Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

availability of freesurfer version 4.0.1
by Burmicz, Ryzarda 07 Nov '08

07 Nov '08

Hello, I have some data which was recon-all'd using 4.0.1 and I have since lost this version of the software. Would it be possible to get hold of 4.0.1 in order to rerun some corrected brains? Thanks, Rysia

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DEALING WITH INTENSITY NORMALIZATION PROBLEMS
by david felps 07 Nov '08

07 Nov '08

Hi Bruce, hi Susan, i was trying to solve the intensity normalization problem using the methods proposed in "How-to Guide for Cortical Inflation using FreeSurfer by Susan Mosher Updated May 25, 2005 " . I was able to add the necessary control points which created, as mentioned in the guide, the "control.dat" file in the right directory. Now i can not erase or remove the selected control points from my wm.mgz in the tkmedit and the following command: % mri_normalize –f $SUBJECT/tmp/control.dat is not working. i ll be thankfull for any hint. _________________________________________________________________ Messenger Online Treff: Spontan chatten, über Hobbies reden, sofort Spass haben? Jetzt klicken! http://redirect.gimas.net/?n=M0811xMOTDE

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mri_binarize download
by Dominic Dwyer 06 Nov '08

06 Nov '08

Hi all, Where I can find a copy of the mri_binarize file? It doesn't seem to be included with 4.0.5, and based on a post from 2007 I looked in ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/ to no avail. I've also checked the site. Since this is my first post I'd also like to send my thanks to the developers for a great program and ongoing support! Dom ------------------------------------------ Dominic Dwyer, PhD candidate Melbourne Neuropsychiatry Centre The University of Melbourne

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Single subj v. group analysis in qdec with covariates-- impossible?
by Laluz, Victor 06 Nov '08

06 Nov '08

Hello, When trying to do a single-subject vs. group qdec study with covariates, I always get errors, such as: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. This error seems quite sensible to me, and I understand why the GLM is unable to deal with it, but is there any way I can "force" it to use the covariates on the single subject, such as is possible in SPM5? Doing uncontrolled analyses are fine (I wouldn't trust the controlled data very much anyway) but it would, in theory anyway, eliminate the hassle of coming up with a well-matched control group for these kinds of analyses. Any help would be appreciated; thanks as always. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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make_average_subject v4.0.0
by Claus Tempelmann 05 Nov '08

05 Nov '08

Hello everybody, please have a look at this email from my collegue Cindy! Claus ----------------------------------------------------------- Dear freesurfers, I would like to do a cortical thickness group comparison of patients and two control groups. Therefore I already pre-processed my data with an older version of freesurfer (I think v3.05). As I tried to create an average subject I realized that there is a bug in the make_average_subject script of v3.0.5 so that no ?h.thickness cards were calculated for my average subject. I learned from the mailing list archive that I could create the thickness cards using mri_surf2surf but was not sure how to define the necessary variables. Just using a newer script (e.g. v4.04) unfortunately was not possible as the older version of freesurfer did not yield all cards necessary during the pre-processing and the resulting average brain looked kind of deformed. Now my question: does anyone still work with the freesurfer version v4.0.0 and could sent me the make_average_subject script of this version? There the mentioned bug should have been fixed... Thanks and greatings Cindy -------- Original-Nachricht -------- > Datum: Mon, 3 Nov 2008 14:35:50 +0100 (CET) > Von: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> > An: Cindy Eckart <Cindy.Eckart(a)gmx.de> > Betreff: Re: freesurfer average > Hallo nochmals, > > ich habe mal kurz in das log-file reingeschaut. Da taucht ja in der ersten > haelfte recht haeufig die Meldung "could not open ..." auf. Bist Du > sicher, dass das nichts mit dem Problem zu tun hat? > > Claus > > ----------------------------------------------------------------------- > Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de > Clinic for Neurology II > MR department Tel.: +49-(0)391-6117183 > OvG University Magdeburg +49-(0)391-6117177 > Leipziger Strasse 44 > 39120 Magdeburg Fax: +49-(0)391-6117178 > Germany > > On Mon, 3 Nov 2008, Cindy Eckart wrote: > >> make_average_subject --subjects <subj1> >subj2> ... <subj36> --echo > --out averagesubject >> >> das "--echo"-Flag ist dabei jedoch irrelevant, weil es nur festlegt, > dass ein dokumentierendes log-file erstellt wird (das hab ich dir > vorsichtshalber auch einmal angehängt) >> >> LG Cindy >> >> -------- Original-Nachricht -------- >>> Datum: Mon, 3 Nov 2008 13:39:37 +0100 (CET) >>> Von: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> >>> An: Cindy Eckart <Cindy.Eckart(a)gmx.de> >>> CC: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> >>> Betreff: Re: freesurfer average >> >>> Hallo Cindy, >>> >>> kannst Du mir dazu noch Deine verwendete Befehlszeile schicken? >>> >>> Danke >>> >>> Claus >>> >>> ----------------------------------------------------------------------- >>> Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de >>> Clinic for Neurology II >>> MR department Tel.: +49-(0)391-6117183 >>> OvG University Magdeburg +49-(0)391-6117177 >>> Leipziger Strasse 44 >>> 39120 Magdeburg Fax: +49-(0)391-6117178 >>> Germany >>> >>> On Mon, 3 Nov 2008, Cindy Eckart wrote: >>> >>>> Hallo Claus, >>>> >>>> hier die beiden Hemisphären des freesurfer average als TIFF-Datei... >>> vielleicht auch noch ganz nützlich, das average wurde anhand von 36 >>> Probanden aus 3 Gruppen erstellt... >>>> >>>> Vielen dank und liebe Grüße >>>> >>>> Cindy >>>> -- >>>> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten >>>> Browser-Versionen downloaden: http://www.gmx.net/de/go/browser >>>> >> >> -- >> GMX Download-Spiele: Preizsturz! Alle Puzzle-Spiele Deluxe über 60% > billiger. >> > http://games.entertainment.gmx.net/de/entertainment/games/download/puzzle/i… >> -- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail

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Creating ROIs from FreeSurfer segmentation
by Barkay, Gavriel 05 Nov '08

05 Nov '08

Dear All, I am using FreeSurfer version 4.0.5 I need to create an ROI mask from aseg.mgz using specific labels (e.g. lt hippocampus). What is the best way to do that? What would be the best way to convert the resulting mask to NIFTI? Thanks, Gabi Barkay

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wmparc.stats
by david felps 05 Nov '08

05 Nov '08

Hi dear freesurfer, my wmparc.stats file contains 815 rows but for many structures listed there, the computed values belonging to the different columns are just null. can somebody please tell me how should i interpret this, or is it just a failure that happened while computing this values?. thank you. _________________________________________________________________ MSN Mobile: Die neuesten Infos aus der Welt der Stars und Sternchen zum Mitnehmen! http://redirect.gimas.net/?n=M0811xMobileDE

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Image deidentification
by Keller, Corey J. 05 Nov '08

05 Nov '08

Hi freesurfers, I have been unable to find a program/method to view the header file on some nifty files made from mri_convert with MPRAGE scans. I want to make sure the files we are creating do not have patient information in the headers. Is there an easy way to check this? Thanks. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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mri_ca_normalize
by Nurunisa Neyzi 04 Nov '08

04 Nov '08

Hi, I am getting an error with the command: mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas -noxform /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/norm_trn1.mgz using MR volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz to mask input volume... using segmentation volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz to generate control points... reading 9 input volumess reading atlas from '8'... reading input volume from /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz... reading input volume from -noatlas... mri_read(): couldn't determine type of file /Users/Nurunisa/Documents/MLS_STUDY/-noatlas mri_ca_normalize: could not read input MR volume from -noatlas end Is the flag -noatlas not valid? Or am I doing something wrong here?

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thickness measurement
by asaf achiron 04 Nov '08

04 Nov '08

Dear Group, in the lh.aparc.stats i can find this variables: SurfArea GrayVol ThickAvg MeanCurv GausCurv what is the difference between them? for the thickness is use the thick avg, right? thank you Asaf

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Freesurfer November 2008