Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Fwd: fMRI time series in surface space
by Kushal Kapse 24 May '12

24 May '12

----- Forwarded Message ----- From: "Kushal Kapse" <kkapse(a)mail.med.upenn.edu> To: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Sent: Thursday, May 24, 2012 9:14:55 AM Subject: Re: [Freesurfer] fMRI time series in surface space hi Bruce, what if I have .feat files from FSL which have already been processed for functional analysis......how can i use transformation tools for going from 4D time series-functional to FS average template surface space for FSL output?..... ----- Original Message ----- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> To: "Kushal Kapse" <kkapse(a)mail.med.upenn.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 8:50:43 AM Subject: Re: [Freesurfer] fMRI time series in surface space Hi KK, mri_vol2surf will take it to individual subject space, then mri_surf2surf can be used to bring it into average space if you want. cheers Bruce On Thu, 24 May 2012, Kushal Kapse wrote: >> Hi Everyone, >> >> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >> >> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >> >> Many thanks, >> kk > _______________________________________________ > 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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extract and display several labels using mri_extract_label?
by Martina Papmeyer 24 May '12

24 May '12

Hello everyone, I guess that this might be a simple question but I couldn't find an answer to my problem yet. I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following: mri_extract_label aseg.mgz 17 18 53 54 filename.mgz (the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file) This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit. Is there any other FS tool I can use? Any form of help would be highly appreciated! Many thanks and all best wishes, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Postdoc Position in Neuroanatomical MRI of Impulsivity
by Andrew Lawrence 24 May '12

24 May '12

*Postdoc Position in Neuroanatomical MRI of Impulsivity* Applications are invited for a 1-year postdoc position, funded by the Waterloo Foundation, in the lab of Andrew Lawrence, School of Psychology, Cardiff University, UK. The successful candidate will investigate neuroanatomical correlates of individual differences in impulsivity in young adults, using high-quality 3T MRI images from T1 and diffusion sequences that have already been collected as part of an imaging genetics project. The position is available from July 1st. Candidates should have a PhD in cognitive or social neuroscience, imaging neuroscience, or a closely related field. Experience with the analysis of neuroanatomical images using e.g. Voxel-based morphometry or cortical thickness analysis (Freesurfer) is essential. Salary will range from a minimum of £30, 122 to a maximum of £35, 938 and will depend on the experience of the candidate. The post-holder will be based in the School of Psychology at Cardiff University. Cardiff Psychology is one of the UK’s largest psychology departments, and was rated top in the UK at the last Research Assessment Exercise (based on research power). The School includes the Cardiff University Brain Research Imaging Centre (CUBRIC). Cardiff has significant capacity in imaging research, including in methods development, cognitive neuroscience and clinical applications, and there are outstanding training opportunities for staff to develop their research skills. For more information visit http://psych.cf.ac.uk. Application forms and further particulars about this position should be obtained by contacting HR Division, Cardiff University, McKenzie House, 30-36 Newport Road, Cardiff CF24 0DE, or emailing vacancies(a)cardiff.ac.ukor by calling 029 2087 4017, citing post reference 128BR. Closing date for applications: *14th June 2012* Informal enquiries may be directed to Prof. Andrew Lawrence ( LawrenceAD(a)Cardiff.ac.uk) For recent related work from the lab, see: Boy F et al. Dorsolateral prefrontal γ-aminobutyric acid in men predicts individual differences in rash impulsivity. Biol Psychiatry 2011; 70:866-72. -- Andrew Lawrence Professor School of Psychology Cardiff University Tower Building, Park Place Cardiff CF10 3AT

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mri_aparc2aseg error during trac-all
by Gabor Perlaki 24 May '12

24 May '12

Hi all! I've just ran the preprocessing for TRACULA analysis, with the command "trac-all -prep -c /home/kutato12/Desktop/dmrirc". It works everything fine, and the output files are correct until the following command: mri_aparc2aseg --s my_subject --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/kutato12/freesurfer/subjects//my_subject/dlabel/anatorig/aparc+aseg+2mm.nii.gz freadFloat: fread failed SUBJECTS_DIR /home/kutato12/freesurfer/subjects subject my_subject outvol /home/kutato12/freesurfer/subjects//my_subject/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0 It fails with the following: freadFloat: fread failed mrisFindNeighbors: /home/kutato12/freesurfer/subjects/my_subject/surf/lh.white: face[1].v[0] = 0, but face 1 not in vertex 0 face list Segmentation fault Linux kutato12 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux The recon-all finished on the MPRAGE without error before trac-all script was started. I've freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 11.04, and I use the trac-all update (2012/01/09). I'd appreciate any help on this issue. Thanks, Gabor

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How to create .license file
by Kan Ding 23 May '12

23 May '12

Hi, All, As instructed by previous post, I typed " pico $FREESURFER_HOME/.license" and was able to place the three lines from my registration email into new window. What should I do after I see " File Name to Write: FREESURFER_HOME/.license" ? How do I pick up the options in this interface? I'm new to FreeSurfer and command interface. Thanks, Kan

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confirm my posting
by Kushal Kapse 23 May '12

23 May '12

just want to confirm if my mail is successfully getting posted on freesurfer

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kkapse@mail.med.upenn.edu
by Kushal Kapse 23 May '12

23 May '12

kkapse(a)mail.med.upenn.edu

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Re: [Freesurfer] mri_convert and --out_orientation (once again)
by Clark Fisher 23 May '12

23 May '12

Thanks Doug, In that case, since everything seems to be working as I want it to, I'm going to leave it as-is. Do you think that this is likely to change back to it's intended (pixel data ignoring) function in future versions, or can I continue to use it like this? -Clark

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wm surface does not follow wm.mgz
by Leon 23 May '12

23 May '12

Hi, FreeSurfer experts I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue. Thanks in advance! Leon

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A question about thickness computation for surfaces not generated by Freesurfer
by Navid Shiee 23 May '12

23 May '12

Hi, I have generated inner and pial surfaces using another method. However, I am interested in computing the cortical thickness using the method implemented in Freesurfer. My surfaces are in vtk format. I was wondering how I can do this, if this is at all possible. Thanks, -- Navid Shiee

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Freesurfer May 2012