Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

surfaces and gifti
by Satrajit Ghosh 09 Dec '11

09 Dec '11

hi all, this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz). a related question. once i have this gifti file how do i get annotations+curvature info also into the file? (the gifti schema supports this right?) essentially i am looking for a way to bundle the surface information into a single gifti container. cheers, satra

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FreeView Gave Errors
by Xinian Zuo 08 Dec '11

08 Dec '11

Freesurfers, Anyone saw some errors below from FreeView? -----------------------------------------------------error message---------------------------------------------------------- freeview.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. ----------------------------------------------------------------------------------------------------------------------------------- I used FS5.1 and ran freeview via VNC client. Any thoughts are highly appreciated! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

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freeview, viewing surfaces
by kelsi 08 Dec '11

08 Dec '11

Hi, when I load my ?h.white, inflated, pial, etc data in freeview, I keep getting this message: "Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces" My command is: freeview -v fsaverage/mri/aparc+aseg.mgz -f fsaverage/surf/lh.inflated Also, is there inherent segmentation in the surface data, or do I have to load it onto an aparc+aseg.mgz file in order to accurately label the areas? Thank you!

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Final result of CVS
by Antonella Kis 08 Dec '11

08 Dec '11

Dear Lilla, I was running the mri_cvs_register with the flag --noaseg and no argument for my target template so as I understood the registration was done on the cvs template as you can see below: mri_cvs_register--mov P01 --noaseg After registration I got 4 files: combined_tocvs_avg35_elreg_norm.m3z combined_tocvs_avg35_elreg_norm_aseg.mgz el_reg_tocvs_avg35.mgz nlalign-norm.m3z nlalign-norm.mgz Is the nlalign-norm.mgz the final result of my CVS and contains contributions from ALL registration steps? Also is the cvs atlas included in the file that you sent me some time ago called: cvs_avg35? Thank you very much for your time and help. Regards, Antonella

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trac-all flag for doing all 3 processing steps?
by Scott Hayes 08 Dec '11

08 Dec '11

Hi, I'm new to tracula, but I'm wondering if I'm overlooking or misunderstanding the flags. It appears that one types in the trac-all command 3 times to process a subject (or group of subjects) >trac-all -prep -c ConfigFile >trac-all -bedp -c ConfigFile >trac-all -path -c ConfigFile Is there a way to specify all three steps w/ one command? That is, could I specify: >trac-all -all -C ConfigFile (I don't see it stated in the help, but maybe it's implicitly understood to work this way?) Thanks for your guidance. Best, Scott

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Re: [Freesurfer] freeview: segmentation fault
by Ruopeng Wang 08 Dec '11

08 Dec '11

I have no problem loading this file in freeview, in both old and new versions. Have you used freeview before on the same system? Did it work? Ruopeng On 12/08/2011 02:33 PM, Xin Zheng wrote: > Hi Ruopeng, > > It seems to be with all files. Attached is one of them. > > Thanks! > Xin > > On Thu, Dec 8, 2011 at 2:22 PM, Ruopeng Wang<rpwang(a)nmr.mgh.harvard.edu> wrote: >> Does it happen with just that file or with other files as well? Would it >> be possible to send us that volume file? >> >> Ruopeng >> >> On 12/08/2011 02:03 PM, Xin Zheng wrote: >>> Hi, >>> >>> We are trying to open something using freeview (ie. freeview -v >>> SubjectID_template/mri/norm.mgz) and would get a segmentation fault. >>> When we tried to open it directly from the freeview GUI, it will load >>> to about 7% and segmentation fault would occur again. We're using >>> Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the >>> problem? >>> >>> Thanks, >>> Xin >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >>

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freeview: segmentation fault
by Xin Zheng 08 Dec '11

08 Dec '11

Hi, We are trying to open something using freeview (ie. freeview -v SubjectID_template/mri/norm.mgz) and would get a segmentation fault. When we tried to open it directly from the freeview GUI, it will load to about 7% and segmentation fault would occur again. We're using Freesurfer 5.1.0 on Fedora 11. Does anyone know what could be the problem? Thanks, Xin

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Re: [Freesurfer] Commands not installed w/ PPC Tiger distribution
by Iain DeWitt 08 Dec '11

08 Dec '11

Yes, this fixes it. Thanks Nick! > you can try downloading and installing this: > > > http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darw… > > > to install, cp this file to /Applications, then type: > > sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz > > n. > > > > On Wed, 2011-12-07 at 14:58 -0500, Iain DeWitt wrote: > > Following up on Ashley's post from 06 Jun 2011 (see below), I also find > > certain commands (see below) are not installed with the current (v5.1) PPC OS > > X Tiger distribution. I had to go back to v4.3 to get a complete set of > > commands. > > > > cheers > > Iain > > > > talairach_avi: Command not found. > > mri_watershed: Command not found. > > mri_segment: Command not found. > > mri_tessellate: Command not found. > > mri_concatenate_lta: Command not found. > > mri_normalize_tp2: Command not found. > > mris_smooth: Command not found. > > mris_inflate: Command not found. > > mris_curvature: Command not found. > > mris_sphere: Command not found. > > mris_fix_topology: Command not found. > > mris_topo_fixer: Command not found. > > mris_ca_label: Command not found. > > mris_euler_number: Command not found. > > mris_make_surfaces: Command not found. > > mris_register: Command not found. > > mris_volmask: Command not found. > > mris_anatomical_stats: Command not found. > > mrisp_paint: Command not found. > > mris_curvature_stats: Command not found. > > mris_calc: Command not found. > > mri_robust_register: Command not found. > > mri_robust_template: Command not found. > > mri_segstats: Command not found. > > > > > > Commands missing in freesurfer directory > > ANN40 > > Mon, 06 Jun 2011 06:22:06 -0700 > > > > Hi all, > > > > I recently downloaded and installed freesurfer for a Mac PowerPC. I tried > > running recon-all on my data and an error message came up saying command > > not found for talairach_avi and many other commands. I looked in my > > /Applications/freesurfer/bin directory and that file wasn't there. All > > the commands that had worked such as mri_convert were. Does anyone know > > what could be causing this problem? > > > > Thanks, > > Ashley > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > > http://www.partners.org/complianceline > . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > >

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tracula and corona radiata
by Cat Chong 08 Dec '11

08 Dec '11

Hello Experts, I would like to be able to get measurements of the anterior portion of the corona radiata using tracula. Is this a possibility? I did not see it as an "option" in paths to reconstruct. thank you very much for your help, catherine

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trackvis, and a separate question about surface transforms
by Colin Reveley 08 Dec '11

08 Dec '11

Hello; first, regarding the information here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms This looks to me very much like snippets of code to help people write their own code to read and transform files, byte by byte, with the help of the trackvis .trk header/file spec. That's great. Thanks. But has anyone written a script or some C or something to actually do that. If not, and if I do that in the form probably of C source, does anyone want the code? second: I'm using freeesurfer for ex-vivo macaque data. It's been a struggle but I've got there. There is something I would like to do: as well as keeping what I have, I would like to tilt the volume's nose up a few degrees (I'd probably use the afni "nudge" plugin for that, or something) and then apply the same transform to my white and pial surfaces. The idea there being to use the surfaces as diagrams in the same cut plane as diagrams in an atlas (the pandya white matter atlas, the paxinos atlas), mark areas and then transform those areas off else where (into diffusion data as masks in fact). I hope that's clear. I just want to apply an arbitrary (actually, a rigid body) linear transform to the surfaces and volumes so that when viewed coronally in sequence in freeview they are in the same plane as diagrams in an atlas, and I can compare the two by eye. the pial and white surfaces together look line like diagrams, and this is very helpful actually. especially if they are in the same cut plane as the atlas diagrams. thanks, Colin

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Freesurfer December 2011