Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

odd tkregister
by Borzello, Mia 29 Mar '13

29 Mar '13

Hi freesurfers, In using tkregister, I generated an odd (see attached): the image not only looks sheered but there is an old white box showing up. I'm not sure how to resolve this. Thanks a lot, Mia

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contrast matrix
by xiangbo_2010 28 Mar '13

28 Mar '13

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang

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Linear Mixed modal
by xiangbo_2010 28 Mar '13

28 Mar '13

Dear experts Whether can the design of contrast in freesurfer 5.2 the same as SPM? it is difficult to make the contrast in freesurfer if the categorical variables were much more, specifically compute the interaction or F-test in study. Thanks！ Bo Xiang

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coregistering- ideal CT type
by Borzello, Mia 28 Mar '13

28 Mar '13

Hi freesurfers, I working on a coregistration right now with a few different CT scans. None of them have looked that good with tkregister (for example when I used one CT scan, the electrodes didn't even show up). Is there an certain CT I need to be using? Thanks, m

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Correlation with cortical thickness
by Martijn Steenwijk 28 Mar '13

28 Mar '13

Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn

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aseg.mgz altered after auto-recon2?
by Joshua Lee 28 Mar '13

28 Mar '13

Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge.

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FSFAST and octave error dfor fast_selxavg3.m
by Mario Ortega 28 Mar '13

28 Mar '13

Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD data, and I have come across the following error. I tried changing files to non .gz extension, and still have this error.. $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ `fast_selxavg3' is a script from the file /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m `fast_ldanaflac' is a function from the file /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m ------------------------- outtop = /media/GOLDIN/FSFAST Extension format = nii.gz error: `MRIread' undefined near line 87 column 7 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/flac_customize.m at line 87, column 5 error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 65, column 7 ------------------------------------------ When I attempt to use fast_selxavg3 standalone in octave, I get this error. octave:1> fast_selxavg3; error: `sess' undefined near line 26 column 19 error: evaluating argument list element number 1 error: evaluating argument list element number 1 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 26, column 8 thanks, Mario Ortega GS4 Washington University in St. Louis, Dept. of Neurology

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mris_thickness & qcache for xhemi surfaces
by Ejoe Yizhou Ma 28 Mar '13

28 Mar '13

Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: "mris_thickness -max 10 subjid ?h thickness_max10" "recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h" To keep with this protocol, my questions are 1) how do I use "mris_thickness" properly so that I don't overwrite the files registered to fsaverage_510? 2) in "recon-all -qcache", will it do the trick by substituting "fsaverage_sym" for "fsaverage_510"? Thank you in advance, Cherry

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spmregister error
by Borzello, Mia 28 Mar '13

28 Mar '13

Hi Freesurfers, I'm in the middle of coregistering a CT and MRI, and after running spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig I get the error that orig.mgz is not found in COR or MGZ formats, but I have an orig.mgz file in my folder. Any help on this would be awesome! Thanks, Mia

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R: Re: R: Re: perirhinal analysis
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

What's meaning "subjet 2with"?Can you shown the correct command line, please? The wrong command line is mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface Many thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-mar-2013 18.32 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] perirhinal analysis If the source subject is subject_prova then you need to spec that subjet 2with --srcsubject (instead of fsaverage) doug On 03/28/2013 01:11 PM, stdp82(a)virgilio.it wrote: > Yes, it is located in > /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. > > > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 28-mar-2013 17.46 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] perirhinal analysis > > It says "no such file or directory" > does rh.perifhyinal.label exist? > > > On 03/28/2013 11:55 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I'm running perirhinal analysis with this error: > > > > mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label > > --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi > > rh --regmethod surface > > > > srclabel = rh.perirhinal.label > > srcsubject = fsaverage > > trgsubject = Con01 > > trglabel = Con01/label/rh.perirhinal.label > > regmethod = surface > > > > srchemi = rh > > trghemi = rh > > trgsurface = white > > srcsurfreg = sphere.reg > > trgsurfreg = sphere.reg > > usehash = 1 > > Use ProjAbs = 0, 0 > > Use ProjFrac = 0, 0 > > DoPaint 0 > > > > SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova > > FREESURFER_HOME /Applications/freesurfer > > Loading source label. > > No such file or directory > > mri_label2label: could not open label file rh.perirhinal.label > > No such file or directory > > ERROR reading rh.perirhinal.label > > > > My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and > > rh.perirhinal.label exist and it is located > > in /Applications/freesurfer/subjects/subject_prova/Con01/label > > > > > > Thanks, > > > > > > Stefano > > > > > > > > _______________________________________________ > > 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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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