Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Re: [Freesurfer] MCSRCH ERROR
by Bruce Fischl 20 Oct '11

20 Oct '11

I just took a look at it, and I think it's still running. How long has it been? There looks like there is a very large topological defect, that will take a long time to correct. The correction has complexity that is quadratic in the convex hull of the largest defect, so large ones can take a *long* time. Usually when there is one this big though it means something failed. Check the rh.inflated.nofix and rh.orig.nofix files to see if there is a connection to the skull or something else. If you have trouble fixing this, upload the subject and we'll take a look. cheers Bruce On Thu, 20 Oct 2011, Kenichiro Tanaka wrote: > Dear Bruce, > > I emailed you the recon-all.log. > Please check it and tell me how wrong something is? > > Thanks, > > Kenichiro Tanaka. > > (2011/10/19 21:26), Bruce Fischl wrote: >> ok, why don't you tar and gzip the subject and put it on our ftp site. You >> can also just email me the recon-all.log and I'll take a look >> Bruce >> On Wed, 19 Oct 2011, Kenichiro Tanaka wrote: >> >> > Dear Bruce, >> > >> > I think they are error. >> > The number of output files is not complete. >> > For example, there are only lh.aparc.a2009s.stats, lh.aparc.stats and >> > lh.curv.stats on stats directory. >> > >> > Thanks, >> > >> > Kenichiro Tanaka. >> > >> > >> > >> > (2011/10/18 21:30), Bruce Fischl wrote: >> > Are you sure they are errors? We see this mysterious message >> > sometimes, but I don't think it is really an error, and usually >> > things are fine >> > >> > cheers >> > Bruce >> > >> > On Tue, 18 Oct 2011, Kenichiro Tanaka wrote: >> > >> > Hello All, >> > >> > While processing a brain image data(.mgz) through >> > ver5.0.0, I got the >> > following errors. >> > I have no idea how to resolve them. >> > I need outputs in stats directory, there are only >> > lh.aparc.a2009s.stats, >> > lh.aparc.stats, and lh.curv.stats. >> > What caused them? >> > How should I resolve them? >> > >> > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF >> > ROUTINE MCSRCH ERROR >> > RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: >> > FUNCTION OR GRADIENT ARE >> > INCORRECT OR INCORRECT TOLERANCESoutof >> > QuasiNewtonEMA: 005: -log(p) = >> > 10318.1 tol 0.000010 >> > . >> > . >> > . >> > inflating to sphere (rms error < 2.00) >> > 000: dt: 0.0000, rms radial error=175.699, avgs=0 >> > 005/300: dt: 0.9000, rms radial error=175.446, >> > avgs=0 >> > 010/300: dt: 0.9000, rms radial error=174.904, >> > avgs=0 >> > 015/300: dt: 0.9000, rms radial error=174.193, >> > avgs=0 >> > 020/300: dt: 0.9000, rms radial error=173.383, >> > avgs=0 >> > 025/300: dt: 0.9000, rms radial error=172.518, >> > avgs=0 >> > 030/300: dt: 0.9000, rms radial error=171.620, >> > avgs=0 >> > 035/300: dt: 0.9000, rms radial error=170.706, >> > avgs=0 >> > 040/300: dt: 0.9000, rms radial error=169.784, >> > avgs=0 >> > 045/300: dt: 0.9000, rms radial error=168.860, >> > avgs=0 >> > 050/300: dt: 0.9000, rms radial error=167.935, >> > avgs=0 >> > 055/300: dt: 0.9000, rms radial error=167.012, >> > avgs=0 >> > 060/300: dt: 0.9000, rms radial error=166.092, >> > avgs=0 >> > 065/300: dt: 0.9000, rms radial error=165.175, >> > avgs=0 >> > 070/300: dt: 0.9000, rms radial error=164.262, >> > avgs=0 >> > 075/300: dt: 0.9000, rms radial error=163.352, >> > avgs=0 >> > 080/300: dt: 0.9000, rms radial error=162.447, >> > avgs=0 >> > 085/300: dt: 0.9000, rms radial error=161.547, >> > avgs=0 >> > 090/300: dt: 0.9000, rms radial error=160.651, >> > avgs=0 >> > 095/300: dt: 0.9000, rms radial error=159.759, >> > avgs=0 >> > 100/300: dt: 0.9000, rms radial error=158.871, >> > avgs=0 >> > 105/300: dt: 0.9000, rms radial error=157.989, >> > avgs=0 >> > 110/300: dt: 0.9000, rms radial error=157.110, >> > avgs=0 >> > 115/300: dt: 0.9000, rms radial error=156.236, >> > avgs=0 >> > 120/300: dt: 0.9000, rms radial error=155.367, >> > avgs=0 >> > 125/300: dt: 0.9000, rms radial error=154.502, >> > avgs=0 >> > 130/300: dt: 0.9000, rms radial error=153.642, >> > avgs=0 >> > 135/300: dt: 0.9000, rms radial error=152.786, >> > avgs=0 >> > 140/300: dt: 0.9000, rms radial error=151.934, >> > avgs=0 >> > 145/300: dt: 0.9000, rms radial error=151.087, >> > avgs=0 >> > 150/300: dt: 0.9000, rms radial error=150.245, >> > avgs=0 >> > 155/300: dt: 0.9000, rms radial error=149.407, >> > avgs=0 >> > 160/300: dt: 0.9000, rms radial error=148.573, >> > avgs=0 >> > 165/300: dt: 0.9000, rms radial error=147.744, >> > avgs=0 >> > 170/300: dt: 0.9000, rms radial error=146.919, >> > avgs=0 >> > 175/300: dt: 0.9000, rms radial error=146.098, >> > avgs=0 >> > 180/300: dt: 0.9000, rms radial error=145.282, >> > avgs=0 >> > 185/300: dt: 0.9000, rms radial error=144.470, >> > avgs=0 >> > 190/300: dt: 0.9000, rms radial error=143.663, >> > avgs=0 >> > 195/300: dt: 0.9000, rms radial error=142.860, >> > avgs=0 >> > 200/300: dt: 0.9000, rms radial error=142.061, >> > avgs=0 >> > 205/300: dt: 0.9000, rms radial error=141.266, >> > avgs=0 >> > 210/300: dt: 0.9000, rms radial error=140.476, >> > avgs=0 >> > 215/300: dt: 0.9000, rms radial error=139.693, >> > avgs=0 >> > 220/300: dt: 0.9000, rms radial error=138.914, >> > avgs=0 >> > 225/300: dt: 0.9000, rms radial error=138.140, >> > avgs=0 >> > 230/300: dt: 0.9000, rms radial error=137.370, >> > avgs=0 >> > 235/300: dt: 0.9000, rms radial error=136.604, >> > avgs=0 >> > 240/300: dt: 0.9000, rms radial error=135.842, >> > avgs=0 >> > 245/300: dt: 0.9000, rms radial error=135.085, >> > avgs=0 >> > 250/300: dt: 0.9000, rms radial error=134.332, >> > avgs=0 >> > 255/300: dt: 0.9000, rms radial error=133.583, >> > avgs=0 >> > 260/300: dt: 0.9000, rms radial error=132.838, >> > avgs=0 >> > 265/300: dt: 0.9000, rms radial error=132.098, >> > avgs=0 >> > 270/300: dt: 0.9000, rms radial error=131.362, >> > avgs=0 >> > 275/300: dt: 0.9000, rms radial error=130.629, >> > avgs=0 >> > 280/300: dt: 0.9000, rms radial error=129.901, >> > avgs=0 >> > 285/300: dt: 0.9000, rms radial error=129.177, >> > avgs=0 >> > 290/300: dt: 0.9000, rms radial error=128.456, >> > avgs=0 >> > 295/300: dt: 0.9000, rms radial error=127.740, >> > avgs=0 >> > 300/300: dt: 0.9000, rms radial error=127.028, >> > avgs=0 >> > >> > spherical inflation complete. >> > . >> > . >> > . >> > epoch 4 (K=1280.0), pass 1, starting sse = 541.21 >> > taking momentum steps... >> > taking momentum steps... >> > taking momentum steps... >> > pass 1 complete, delta sse/iter = 0.32/19 = 0.01710 >> > finalwriting spherical brain to >> > ../surf/lh.qsphere.nofix >> > spherical transformation took 0.10 hours >> > distance error %100000.00 >> > . >> > . >> > . >> > pass 1: epoch 1 of 3 starting distance error %21.36 >> > pass 1: epoch 2 of 3 starting distance error %21.04 >> > unfolding complete - removing small folds... >> > starting distance error %20.80 >> > removing remaining folds... >> > final distance error %20.81 >> > 364: 0 negative triangles >> > . >> > . >> > . >> > >> > >> > Thanks, >> > >> > Kenichiro Tanaka. >> > >> > _______________________________________________ >> > 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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[Major Upgrade] - iSurf Brainview 4.0.0
by Pedro Paulo de Magalhães Oliveira Junior 20 Oct '11

20 Oct '11

Today it was released the version 4.0.0 of iSurf Brainview, it's a majorversion release for IPad, IPhone and IPod Touch. It's also a landmark release. Major New Features - 3D Visualization of Cortical structure - 3D Model is fully "touchable" and displays the name of touched structure using aparc.annot Minor Changes - iOS5 compliance - Memory usage improvement - Versioning As usual suggestions and feedbacks are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… A personal note: This App is being used in the Radiology course. All med students in São Paulo University now have basic MRI neuroanatomy training using iSurf --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Subcortical segmentation atlas
by cloud.ctrl＠me.com 19 Oct '11

19 Oct '11

Hello, I am working on comparing hand-drawn subcortical volumes to those output automatically by FreeSurfer. While reading about the segmentation process on the wiki, I came across this line: "The final segmentation is based on both a subject-independent probabilistic atlas and subject-specific measured values. The atlas is built from a training set, i.e., a set of subjects whose brains (surfaces or volumes) have been labeled by hand. These labels are then mapped into a common space (Talairach space for volumes..." (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview) Because of the way we decided to delineate our ROI, we need to compare the shapes we defined in AFNI to those defined by this training set and output by FreeSurfer. I've been looking for more information about this probabilistic atlas, but I cannot find any more information about it. The only thing I found was the last line of this thread from the mail archives: Am 23.08.2011 um 04:03 schrieb Anthony Dick: > The subcortical segmentation identifies subcortical structures such as > thalamus, basal ganglia structures, hippocampus, amygdala, and > cerebellum. The cortical parcellation delineates different areas of the > cortex, such as the superior temporal sulcus, the central sulcus, the > pars triangularis, opercularis, and orbitalis of the inferior frontal > gyrus. A recommendation is to get a copy of the Duvernoy atlas, which > covers definitions of different parts of the cortex. The Mai atlas is > good for learning subcortical structures. Was the Mai atlas used to create the define the structures in the training set? Could you provide me with any more information regarding the training set?

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Re: [Freesurfer] Group Average of Retinotopy Results
by Michelle Umali 19 Oct '11

19 Oct '11

Hi Doug and the Freesurfers, Thanks for your help. I have 2 questions.: 1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data: e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group_polar_lh but how do you do this for the fieldsign analysis, since the cess.nii and other files don't exist? 2) So when trying to run a group mri_glmfit on the polar and eccen maps with: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir group_eccen_lh.wls --nii.gz I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each. I am not sure how this happened. I only have one run each of polar and wedge data. What may have generated these two files and which one do I use? Thanks. Michelle On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > wrote: > When you run preproc-sess use -surface fsaverage lhrh instead of -surface > self lhrh. Then create a new analysis with the same parameters, except use > -surface fsaverage lh instead of -surface self lh. > doug > > Michelle Umali wrote: > >> Hi Doug, >> I'm a little confused as to how to assign functional data to the fsaverage >> space. >> 1) Do you mean just change each subject's subjectname file to fsaverage >> and then do the same thing as before for each person? >> 2) Also, when I specify the analysis do I change -rtopy.self.lh to >> rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? >> >> e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy >> 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force >> >> then the same for selxavg3-sess and fieldsign-sess >> >> and then isxconcat-sess would be: >> isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh >> >> >> Thanks. >> Michelle >> >> On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> If you want to combine across subjects, then you need to run the >> analysis on fsaverage (ie, rerun preproc-sess, create a new >> analysis, run selxavg3-sess, and then isxconcat-sess). >> doug >> >> Michelle Umali wrote: >> >> Dear Freesurfers, >> I've generated individual polar, eccentricity, and fieldsign >> maps for each of my subjects. I would like to generate group >> average maps of these that I can visualize on the fsaverage brain. >> >> When I ran: >> isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh >> >> I got: >> ERROR: analysis space is self surface, not supported >> >> How do I do a group average for the 3 different maps? >> >> Thanks. >> Michelle >> >> For each person I ran recon-all and flattened occipital patches. >> Then: >> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 >> -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold >> -force >> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 >> -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold >> -force >> >> preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd >> bold -force >> >> selxavg3-sess -a rtopy.self.lh -s sjXX -force >> selxavg3-sess -a rtopy.self.rh -s sjXX -force >> >> fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX >> fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX >> >> ------------------------------**------------------------------** >> ------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >> <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >

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FreeSurfer Questions
by Christopher McCarthy 19 Oct '11

19 Oct '11

Dear FreeSurfer Gurus, We are looking for a way to normalize the intensity histogram for our subjects. In the past we have used Brain Image Java, using FSL-Fast inhomogeneity corrections. Unfortunately we are unable to open the output files (.img, .hdr) in FreeSurfer. When trying to import the files (after converting them to nii) we get a talaraich error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) here is the mri_info for a subject we get this error with: Volume information for S029_nii type: nii dimensions: 256 x 256 x 100 voxel sizes: 0.9375, 0.9375, 1.5000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.9375 0.0000 0.0000 120.0000 0.0000 0.9375 0.0000 -120.0000 0.0000 0.0000 1.5000 -75.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.31836 ras to voxel transform: -1.0667 0.0000 0.0000 128.0000 -0.0000 1.0667 -0.0000 128.0000 -0.0000 -0.0000 0.6667 50.0000 0.0000 0.0000 0.0000 1.0000 We are either looking to get the files we currently have to import correctly in FreeSurfer, or import our DICOM files into a program and normalize the intensity histogram and output a file freesurfer can read. We are looking to get rid of hyper intensities in the temporal and frontal lobes that cause main and pial surface errors. Thanks for whatever help you can give, now and in the future. Chris McCarthy

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problem with generating cesvar.nii
by SHAHIN NASR 19 Oct '11

19 Oct '11

Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. > mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: > mris_calc -o diff_map1/rh.cesvar.nii map1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: "Error: MRInormWeights: values less than or eq to 0" which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] reg-feat2anat failure
by Douglas N Greve 19 Oct '11

19 Oct '11

This file is created when you run reg-feat2anat and should be the one that gets changed with --manxfm func2anat. You can handle this differently if you 1. Manually edit the anat2exf.register.dat so that it is relatively close (no need to be perfect) cd feat/reg/freesurfer tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat --surfs 2. Run bbregister: cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup bbregister --mov ../../example_func.nii.gz --init-reg anat2exf.register.dat --reg anat2exf.register.dat --bold this second step will fine-tune your hand-edited version. Then go back and run aparc2feat, etc. doug Michelle Umali wrote: > Hi Doug, > The file that changed was exf2std.register.dat. How do I specify > that I wanted that anat2exf.register.dat is supposed to be edited? At > what point in the processing stream does this occur? > > Did editing exf2std.register.dat do anything? > > Thanks. > Michelle > > > > On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The registration that should be used for all of these is > anat2exf.register.dat found in feat/reg/freesurfer. Can you verify > that that was the one that you manually changed? Look at the time > stamp as compared to the other files in that folder. > doug > > Michelle Umali wrote: > > Hi Doug, > I am using reg-feat2anat on the feat directory of each run. > reg-feat2anat --feat feadir.feat --subject XX > Then I checked and adjusted the registration with: > reg-feat2anat --feat featdir.feat --manual > Next I checked and adjusted the registration to the standard with: > reg-feat2anat --feat featdir.feat --manxfm func2std > > To generate cortical binary masks I used: > aparc2feat --feat featdir.feat --annot BA > fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 > -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz > > To generate subcortical binary masks I did: > aseg2feat --feat featdir.feat --aseg aparc+aseg > fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz > -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz > > When I looked at the masks in FSLview and checked the masks > against the other atlases, everything was off even after > painstakingly editing the registrations. > Is there something I am doing wrong? > > Thanks. > Michelle > > On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > How are you generating the masks? > doug > > Michelle Umali wrote: > > Hi Freesurfers, > I've run reg-feat2anat on several subjects in order to > generate binary masks to use in an FSL ppi. > For 3 subjects, this completely failed. > > When I looked at the fsl's own registration of fsl feat 2 > standard (via tkregister2), the registration is fine, but > after running reg-feat2anat, the registration of the > feat to > the freesurfer anatomical and the feat to standard are > completely off. > > I manually fixed and saved the registration edits via > reg-feat2anat --manual, but when I generated the masks > again, > they were totally wrong still. > When looking at freesurfer's feat to standard > registration, it > looks like all the brains weren't tall enough in the > saggital > view. Am I supposed to stretch the feat brain to fit? > > How can I fix this so that the masks are accurate? > > Thanks. > Michelle > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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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Re: [Freesurfer] QDec questions
by Douglas N Greve 18 Oct '11

18 Oct '11

Yes, see the answer to your first question below. doug krista kelly wrote: > Am I able to do vertex-by-vertex analyses using freesurfer if I have > more than 2 discrete variables? If so, how? > > Is it also ok to use the unsmoothed data when doing surface area label > analyses? > > Thanks! > > On Tue, Oct 18, 2011 at 3:14 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Sorry, I meant to say that you cannot use QDEC with more than 2 > discrete variables (you have 3). You do not need to extract data > from the smoothed thickness files, but the results you get from > your ROI analysis may then differ a bit from that you get from the > QDEC analysis. > doug > > krista kelly wrote: > > Thanks Doug! Just a few more things: > > I only have two groups, so my contrast was wrong. Should it > only be 1 -1, even if I have other variables I want to control > for? Or should I have a contrast file for each discrete variable? > > How would I extract the smoothed data using mri_anatomical_stats? > > I realize the importance of smoothing data while doing a > vertex-by-vertex analysis in QDec, but if I'm doing an ROI > analysis by extracting the average thickness in a certain > label (i.e. v1), is it necessary to do the stats on the > smoothed data from each participant? > > Thanks! > > > On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > krista kelly wrote: > > Hi, just wondering if anyone has any advice on the > following > questions: > > I'm using QDEC to analyze cortical thickness differences > between groups and I have a few questions: > > 1) There are a few variables that I need to control > for. First > variable is scanner - I used two different scanners of > different field strengths (1.5T GE and 3T Siemens) so I > wanted > to control for scanner. I also wanted to control for > age and > gender. Here's my ideal design setup: > > discrete variables - groups, scanner, gender > nuisance variable - age > > contrast would be 1 -1 0 0 0 0 > I realize that scanner, gender, and group are all discrete > variables, and that age would be a continuous one. > However, in > the design tab, I am not able to select all 3 discrete > variables (groups, scanner, and gender). Should I designate > scanner or gender as a nuisance variable instead? Would it > matter which one I use as the nuisance variable? > Possible setup: > > discrete vars - groups, scanner > nuisance vars - age, gender > > contrast - 1 -1 0 0 (Correct?) > > Unfortunately, you cannot use QDEC if you have three groups. > You'll have to create an FSGD file and contrasts by hand, > then run > mri_glmfit. Do a search for FSGD on our wiki and go to the > examples page. I think there is an example there for what > you want > to do. > > > 2) If I use DODS, should I demean the ages if age is a > nuisance variable? > > You should actually test whether there is an interaction > between > age and your group contrast of interest (using the DODS > model). If > there is not interaction, then switch to a DOSS where demeaning > does not matter. > > > 3) If I use a smoothing kernel during the analysis, then > create an ROI and map that ROI to each individual subject, > will the resulting .stats file in each subjects stats > folder > reflect the smoothed data or does mapping onto each ROI > just > extract the raw unsmoothed data from each vertex? > > It depends on how you do the extraction. If you are using > mris_anatomical_stats on each individual's unsmoothed data, > then > it will reflect the unsmoothed. > > doug > > > Thanks! > Krista > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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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Re: [Freesurfer] Surface area measure
by Douglas N Greve 18 Oct '11

18 Oct '11

I don't know if that has ever been explored. doug krista kelly wrote: > Great! Do you know if it is better to use one surface area (i.e. WM or > pial) over the other when investigating differences between groups? > > On Tue, Oct 18, 2011 at 2:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The white surface. > doug > > krista kelly wrote: > > When I extract surface area data using the following > commands, which measure of surface area am I getting, the pial > surface, the WM surface, or the total of both combined? > > aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi > rh --meas area --tablefile aparc_stats_rh.txt > > Thanks! > Krista > || > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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. > > -- 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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Re: [Freesurfer] QDec questions
by Douglas N Greve 18 Oct '11

18 Oct '11

Sorry, I meant to say that you cannot use QDEC with more than 2 discrete variables (you have 3). You do not need to extract data from the smoothed thickness files, but the results you get from your ROI analysis may then differ a bit from that you get from the QDEC analysis. doug krista kelly wrote: > Thanks Doug! Just a few more things: > > I only have two groups, so my contrast was wrong. Should it only be 1 > -1, even if I have other variables I want to control for? Or should I > have a contrast file for each discrete variable? > > How would I extract the smoothed data using mri_anatomical_stats? > > I realize the importance of smoothing data while doing a > vertex-by-vertex analysis in QDec, but if I'm doing an ROI analysis by > extracting the average thickness in a certain label (i.e. v1), is it > necessary to do the stats on the smoothed data from each participant? > > Thanks! > > > On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > krista kelly wrote: > > Hi, just wondering if anyone has any advice on the following > questions: > > I'm using QDEC to analyze cortical thickness differences > between groups and I have a few questions: > > 1) There are a few variables that I need to control for. First > variable is scanner - I used two different scanners of > different field strengths (1.5T GE and 3T Siemens) so I wanted > to control for scanner. I also wanted to control for age and > gender. Here's my ideal design setup: > > discrete variables - groups, scanner, gender > nuisance variable - age > > contrast would be 1 -1 0 0 0 0 > I realize that scanner, gender, and group are all discrete > variables, and that age would be a continuous one. However, in > the design tab, I am not able to select all 3 discrete > variables (groups, scanner, and gender). Should I designate > scanner or gender as a nuisance variable instead? Would it > matter which one I use as the nuisance variable? Possible setup: > > discrete vars - groups, scanner > nuisance vars - age, gender > > contrast - 1 -1 0 0 (Correct?) > > Unfortunately, you cannot use QDEC if you have three groups. > You'll have to create an FSGD file and contrasts by hand, then run > mri_glmfit. Do a search for FSGD on our wiki and go to the > examples page. I think there is an example there for what you want > to do. > > > 2) If I use DODS, should I demean the ages if age is a > nuisance variable? > > You should actually test whether there is an interaction between > age and your group contrast of interest (using the DODS model). If > there is not interaction, then switch to a DOSS where demeaning > does not matter. > > > 3) If I use a smoothing kernel during the analysis, then > create an ROI and map that ROI to each individual subject, > will the resulting .stats file in each subjects stats folder > reflect the smoothed data or does mapping onto each ROI just > extract the raw unsmoothed data from each vertex? > > It depends on how you do the extraction. If you are using > mris_anatomical_stats on each individual's unsmoothed data, then > it will reflect the unsmoothed. > > doug > > > Thanks! > Krista > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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. > > -- 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

1 0

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Freesurfer October 2011