Freesurfer

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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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qdec-calculate the value of the slope
by asaf achiron 10 Jun '10

10 Jun '10

Hello Support, how can i calculate the value of the slope of a a plot when displaying the data for a particular vertex in qdec? thank you

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Across Scanner Comparisons
by blazey＠artsci.wustl.edu 10 Jun '10

10 Jun '10

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

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

10 Jun '10

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

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Registration of talairach and original space?
by Dickinson, Annelise (NIH/NIMH) [F] 10 Jun '10

10 Jun '10

Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen ***************************************************** 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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Calc stats on ROI in qdec
by Jeff Sadino 09 Jun '10

09 Jun '10

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff

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Snowy background for T1 images
by Dave Brohawn 09 Jun '10

09 Jun '10

Hello, I keep seeing a snowy background for my T1 structural images. Here is my info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ cd /space/seymour/1/users/folate_subjects The command I entered and one of the subjects we are seeing this with - tkmedit-sess -s FB0011089A -a fmcsm5_functionals -c Cond1vFix Is this a problem? What can I do to fix this? Dave Brohawn

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