Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] Viewing volumes and surfaces in Native Space
by Douglas N Greve 08 Mar '13

08 Mar '13

Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote: > Hi Doug, > > Thank you for your reply. > > I tried FreeView and have attached screenshots of results. > > freeview_native_brain.jpg - snapshot of native brain > > freeview_aseg.jpg - aseg.mgz added. This appears to correspond with > native brain > > freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar > to aseg.mgz. Slightly different, as I'd expect, corresponds well to > native brain. > > freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. > This is the FreeSurfer output, ie not reoriented. It corresponds well > to aseg.mgz and native brain > > freeview_native_brain_lh_pial_native.jpg - The pial (left) surface > that I created using register.dat and mri_surf2surf is shown. This > does not correspond to the native brain. > > I wonder if there are some FreeView options that I should be using? > > Best regards, > -Tim > > > > On Thu, 7 Mar 2013, Douglas N Greve wrote: > >> Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit >> rigid and expects things to be a certain way (ie, not in native space). >> Try using freeview instead. >> doug >> >> On 03/07/2013 03:19 PM, Timothy Brown wrote: >>> Dear FreeSurfer users, >>> >>> I wish to view volumes and surfaces in native space. >>> >>> I used the information at: >>> >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>> >>> to convert volumes. >>> >>> I then used: >>> >>> tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg >>> register.dat >>> cp register.dat ../surf/ >>> mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native >>> --tval-xyz --hemi lh --s 1158119_3_6 >>> >>> When I use tkmedit to view the surfaces and volumes, the surface that >>> I thought would be in native space does not seem to correspond with >>> the "native space" volumes. (graphic attached) >>> >>> Can you let me know the steps/procedure to do this? >>> >>> Many thanks, >>> >>> -Tim >>> >>> Timothy Brown email: timothy(a)cis.jhu.edu >>> Computational Anatomist phone: 410.516.7551 >>> Center for Imaging Science fax: 410.516.4557 >>> Johns Hopkins University >>> 301 Clark Hall >>> 3400 N. Charles Street >>> Baltimore, MD 21218 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: 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 >> 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. >> > > Timothy Brown email: timothy(a)cis.jhu.edu > Computational Anatomist phone: 410.516.7551 > Center for Imaging Science fax: 410.516.4557 > Johns Hopkins University > 301 Clark Hall > 3400 N. Charles Street > Baltimore, MD 21218 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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cortical thickness of ROIs derived from VBM results
by ZhiLiangLong 08 Mar '13

08 Mar '13

Hi all: I got some regions of interest showing significant diffencese in VBM between two groups. Now, i attemp to compare cortical thickness of these ROIs. However, i don't know how to map the ROIs to cortical surface and extract cortical thickness values? I need help.

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roi analysis on longit. processed data
by Andreas Werner 08 Mar '13

08 Mar '13

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Mirror a label from left hemi to right.
by Chao Suo 08 Mar '13

08 Mar '13

Hi Freesurfers, I have created a label on left hemi. Is there a command could mirror this label to the right hemi? I have tried mris_reserve, it doesn't work. Thanks Chao Suo School of Psychiatry, UNSW RNG, BMRI, Usyd.

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Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
by Andrew Bock 08 Mar '13

08 Mar '13

Hello, I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock(a)u.washington.edu

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Re: [Freesurfer] new tracula
by Anastasia Yendiki 08 Mar '13

08 Mar '13

Hi Andi - You can try, but the trac-* files are just wrapper scripts that call the executables of tracula, which are the dmri_* files. You should also replace the entire $FREESURFER_HOME/trctrain directory with the new version. Hope this helps, a.y On Fri, 8 Mar 2013, Andi Heckel wrote: > Hi Anastasia, > > thank you your reply! > > Can I actually use the new tracula also within the previous Freesurfer > release (v.5.1) ? > I mean by simply copying the new trac-all , trac-paths, > trac-preproc > to the freesurfer/bin directory of v.5.1 ? > > kind regards, > andi > > > -----Original Message----- > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Andi Heckel <ahheckel(a)aol.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tue, Mar 5, 2013 12:07 am > Subject: Re: [Freesurfer] new tracula > > Hi Andi - You're very welcome! I hope you'll find it useful. > > That's correct, if you turn off these pre-processing options then trac-all > will simply copy your DWIs, gradient table and b-value table from the > location that you specify to the dmri/ directory and continue from there. > > You can certainly use a past dmrirc file, trac-all is backwards compatible > that way. But some of the defaults have changed, and you want to make sure > you're not overriding the new defaults unless you have a reason to do so. > > I've updated the page of the example dmrirc with the new defaults but also > put a link in there to the old defaults so you can compare: > http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc > > The tutorial hasn't been updated yet to reflect the 5.2 defaults (ick!) > but I'll get to that soon. > > a.y > > On Mon, 4 Mar 2013, Andi Heckel wrote: > > > Dear Tracula Team, > > > > first, thank you very much for the new version with its many improvements > ! > > > > I have dwi data (as nii.gz) that have already been unwarped and > eddy-corrected, the bvector-textfiles have also been rotated > > accordingly. > > So, I guess, when I use TRACULA on these data, I simply set dob0=0, and > doeddy=0 and dorotbvecs=0 > > to indicate that these steps have already been performed outside of tracul > a, > correct ? (just want to be sure...) > > > > btw. is it safe to use the dmrirc config file from the previous version in > the > new version ? > > > > thank you very much and kind regards, > > andi > > > > > > > > > > > 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-mai > l > contains patient information, please contact the Partners Compliance HelpLin > e at > http://www.partners.org/complianceline . If the e-mail was sent to you in er > ror > but does not contain patient information, please contact the sender and prop > erly > dispose of the e-mail. > >

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Rejoindre mon réseau sur LinkedIn
by Bin Lv via LinkedIn 07 Mar '13

07 Mar '13

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make_average_subject error: talairach.m3z does not start as 'MNI Transform File'
by Xiaowei Song 07 Mar '13

07 Mar '13

Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error. mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest I found another same question asked before, but no answer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html Any hint or help will be appreciated. Thank you. -- Xiaowei Song

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Re: [Freesurfer] FS workshop registration link
by zkaufman＠nmr.mgh.harvard.edu 07 Mar '13

07 Mar '13

Hello Nooshin, The email containing the registration page went out today at 11am EST. It can be found here: https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.7678.cgi Unfortunately, the course was filled within the first two hours of opening registration, but there is a waitlist and you are free to sign up for that. I see your name and email in our email list so you should have received today's announcement. Maybe check your spam folder? -Zeke > Dear All > > I have a question about upcoming Freesurfer course registration (April 29 > _ > May 1). The registration link was supposed to be open and sent by today, > but I still have not received it. > I was wondering if you have any information and can help me. > > Thanks a lot > Nooshin > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer
by Jon Wieser 07 Mar '13

07 Mar '13

Hi Nicole, It looks like recon-all -autorecon2 had trouble segmenting the gray/white matter. you can try using 3duniformize to make the gray,white matter more uniform, before doing the freesurfes recon-all. you can also try skullstrippong in afni with 3dskullstrip first, before freesurfer processing. I have attached script files for the uniformize and skullstrip. if this does not fix it, I can come to help you, or you can e-mail the problem to the freesurfer people at freesurfer(a)nmr.mgh.harvard.edu . They are very helpful and will response relatively quickly. Jon ----- Original Message ----- From: "Nicole T Nowak-Saenz" <nowaksae(a)uwm.edu> To: "Jon Alan Wieser" <wieser(a)uwm.edu> Sent: Thursday, March 7, 2013 12:35:57 PM Subject: Freesurfer Hi Jon, I think you mentioned working with Freesurfer. Have you ever seen anything like this? I'm hoping the problems with segmentation, and white/pial lines are due to the recon-all somehow leaving out half the brain (e.g., temporal lobes). To me it looks like half the brain is missing, yet some skull remains. I have a feeling this will require more than adjusting a watershed parameter. Any clue how these errors occured or what to do about them? I should mention I had to use a flag which was provided in the failed recon-all log to correct an error like this one: DICOM WARNING: file 00020002.dcm has Rescale tags. If this is something you know something about and have a few minutes to address, I would appreciate it. If not, I completely understand. Nicole

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Freesurfer March 2013