothing at all. > > If someone could shed some light on the matter I'd be extremely > grateful. > > Thank you > > > > >

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question about aseg
by Gabriel Go.Es. 28 Sep '09

28 Sep '09

hello Freesurfers i have a doubt, i have read on the mail archive that you were working on get a segmentation of the vermis, i have the V 4.2 of freesurfer wich hav not this region,and i like to have that region, is there any way to get it? is it in another version of FS? or does any one have it? Best Regards Gabriel _________________________________________________________________ ¿Quieres ver los mejores videos de MSN? Enciende Messenger TV http://messengertv.msn.com/mkt/es-es/default.htm

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Re: [Freesurfer] Question about baseid
by Nick Schmansky 28 Sep '09

28 Sep '09

Brian, When you specify a subject name, it will create the folder for you. You command string below is failing because it includes the characters ... If you eliminate those, it will create a subject named Sub1 (although I would give it a name with the letters 'base' in it). Nick On Mon, 2009-09-28 at 16:35 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > Do I create a folder where the subjects are and then put that name in place of baseid? > > I created a folder named Sub1 in the subjects folder with all the other scans and tried it but it gave me this > > brianweisinger$ recon-all -base Sub1 -tp 00308 -tp 01150 ... -allERROR: Flag ... unrecognized. > -base Sub1 -tp 00308 -tp 01150 ... -all > Darwin CHP-MP2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 > > recon-all exited with ERRORS at Mon Sep 28 16:33:07 EDT 2009 > > Any ideas? > > > > On 9/28/09 4:25 PM, "Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> wrote: > > Brian, > > You decide on the name. It is a new subject composed of data from tp1id > and tp2id. Once that 'base' subject is created, then you run your > longitudinal analysis against that base: > > recon-all -long tp1id baseid -all > recon-all -long tp2id baseid -all > > then compare tp1id.long.baseid to tp2id.long.baseid. > > See: > > http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing > > Nick > > > > On Mon, 2009-09-28 at 16:08 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > > I am trying to run a longitudinal stream and I have already run all the scans through recon all already. I am on the second step > > > > > > 2. "-base" create the base template and process it cross sectionally: > > > > recon-all -base <baseid> -tp <tp1id> -tp <tp2id> ... -all > > > > > > > > Where do I find the baseid to put in the <baseid> spot? > > > > Thanks in advance for any help with this. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >

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Question about baseid
by Weisinger, Brian (NIH/OD) [E] 28 Sep '09

28 Sep '09

I am trying to run a longitudinal stream and I have already run all the scans through recon all already. I am on the second step 2. "-base" create the base template and process it cross sectionally: recon-all -base <baseid> -tp <tp1id> -tp <tp2id> ... -all Where do I find the baseid to put in the <baseid> spot? Thanks in advance for any help with this.

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anatomical_stats on 3D volumes
by Narly A Golestani 28 Sep '09

28 Sep '09

Dear all, I have some 3-D volumes (labelled regions of interest) generated manually on *normalised* structural images. I would like to use freesurfer to run the anatomical_stats command on these volumes. Is this possible? These labels (volumes) were not generated using freesurfer. Can I transform them into the required format for this purpose? I assume I'll also have to run recon_all on the *normalised* T1s in order to have the measures needed for this? thanks in advance for any input you might have, best wishes, Narly.

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CPs and Pial Surfaces
by Sherri Novis 28 Sep '09

28 Sep '09

Hello - My previous email was either lost in the shuffle or a bad q - pls let me know if it's the latter. I am adding white matter control points, and rerunning autorecon-all - however the pial surfaces are not changing after I add CPs. I am adding them slice by slice. The log file shows the CPs are recognized. log file attached. I can't find any info in the tutorials of archives as to exactly how CPs and pial surfaces interact. Are there specific ways the CPs need to be added to force new pial boundaries? Or do they not not interact the way I think they do.. This is what I'm loading to edit CPs: tkmedit [SubjectID] brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white. Thank you - Sherri

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Summing ROIs on fsaverage surface
by Holly Bridge 28 Sep '09

28 Sep '09

We have an ROI for V1 of each of 10 subjects that we have transformed onto the surface of fsaverage with mri_surf2vol. Now we would like to sum these binary masks to produce a single mask with values from 0 to 10 corresponding to the overlap of the individual masks on the average surface. Is there a way to do this with freesurfer tools or do we need to invoke fslmaths from the FSL tools? Thanks, Holly --------------------------------------------------------------------------------------------------- Dr Holly Bridge Royal Society University Research Fellow FMRIB Centre Tel: +44-1865-222582 John Radcliffe Hospital Headington Oxford OX3 9DU Email: hb(a)fmrib.ox.ac.uk Lecturer and JRF, New College ---------------------------------------------------------------------------------------------------

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Freesurfer September 2009