Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

error longitudinal processing
by Rashmi Singh 24 May '12

24 May '12

Hello, I ran longitudinal processing which exited with errors. I am attaching the output file. Please advise why this error occurred. The recon –all run ran perfectly for all the time points for this subject. My command was as follows: recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all </dev/null&> FSAA510.long & My all other subjects longitudinal run completed without error. Thanks, Rashmi ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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feat2surf
by Kushal Kapse 24 May '12

24 May '12

hi, i am performing feat2surf after i successfully performed reg-feat2anat.......for some reason it gives me "ERROR: cannot find any .img, .nii, .nii.gz files"....although the stats file is in reg folder.....may i please get suggestion on how to proceed from here thanks kk

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how to save screen shot (using TCL) without X11
by Natalie Han 24 May '12

24 May '12

Hi, I have a tcl script to save multiple tkmedit screen shots, but I wonder if there is a way to suppress the pop out tkmedit windows everytime I want to save the tif. Basically, if I don't have a X11 window when ssh, how can I save the tkmedit screen shots with tcl script? Is there an option in tcl script or tkmedit to render virtually instead of display to the screen? Thanks a lot. -Natalie

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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: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> Sent: Thursday, May 24, 2012 11:45:14 AM Subject: Re: [Freesurfer] fMRI time series in surface space run preprocessing of FS-FAST and do sampling on surface seems a good way to give a try....i am having confusions with directory structure for FS-FAST....Project/sess01/bold/001/f.nii this is how my anatomical directory structure is originally: data/server/controls/14987_4589/ 14987_4589 is one of the subject in controls folder for me i m confused with following thing around FS-FAST: 1- the "project" directory of FS-FAST is supposed to be within 14987_4589 directory???? because as per the tutorial, "sess01" directory is supposed to be subjects directory with bold folder containing functional runs of that subject called as "sess"....... please let me know thanks kk ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, 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 > > -- 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 _______________________________________________ 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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Re: [Freesurfer] extract and display several labels using mri_extract_label?
by Martina Papmeyer 24 May '12

24 May '12

Thanks for your help, Bruce! Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions? Many thanks, Martina Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> on Thu, 24 May 2012 08:53:14 -0400 (EDT): > Hi Martina > you can use mri_binarize --match 17 --match 18... to do this. > > cheers > Bruce > > > > On Thu, 24 May 2012, Martina Papmeyer wrote: > >> 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 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. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [Freesurfer] extract and display several labels using mri_extract_label?
by Bruce Fischl 24 May '12

24 May '12

probably easiest to do in matlab: [v,M,mr] = load_mgh('aseg.mgz'); ind = find(v ~= 17 & v ~= 53 & v ~= 18 & v ~= 54) ; v(ind) = zeros(size(ind)); save_mgh(v, 'aseg.mtl.mgz', M,mr); cheers Bruce On Thu, 24 May 2012, Martina Butt wrote: > Thanks for your help, Bruce! > > Unfortunately, this also leads to a mgz.file where hippocampus and amygdala > are "merged" together so that I can't see anymore what is hippocampus and > what is amygdala (both have same value). I tried some other things but > nothing appears to work. Any other suggestions? > > Many thanks, Martina > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> on Thu, 24 May 2012 > 08:53:14 -0400 (EDT): > >> Hi Martina >> you can use mri_binarize --match 17 --match 18... to do this. >> >> cheers >> Bruce >> >> >> >> On Thu, 24 May 2012, Martina Papmeyer wrote: >> >>> 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 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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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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Freesurfer