Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Longitudinal processing; problem with template creation
by Per Selnes 21 Jun '10

21 Jun '10

Hi, I keep having problems when processing templates in the longitudinal run in FreeSurfer 4.5 on 64bit Linux. For most subjects, the templates seem nearly perfect, but for some, even though the time point recons seem fine, the surfaces of the templates are completely garbled, and it seems as if the posterior part of the brain is chopped off, i.e. outside the image. See enclosed screenshot with the two time points above, and the template below. According to the log, recon-all completed without errors. Might this be related to this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12187.html Thanks a lot in advance! Regards, Per Selnes

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Re: [Freesurfer] extracting anatomical ROI in native space
by Doug Greve 19 Jun '10

19 Jun '10

Try using nifti output, ie, "--o label1.nii" doug On Sat, 19 Jun 2010, Hwee Ling Lee wrote: > Dear all, > > > > Apologies for my ignorance. > > I'm trying to extract the transverse gyrus, transverse sulcus, planum > temporale and temporal pole from the inflated surface created by freesurfer. > What I intend to do, is to convert these labels into spm analyze format > files in native space, and apply the deformation parameters from DARTEL into > standard space. > > > > Until now, I have created new labels for these regions, and using the > mri_label2vol command line: > > > > mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz > -fillthresh .5 -o label1.bshort > > > > However, it prompted me for a register.dat file and I do not have this. > Using the advice from Dr. Doug Greve, I have tried to use the -identity: > > > > mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz > -identity -fillthresh .5 -o label1.bshort > > > > When I did this, I get 256 files for label1. > > > > So I think I might have done something wrong here. > > > > Could someone please advise me how to do this? I'm lost here. > > Thank you very much in advance! > > > > Best regards, > > HweeLing > > > > -- 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

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extracting anatomical ROI in native space
by Hwee Ling Lee 19 Jun '10

19 Jun '10

Dear all, Apologies for my ignorance. I'm trying to extract the transverse gyrus, transverse sulcus, planum temporale and temporal pole from the inflated surface created by freesurfer. What I intend to do, is to convert these labels into spm analyze format files in native space, and apply the deformation parameters from DARTEL into standard space. Until now, I have created new labels for these regions, and using the mri_label2vol command line: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -fillthresh .5 -o label1.bshort However, it prompted me for a register.dat file and I do not have this. Using the advice from Dr. Doug Greve, I have tried to use the -identity: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -identity -fillthresh .5 -o label1.bshort When I did this, I get 256 files for label1. So I think I might have done something wrong here. Could someone please advise me how to do this? I'm lost here. Thank you very much in advance! Best regards, HweeLing

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2nd Level Analyses in FreeSurfer
by Andrew Jahn 18 Jun '10

18 Jun '10

Hi all, I am interested in using Freesurfer to project volume data onto the inflated brains run through the FS pipeline. I am using SPM and have been able to project 1st level con and spmT images onto the corresponding subject's inflated anatomical. My question is, if I wanted to look at 2nd level SPM results on an inflated brain, would it make the most sense to project them onto fsaverage? For example, spmregister --s fsaverage --mov spmT_0001.hdr --reg register.dat Or, is there a way to average the surfaces of the subjects in the study and then project their second levels onto that averaged surface? Thanks! -Andrew

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MAP FUNCTIONAL OF SINGLE SUBJECTS INTO TAILARACH (MNI305) SPACE (fsaverage)
by caspari＠clipper.ens.fr 18 Jun '10

18 Jun '10

Hi! This is maybe something very easy: but I am not sure whether I did it the right way: To map the activation from the subject anatomy to the fsaverage volume I used the sig.nii file out of my contrast folder (humBod-vs_humObj) together with the command mri_vol2vol: mri_vol2vol --mov ../all_days_ss2/bold/all_days_ss2/humBod_vs_humObj/sig.nii --reg ../all_days_ss2/bold/register.dat --o HB-HO-in-tal.2mm_ss2.nii --tal --talres 2 (my functional image is also 2mm isotropic) Can this be done like that? When I remapp the volume activation of my single subject (which has been remapped by the above command onto fsaverage space?) onto the fsaverage surface, and visualize it with tksurfer, actually my main activation (ROI of interest) nearly dissappears, but all the rest looks quite similar- how can this be? I'm not sure whether I proceed in the right way. would be great If someone could help me out! Natalie xxx

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are paired compairisons possible using QDEC
by Mira Michelle Raman 18 Jun '10

18 Jun '10

Hi, I have a group of siblings (one disorder, one unaffected). Is it possible for me to set up the group analysis in a way so that siblings are compared to their sibling, something analogous to a paired t-test, and if so do you have a tutorial or example to which you could direct me. Thank you, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620

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Parametrics in FreeSurfer
by Andrew Jahn 18 Jun '10

18 Jun '10

Hi FreeSurfer experts, I was wondering whether you are able to use parametric modulators during FS-FAST. All I can see from the mkanalysis-sess gui is setting up contrasts, but I would also like to see how other parameters affect the size and shape of the bold response. Is there any way to do this in Freesurfer? If not, is there a way to visualize parametric analyses done in another software package (e.g., SPM) on a brain processed in freesurfer? Thanks! -Andrew

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Re: [Freesurfer] deepest zone in a sulcus
by Lena Palaniyappan 18 Jun '10

18 Jun '10

Thanks for the help, will try lh.sulc, for proxy 'depth' measure cheers On 18/06/2010 19:50, "Donna Dierker" <donna(a)brainvis.wustl.edu> wrote: > I would think lh.sulc might be better for this purpose. > > If neither works, you can try importing into Caret and using sulcal > depth. Hopefully lh.sulc will do the job. > > On 06/18/2010 08:49 AM, Lena Palaniyappan wrote: >> Hi all >> >> I am trying to determine a 'sulcal pit' - the deepest point in central >> sulcus. The lh.curv file gives curv values of all vertices, but how can I >> display the depth as a color map localised to central sulcus only? With such >> a display will I be able to identify the zone with maximum 'depth' as >> defined by lh.curv values? >> >> Cheers >> Lena >> >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

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regeneration of a aseg.stats file...
by Gonzalo Rojas Costa 18 Jun '10

18 Jun '10

Hi: I deleted the aseg.stats file by mistake (only that file)... How can I regenerate that file ?... I have the complete processing of that patient... Sincerely, Gonzalo Rojas Costa

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how to check the version of freesurfer?
by Dalwani, Manish 18 Jun '10

18 Jun '10

Sorry for this lame question but how can I check the current version of freesurfer? Regards, Manish Dalwani

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