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30132 discussions

Fwd: subcortical segmentation
by Liane Hunter 16 Jul '13

16 Jul '13

---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Tue, Jul 16, 2013 at 12:44 PM Subject: Re: [Freesurfer] subcortical segmentation To: Liane Hunter <liane.hunter(a)med.einstein.yu.edu> Hi Liane can you cc the list so others can answer? You will get better and faster answers that way, and also others will be able to learn from the replies. thanks Bruce On Tue, 16 Jul 2013, Liane Hunter wrote: Thanks so much.As as clarification: should I make edits to the > brainmask.mgz > > or norm.mgz file. > Likewise, is this the correct command to run to fix edits to the > subcortical > segmentation: > > normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. > > Thank you again for all of your help > Liane > > > > On Tue, Jul 16, 2013 at 11:40 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > > wrote: > Hi Liane > the brainmask is not for subcortical segmentation - use the > norm.mgz if you want to visualize subcortical structures > > cheers > Bruce > On Tue, 16 Jul 2013, Liane Hunter wrote: > > > Hello, > I noticed that when I am checking the subcortical > segmentation the brainmask does not accurately display the > subcortical structures > ( ie. the putamen is too small). The segmentation appears > to be correct when I compare it to the original > file. Does anyone know why this is the case? > Also, if I make changes to the subcortical segmentation > based on the original file will this change accurately > edit the brainmask? > > Thank you. > Sincerely, > Liane > > Liane HunterMD/Ph.D Candidate > Albert Einstein College of Medicine > > > > > 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. > > > > > -- > Liane HunterMD/Ph.D Candidate > Albert Einstein College of Medicine > > -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Button Press Regressor
by Nicholas Paul Denisuk 16 Jul '13

16 Jul '13

Dear Freesurfer Users, I have opened up the X.mat file from the analysis. I think that the button regressor is the third column in the file, but I am not 100% sure. Do you know which column the button regressor is? Below is the background info to this question. >>I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick >>Hi Nick, please remember to post to the list and not to us personally. To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work. doug

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Segfault error
by Rune Frandsen 16 Jul '13

16 Jul '13

I have just installed Freesurfer and wanted to try tkmedit I get a Segfault error and it asked me to write to this mail. The .xdebug_tkmedit is tkmedit started: Wed Jul 10 10:53:23 2013 /usr/local/freesurfer/tktools/tkmedit.bin $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Segfault Creating main window xDebug stack (length: 2) 01: main() 01: Creating main window 00: 00: My system is a fresh install of CentOS 6.4 64bit installed in VirtualBox. The only other program installed is FSL. The base machine is a HP Envy dv6 i7 16GB with Win8 64bit. Is this a known problem? Best regards Rune Frandsen (MD, phd student) Danish Center for Sleep Medicine runefrandsen(a)gmail.com

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mritotal vs. talairach_avi scripts
by Mark Plantz 16 Jul '13

16 Jul '13

Hello, I have a quick question about talairach transform. I know that FreeSurfer previously used mritotal to create the linear talairach transform. You could check the "final objective function value" in the mritotal.log file. I think the ideal value was in the ballpark of 0.06. Is there a way to check for this value in the current talairach_avi script? If so, where would it be found? Possibly in the recon-all.log? Thank you for the help. - Mark

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Articles regarding using FreeSurfer manual interventions
by Liane Hunter 16 Jul '13

16 Jul '13

Hello, I wanted to inquire if anyone knows of any articles in the literature that quantify the differences between using FreeSurfer with and without manual intervention. Thank you Liane -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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subcortical segmentation
by Liane Hunter 16 Jul '13

16 Jul '13

Hello, I noticed that when I am checking the subcortical segmentation the brainmaskdoes not accurately display the subcortical structures ( ie. the putamen is too small). The segmentation appears to be correct when I compare it to the original file. Does anyone know why this is the case? Also, if I make changes to the subcortical segmentation based on the original file will this change accurately edit the brainmask? Thank you. Sincerely, Liane Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Re: [Freesurfer] Xhemi question
by Boratyn, Daria A. 16 Jul '13

16 Jul '13

Couple of quick things in regards to smoothing prior to calculating the LI. I'm just trying to use the fsaverage_sym atlas and improve my xhemi registration, not conduct a thickness asymmetry analysis. Should the smoothing be done before the xhemi registration? If so, do you have a recommendation for the smoothing kernel? Also, how many vertices are there in fsaverage_sym's surface? Thank you, Daria Daria A. Boratyn, Clinical Research Coordinator MS Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Date: Fri, Jun 7, 2013 at 1:31 PM Subject: Re: [Freesurfer] Xhemi question To: Daria Boratyn <boratyn(a)nmr.mgh.harvard.edu<mailto:boratyn@nmr.mgh.harvard.edu>>, "Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>" <Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding xhemi to our processing stream. Is there > is a way to QC the results at an individual subject level? > > Best, > Daria > > > Daria A. Boratyn, > Clinical Research Coordinator > MS Imaging Lab > Massachusetts General Hospital > 149 13th Street | Boston, MA 02129 > 617-726-7531<tel:617-726-7531> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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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rtview.sh & fsig
by Michael Bannert 16 Jul '13

16 Jul '13

Dear Freesurfer experts, I have been using Freesurfer in combination with rtview.sh to visualize my retinotopic mapping results (rotating wedge) and to define masks for individual visual areas. The command that I use for this is something like: rtview.sh --s *subj_id* --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz I was under the impression that by specifying fsig, Freesurfer would internally threshold the resulting polar map according to an F-test to show only significant vertices. Is this true? I actually doubt that this is the case because I noticed in the "configure overlay display" that the maps are seemingly arbitrarily thresholded at a "Min" of 0.4. Is this threshold derived based on statistical principle? How can I do proper statistics with fsig.nii.gz in Freesurfer, i.e. define alpha, correct for multiple comparisons etc.? Thanks, Michael P.S.: Just to provide some context for my question... imho it doesn't matter much if a given vertex is significantly activated if the only purpose is to define boundaries between visual areas. However, an exception would be the definition of such boundaries in the cortical surface near the fovea where boundaries between areas cannot be identified as reliably as in more eccentric regions. I was thinking that by focusing only on significant vertices, I would be able to isolate only those voxels that can clearly be assigned to a single visual area - even if that means that I may have to discard some vertices near the fovea. -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031

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ROI info in the DK atlas
by Yang, Daniel 16 Jul '13

16 Jul '13

Dear FreeSurfer Expert, I would like to draw the specific ROI of the DK atlas (not specific individual, but this ROI in general). I'm wondering how this ROI can be extracted/created as a mask so that I can draw it on the brain using some software? Could you please advise? Thanks a lot, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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tracula -path option 0 unknown
by Gerit Pfuhl 16 Jul '13

16 Jul '13

Dear Freesurfer experts, for one subject (out of over 80 already processed) I get i nthe last step an error I am unable to locate. The output from the tracula -path command says at the end: option 0 unknown. There are no reported problems in -prep, and -bedp. The script uses default values (I run this subject 3 times, always gets stuck on -path, not before). The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use bbr Excerpt of the output ... /igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt ERROR: Option 0 unknown Thanks for all help to understand this Gerit

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