Freesurfer

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30132 discussions

Re: [Freesurfer] tkregister2 error on lion
by Nick Schmansky 15 Nov '12

15 Nov '12

Rito, Hi, tkregister2 works for me on lion. do tkmedit and tksurfer work? did you install XQuartz via these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer Actually i dont know if it necessary for lion to install XQuartz, but that is what i am running on my lion system (because i upgraded it from snow leopard when XQuartz was required to run tksurfer). Nick > Hi All, > > I have freesurfer 5.1 installed on my laptop running Lion. When I tried to > use tkregister2, the program doesnt load up the GUI. It failed even after > installing XQuartz. > It loaded successfully in a machine running Snow Leopard. > Any suggestions on how to get around it or are there any fixes available ? > > Thanks a lot > > Ri > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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interpretation of vertexwise thickness, area, volume analysis
by Mahinda Yogarajah 14 Nov '12

14 Nov '12

Dear Experts, Given that volume is area x thickness, how would one explain significant reductions in volume in a qdec anaysis comparing patients and controls, but not significant differences in area or thickness in the same regions where volume differences are seen. All analyses use the same parameter settings. Thanks. Mahinda

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SPM complications - moving parcels into native space
by Terri Scott 14 Nov '12

14 Nov '12

Dear all, I'm new to freesurfer and I'm trying to move a set of parcels from mni space to the native space of a subject. The parcels were created in SPM but I was going to try to register them to the subject using cvs. I registered my subject to an mni template with cvs. I converted the .img parcel file to .nii.gz, and changed the voxel size and orientation to match the mni template I used for the cvs registration of my subject. I then run this: mri_vol2vol --inv-morph --noDefM3zPath --interp nearest --no-save-reg --mov ' subj_anat_vol ' --targ ' cvs_input ' --o ' in_anat_output ' --m3z ' morph_fullpath ' >> ' log_fullpath where cvs_input is my parcel. When I run it, the parcels don't register well and come out distorted/in the wrong spot/etc. The parcel volume size is very different from the 256x256x256 template, but I don't know how to handle this problem. Any help you can give is greatly appreciated! Thanks! Terri

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Rejoindre mon réseau sur LinkedIn
by Steven Lehar via LinkedIn 14 Nov '12

14 Nov '12

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tkregister2 error on lion
by Ritobrato Datta 14 Nov '12

14 Nov '12

Hi All, I have freesurfer 5.1 installed on my laptop running Lion. When I tried to use tkregister2, the program doesnt load up the GUI. It failed even after installing XQuartz. It loaded successfully in a machine running Snow Leopard. Any suggestions on how to get around it or are there any fixes available ? Thanks a lot Ri

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aparc+aseg voxels labeled as "unknown"
by Nikhil Chandra 13 Nov '12

13 Nov '12

Hello, After completing the FreeSurfer Recommended Reconstruction, we have noticed that in aparc+aseg, many subjects exhibit small clusters of voxels in the medial temporal lobe that are labeled as "ctx-lh-unknown" or "ctx-rh-unknown". These clusters are mostly found on the boundaries between the amygdala, hippocampus, inferior lateral ventricles, and cerebral white matter. Please refer to the attached screen shot for an example. How can we deal with this problem? One possible solution that we thought of was to apply the corresponding label in aseg.mgz for each affected voxel in aparc+aseg.mgz, but we thought we would ask if there is a better way. Thank you, Nikhil Chandra

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Fwd: bad acquisition and noise problem.
by youngmin huh 13 Nov '12

13 Nov '12

---------- Forwarded message ---------- From: youngmin huh <ymin1123(a)gmail.com> Date: 2012/11/14 Subject: Re: bad acquisition and noise problem. To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Thanks for your comment. I would appreciate if you could take a look. Do you want a whole folder of the subjects, or just 001.mgz and log file? Thanks, Youngmin. 2012/11/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > it's not a question of SNR, the problem appears to me to be that the B0 > distortions are so bad that a bunch of the temporal lobe is piled up on top > of itself. There's no way to fix that posthoc. If you upload the full > volume I'm happy to take a look > > > On Wed, 14 Nov 2012, youngmin huh wrote: > > I'm not engaged in obtaining images, so I don't have any details about the >> images.I wonder the method which you commented can be applied to images I >> >> already earned. >> If it's not, is there any way to recover SNR after image scanning? >> >> Thanks, >> >> Youngmin Huh. >> >> >> 2012/11/13 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what is the bandwidth? The typical way to fix it is to increase >> the bandwidth. You can probably recover some of the SNR you will >> lose by reducing your flip angle, which is pretty far from the >> Ernst angle. >> Also, minimize your TE (if 4ms is not already the min) >> cheers >> Bruce >> >> >> On Tue, 13 Nov 2012, youngmin huh wrote: >> >> Hi, >> 3D SPGR sequences were used. (TR=22, TE=4, >> thickness=1.4, FOV=240*240, >> FA=40) >> If the artifacts are due to B0 distortion, I wonder >> how I can fix it. >> >> Thanks, >> Youngmin Huh >> >> >> >> 2012/11/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Can you give us the acquisition details? I >> suspect this is not >> noise, but rather B0 distortion. >> what is the acquisition? And what bandwidth? >> >> >> On Nov 8, 2012, at 2:53 AM, youngmin huh >> <ymin1123(a)gmail.com> >> wrote: >> >> > Dear all, >> > >> > I'm working with some images, and they have >> so much noises on >> temporal areas. >> > I just ran recon2, but not sure if they'll >> be segmented >> properly. >> > Does anyone have a recommendation for >> dealing with it? >> > I wonder if there is any flag or option for >> this occasion. >> > I would appreciate any comments or help. >> > I attached an example. >> > >> > Thanks, >> > >> > Youngmin Huh >> > <temporal_001.jpg> >> >> >> 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<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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Re: [Freesurfer] bad acquisition and noise problem.
by youngmin huh 13 Nov '12

13 Nov '12

Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Can you give us the acquisition details? I suspect this is not noise, but > rather B0 distortion. > what is the acquisition? And what bandwidth? > > > On Nov 8, 2012, at 2:53 AM, youngmin huh <ymin1123(a)gmail.com> wrote: > > > Dear all, > > > > I'm working with some images, and they have so much noises on temporal > areas. > > I just ran recon2, but not sure if they'll be segmented properly. > > Does anyone have a recommendation for dealing with it? > > I wonder if there is any flag or option for this occasion. > > I would appreciate any comments or help. > > I attached an example. > > > > Thanks, > > > > Youngmin Huh > > <temporal_001.jpg> > > > 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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Subgenual ACC - part of the Desikan rostral ACC?
by Amanda Schlesinger 13 Nov '12

13 Nov '12

Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under the genu of the CC and that the caudal boundary there at the genu marks the rostral edge of the subgenual ACC/BA 25? Clarification would be much appreciated! thanks! - Amanda ---------------- Amanda Schlesinger, MD Department of Psychiatry University of Minnesota Medical School schle248(a)umn.edu

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Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl
by Clark Fisher 13 Nov '12

13 Nov '12

Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark

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