Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

brain regions
by Ahmed, F, Me <fahmed＠sun.ac.za> 12 Jun '10

12 Jun '10

Hello FS experts, A quick question, I'm looking for specific brain regions, but I can't seem to find them in the files once processing has been completed, I'm just wondering if FS does processing for areas including prefrontal cortex and corpus collosum? Thanks, Fatima

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cortical and subcortical lesions
by Natalie Marchant 12 Jun '10

12 Jun '10

Hello, I have a couple of questions about lesions: 1. I would like to define cortical lesions and white matter lacunes in freesurfer using T1 and FLAIR images; maybe by combining the aseg results with the FLAIR images? I read some old threads about this topic and saw mention of something that the freesurfer team was working on to do this. Is this program now available? If not, has anyone tried to do this and had success? 2. Some of the cortical lesions extend into the white matter, technically causing a discontinuation in the grey matter surface. Following the tutorial, I filled in the area of the stroke, but after rerunning recon2 freesurfer still represents a pial line around this area. Is there a way to fix this? I have attached a screenshot. Thanks for your help, Natalie

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Re: [Freesurfer] Across Scanner Comparisons
by Pedro Paulo de Magalhães Oliveira Junior 12 Jun '10

12 Jun '10

With distinct fields/gradients and FS 4.01 I think you can have quite distinct results. My guess: 10% difference. Bruce can give you a more accurate figure. At http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes notice: "-norandomness is the the default. The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results. The -randomness flag can be used to allow usage of a random seed." I suggest you to upgrade to 4.5.0 cheers ---------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile 2010/6/10 <blazey(a)artsci.wustl.edu> > One scanner is a Siemens Vision 1.5T and the other is a Siemens Trio 3T. > We used FreeSurfer 4.01 for the cross-sectional processing. > > Thanks, > > - Tyler > > > It's hard to know without the info about scanner type > > (Manufacturer/Field/Sequence) and FreeSurfer version. > > > > I usually see 3-5% difference in measurements. Phillips 3T with common > > fSPGR. > > ---------------------------------------------------------- > > Pedro Paulo de M. Oliveira Junior > > Diretor de Operações > > Netfilter & SpeedComm Telecom > > -- For mobile: http://www.netfilter.com.br/mobile > > > > > > > > > > On Thu, Jun 10, 2010 at 12:03, <blazey(a)artsci.wustl.edu> wrote: > > > >> Hi All, > >> > >> Our group recently scanned subjects with two different scanners in order > >> to determine how reliable FreeSurfer comparisons between the two > >> scanners > >> are. After putting each session through the regular cross-sectional > >> Freesurfer pipeline, we noticed that there is much greater variability > >> between the two scanners when we compare structures in the right > >> hemisphere than in the left. Is there any FreeSurfer related reason for > >> this? > >> > >> Also, we are currently running each subject through the longitudinal > >> pipeline (i.e. Scanner 1 as TP1, Scanner 2 as TP2). Is there any reason > >> to > >> think that this will help reduce the variability seen between the two > >> scanners? > >> > >> Thanks in advance for any help. > >> > >> - Tyler Blazey > >> > >> > >> > >> _______________________________________________ > >> 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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CT registration
by Gregory Dierksen 12 Jun '10

12 Jun '10

Does FreeSurfer (or FSL) have any commands that support CT registration? --

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how the -nonuintensitycor flag work?
by Guang Zeng 12 Jun '10

12 Jun '10

Hi, there, I wan to use the -nonuintensitycor option of the recon-all command, my command line is: recon-all -s subjid -all -nonuintensitycor, But the process failed because in the following step, they can not find nu.mgz, so I need to create my own nu.mgz before running my recon-all command, is it correct? Thanks! Guang _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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How means all the output file from a segmentation?
by Leonardo Chesi 12 Jun '10

12 Jun '10

Hi, after the segmentation process, we obtain a lots of file that I can't understand what they represent. Infact I know the mean of the file aseg.mgz (that is a mask of the segmentation) and norm.mgz but for example I can't understand the difference between brainmask.mgz and brainmask_auto.mgz. Can you help me with a list of the output? And can I obtain the volume rendering of only one part of the segmented structure? (es. Hippocampal)?? Thanks for your help Leonardo

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ERROR "Could not determine file type" during mri_vol2surf AND opening a talairach.xfm in tkmedit
by Dickinson, Annelise (NIH/NIMH) [F] 11 Jun '10

11 Jun '10

Hi all, Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error: >> mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh >>ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file): mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm Has anyone seen such an error before and/or know how to fix it? Please let me know! Thank you!!! -Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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Fwd: advise on generating individual standard deviation map
by Michael Scheel 11 Jun '10

11 Jun '10

Hi Doug, I think I solved the registration issue. This is my command: mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval bert/surf/lh_av.thickness --trg_type curv Any objections? Thanks, Michael Begin forwarded message: > From: Michael Scheel <scheelmichael(a)googlemail.com> > Date: 10. Juni 2010 22:45:10 MESZ > To: Doug Greve <greve(a)NMR.MGH.HARVARD.EDU> > Subject: Re: [Freesurfer] advise on generating individual standard deviation map > > Hi Doug, thanks for you reply. That is exactly what I want to do so many thanks for explaining that. > However I have problems with the usage of mri_surf2surf > > michael$ mri_surf2surf --srcsubject bert --srcsurfval bert/surf/lh.thickness --trgsubject fsaverage --trgsurfval bert/surf/lh.thickness_average --hemi lh > ERROR: could not determine type of bert/surf/lh.thickness_average > > Also when I run the example from the FS wiki site i get the following error (see below). Any idea what I'm doing wrong here? > > Thanks, Michael > > michael$ mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval bert-thickness-lh.img --trg_type analyze4d > srcsubject = bert > srcval = thickness > srctype = curv > trgsubject = ico > trgval = bert-thickness-lh.img > trgtype = analyze4d > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > Reading source surface reg /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.sphere.reg > Loading source data > Reading curvature file /Users/michael/Desktop/TEST_FREESURFER/bert/surf/lh.thickness > Reading icosahedron /Applications/MriSoftware/freesurfer/lib/bem/ic7.tri > Done > Mapping Source Volume onto Source Subject Surface > surf2surf_nnfr: building source hash (res=16). > Surf2Surf: Forward Loop (163842) > > surf2surf_nnfr: building target hash (res=16). > Surf2Surf: Reverse Loop (131122) > Reverse Loop had 21908 hits > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 146869, nTrgMulti = 16973, MnTrgMultiHits = 2.29076 > nSrc121 = 89131, nSrcLost = 0, nSrcMulti = 41991, MnSrcMultiHits = 2.30095 > Saving target data > ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 > > > > > On 10.06.2010, at 12:05, Doug Greve wrote: > >> >> I don't have anything explicitly that will compute a map of z-scores, >> but you could do a two "group" analysis with your subject as the only >> one in one group and then do a group analysis. Alternatively, you can >> transform you individual to the fsaverage space (mri_surf2surf), then >> compute the z using fscalc.fsl. You'd have to compute the group mean >> and stddev using mri_concat (--mean and --std), then use fscalc.fsl, >> something like >> >> fscalc.fsl --surf fsaverage lh lh.thickness.fsaverage.mgh -sub >> groupmean.mgh -div groupstd.mgh zscore.mgh >> >> doug >> >> >> >> >> >> On Wed, 9 Jun 2010, Michael Scheel wrote: >> >>> Dear FS experts, >>> >>> could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. >>> >>> Thanks, Michael >>> _______________________________________________ >>> 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 >> >> >> 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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MRIread and MRIwrite
by Seok Lew 10 Jun '10

10 Jun '10

Hi, I am using matlab functions of MRIread and MRIwrite for a MRI correction. When running mri_normalize with the corrected MRI, I came up with the error like 'unsupported src format 3'. For a debug, I simply MRIread a mri and MRIwrite the mri without anything done, but had the same src format error. Anyone know what went wrong ? Thanks, Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School slew(a)nmr.mgh.harvard.edu

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retinotopy: MGH vs UCSD
by francesca strappini 10 Jun '10

10 Jun '10

Hi all, I would ask you about freesurfer and retinotopy. I'm going to begin the analysis of some retinotopic data. I would ask if you know if the retinotopic analysis made by MGH freesurfer is qualitatively comparable to, or it's good as, that made by USCD freesurfer (old freesurfer). Thank you kindly in advance. Francesca

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