Freesurfer

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Re: [Freesurfer] How to register FLAIR to T1?
by Ed Gronenschild 24 Jul '12

24 Jul '12

Hi Doug, I've found a solution to the problem: I converted T1.mgz and FLAIR.mgz to nii.gz and then applied flirt directly with the same options as in flsregister called by bbregister, so flirt -cost corratio -dof 6 -searchx -90 90 -searchy -90 90 \ -searchz -90 90 -in FLAIR.nii.gz -ref T1.nii.gz \ -out FLAIR_to_T1.nii.gz This perfectly matched the T1. Cheers, Ed On 16 Jul 2012, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 18 > Date: Mon, 16 Jul 2012 11:32:06 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] How to register FLAIR to T1? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <500433F6.8010102(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Often with FLAIR there is not enough gray-white contrast to run the > registration. Try using the pial surface instead, with "-surf pial > --t1" > This tells it to use the pial surface as a boundary. The --t1 is > needed > because the intensity should go from bright to dark. Let me know if > that > does not fix the problem. > doug > > On 07/10/2012 11:58 AM, Bruce Fischl wrote: >> glad to hear it :). You may need to repost (and possibly upload your >> data) >> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >> >>> Hi Bruce, >>> >>> It is indeed from the same scan session. >>> I'll wait patiently, let Doug enjoy his vacation before >>> he gets bothered again by all our questions. >>> >>> Cheers, >>> Ed >>> >>> On 10 Jul 2012, at 16:57, Bruce Fischl wrote: >>> >>>> Hi Ed, >>>> >>>> sorry, you'll have to wait until Doug is back from vacation. Is >>>> this from >>>> the same session? I've always had it work on flair images using >>>> one of the >>>> types of initialization. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> Unfortunately, this has no effect. >>>>> >>>>> Ed >>>>> >>>>> On 10 Jul 2012, at 16:40, Bruce Fischl wrote: >>>>> >>>>>> Hi Ed >>>>>> >>>>>> you are using -t2, right? You can also try -init-header >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Tue, 10 Jul 2012, >>>>>> Ed Gronenschild wrote: >>>>>> >>>>>>> Hi Bruce, >>>>>>> >>>>>>> It is slightly better but still displacements >>>>>>> in all directions and rotations too exist. >>>>>>> >>>>>>> Ed >>>>>>> >>>>>>> On 10 Jul 2012, at 16:13, Bruce Fischl wrote: >>>>>>> >>>>>>>> try -init-spm >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I would like to register FLAIR to T1. >>>>>>>>> Specifications FLAIR: >>>>>>>>> axial acquisition, 24 slices, >>>>>>>>> pixel size = 0.45 * 0.45 mm^2 >>>>>>>>> slice thickness = 5.50 mm (no gap). >>>>>>>>> >>>>>>>>> The slices run from the top of the brain >>>>>>>>> to just below the eyes. This is contrary >>>>>>>>> to the T1 scan which covers the full head >>>>>>>>> down to the neck. >>>>>>>>> I have tried bbregiser as follows: >>>>>>>>> >>>>>>>>> bbregister --s 001 --mov 001_FLAIR.mgz \ >>>>>>>>> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >>>>>>>>> >>>>>>>>> and inspected the result with >>>>>>>>> >>>>>>>>> tkregister2 --mov 001_FLAIR.mgz \ >>>>>>>>> --reg 001_register.dat --surf >>>>>>>>> >>>>>>>>> The result looks bad, it is displaced and rotated >>>>>>>>> by about 20 degrees with respect to T1. >>>>>>>>> >>>>>>>>> It makes hardly any difference if instead of --t1 >>>>>>>>> --t2 as contrast setting was used. >>>>>>>>> >>>>>>>>> Is there a better way to do this registration? >>>>>>>>> For instance, should I crop T1 to about the >>>>>>>>> same space as covered by FLAIR? >>>>>>>>> >>>>>>>>> (FreeSurfer v4.5.0, MacOSX 10.5) >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> Ed >>>>>>>>> _______________________________________________ >>>>>>>>> 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. >>>>>>>> >>>>>>> >>>>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >

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tracula processing time ?...
by Gonzalo Rojas Costa 24 Jul '12

24 Jul '12

Hi: How much time (aprox) take each step of tracula processing ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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(no subject)
by Vincenzo Pierro 24 Jul '12

24 Jul '12

Please, could anyone let me know how to perform statistical analysis in QDEC to look at the interaction between two genes on cortical thickness? Vincenzo Pierro

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Re: [Freesurfer] Measuring total cortical volume
by Douglas N Greve 24 Jul '12

24 Jul '12

Those are the values I mentioned before (lhCortex, etc, see below). I don't understand your concern about the deep structures. doug ps please remember to post to the freesurfer list and not to me directly. thanks! On 07/24/2012 06:56 AM, Emelie Andersson wrote: > Thank You for your answer. > > I have another question: If i want to measure only the cortical volume > (i.e not the deep grey structures such as the basal ganglia) - how do > I do? How are the deep grey structures and ventricles excluded from > the WM volume? > > Look forward to hear from You, > > Best regards > Emelie > > On Tue, Jul 17, 2012 at 5:41 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > This is computed by computing the volume inside the pial surface > and subtracting the volume inside the white surface (and > accounting for small amounts in the "unknown" region). > doug > > > On 07/17/2012 04:47 AM, Emelie Andersson wrote: > > Thank You Douglas, > > May I ask if You know how the numbers were calculated? > > best regards > Emelie > > On Mon, Jul 16, 2012 at 6:11 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: > > In the aseg.stats file, there will be these values > > # Measure lhCortex, lhCortexVol, Left hemisphere cortical > gray matter > volume, 218425.204942, mm^3 > # Measure rhCortex, rhCortexVol, Right hemisphere cortical > gray matter > volume, 212261.052152, mm^3 > # Measure Cortex, CortexVol, Total cortical gray matter > volume, > 430686.257094, mm^3 > > does this work for you? > doug > > > On 07/16/2012 03:17 AM, Emelie Andersson wrote: > > Hello, > > > > We have a some doubts about how to measure the total cortical > volume. > > Is it recommendable to use GM = pial surface - white matter? > > > > Hope to hear from You, > > > > Best regards > > Emelie > > > > > > _______________________________________________ > > 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> > > _______________________________________________ > 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 > > > 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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questions about SurfArea and meancurv
by Yang, Daniel 24 Jul '12

24 Jul '12

Dear Freesurfer, I am new to freesurfer and have a number of beginner's questions. After recon all the subjects and running the freesurferstats2table<http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table> script, I am looking at the two files: aparc_area_lh.txt and aparc_meancurv_lh.txt. Everything goes by default. My questions are, 1. In the aparc_area_lh.txt, is the surface area based on the pial surface, the white surface, or both? 2. In the aparc_meancurv_lh.txt, is it based on the Gaussian Curvature of the white surface or the pial surface? I cannot find the relevant documentation in the freesurfer wiki. Any comments are highly appreciated! Best Regards, Daniel -- Daniel Yang, PhD Postdoctoral Researcher Child Study Center Yale University 203-737-5454

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Hippocampal subfields and aseg
by Murray, Michael 24 Jul '12

24 Jul '12

Hello, In several of our subjects, we've noticed on the aseg that the hippocampus extends into the fusiform gyrus. I've attached an image showing this in the left hippocampus. Looking at the wm.mgz volume, there seem to be wm voxels in that region that shouldn't be there (image attached). Could these be what are causing the incorrect segmentation (in which case the voxels can just be removed from wm.mgz)? If not, do you have any other ideas as to how to fix this problem? Otherwise, it seems as though the aseg would have to be edited, which would be a large and tedious edit to make in our very large set of subjects. This is particularly a problem because we are interested in the subfields, and the issue carries over when that processing is performed. In the same subject as discussed above, the CA1 subfield of the left hippocampus also overextends into the fusiform gyrus (image attached). Since we are primarily interested in using the total subfield volume (rather than the aseg volume), it would also work if we could just specifically edit whatever the input to the subfield stream is. Would this just be aseg, or are there other volumes that would need to be edited before running the subfields flag? That may be a question for Koen, but any advice that anyone could offer would be very helpful. Thank you, Michael Murray

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Interaction between two genes on cortical thickness
by Vincenzo Pierro 24 Jul '12

24 Jul '12

Please, could anyone let me know how to perform statistical analysis in QDEC to look at the interaction between two genes on cortical thickness? Vincenzo Pierro

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Sample size estimates for well-powered cross-sectional cortical thickness studies
by Heath Pardoe 24 Jul '12

24 Jul '12

Hi all, Some work my colleagues and I did investigating how many subjects should be included in a study has been recently published in Human Brain Mapping ( http://www.ncbi.nlm.nih.gov/pubmed/22807270) The paper should be freely available on pubmed central fairly soon if you don't have access to Human Brain Mapping early view. Or I can send you a copy. I've provided some instructions on how to carry out a similar analysis using your own Freesurfer-processed control data here: http://www.brain.org.au/software/cortex/power The R package provided at the above link contains a function "load.mgh.R" which can be used to load mgh surface files into R & do whatever sophisticated statistical analysis takes your fancy. Let me know if you've got any questions. Best wishes Heath -- Heath R. Pardoe, PhD Florey Neuroscience Institutes Melbourne Brain Centre 245 Burgundy Street, Heidelberg 3084 Australia Phone: (+61 3) 903 57053 Email: h.pardoe(a)brain.org.au

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Re: [Freesurfer] stats
by Douglas Greve 23 Jul '12

23 Jul '12

Neither of these tables is the one you want. Those are tables of standard freesurfer ROIs and are unrelated to your map-based analysis. You will need to do the cluster-wise correction for multiple comparisons using the voxel-wise threshold that FDR found. Set the cwp (cluster-wise p-value) threshold to 1 so that you get all of the clusters. When you do the clusterwise correction, it will produce a file with the values you want. doug On 7/23/12 2:44 AM, Oertel, Viola wrote: > Hi Doug, > I did the correction for multiple comparisons (FDR 0,05). Then, I have seen significant clusters in the map. After that, I run the generate tables stat (or so on) button and got two tables with thickness values. But I don't know which one of the tables is the right one because this step produced two files: > > > lh.aparc.a2005s.thickness.stats and > lh.aparc.thickness.stats > > May you tell me which one is the right, and are these results only the significant areas, or all computed once? > > > Thanks, > Viola > > ________________________________________ > Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Gesendet: Freitag, 20. Juli 2012 21:26 > Bis: Oertel, Viola; Freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: AW: [Freesurfer] stats > > Hi Viola, those stats tables are unrelated to your map-based exploratory > analysis. If you have clusters in your map, you should run the > correction for multiple comparisons. This will give you significant > clusters. It will also produce a table of mean thicknesses in each > cluster for each subject which you can then import to SPSS. > doug > > On 07/19/2012 04:35 PM, Oertel, Viola wrote: >> Yes. I did the contrast pat. vs. cont and see some significant regions on the display. After that, I did this "generate" stats table. My idea was to put this scores into SPSS and run the inferential statistics there. But I am not sure which table I have to use. What I want to use are the thickness values of each participant of all significant regions which I can see on the template. >> Currently, I am not sure what kind of regions the tables show? Are that all regions, only the significant ones of the specific contrast I compute? I have seen that both tables show different regions. But I currently don't how the selection works. >> >> May you help with that? >> >> Thanks and best regards, >> >> Viola >> >> ________________________________________ >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Gesendet: Donnerstag, 19. Juli 2012 17:30 >> Bis: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] stats >> >> Those stats tables just gives statistics (means, standard deviations) >> for thickness in different regions. They do not have inferential >> statistics. Have you run an analysis on patients vs controls? >> doug >> >> On 07/19/2012 09:27 AM, Oertel, Viola wrote: >>> Dear Doug, >>> >>> I have a question: when I create the stats tables, there are two tables: >>> >>> lh.aparc.a2005s.thickness.stats and >>> >>> lh.aparc.thickness.stats >>> >>> which one is the right one if I want to get the thickness values of >>> the significant clusters from the main effect (pat. / controls)? >>> >>> Thanks and best regards, >>> >>> Viola >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > >

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Directed search for group analysis
by Jeni Chen 23 Jul '12

23 Jul '12

Hello Freesurfer experts, I've been trying to figure out a way to run a directed search in a group analysis. I read the tutorial on ROI analysis and some of the posts here, but we can only do it with individual subject. Simply pout, I want to restrict my search areas to 4 ROIs (determined from the fsaverage or common template) when I run the group analysis (thus lowering the corrected stats threshold based on search criteria). What's the best way of doing it? Also, some posts suggests using the --mask option when running the glmfit command, but it seems some people also used the --label option. What is the difference? Thank you for your help. Jeni

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