Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

non-stationarity in CTh maps
by Hugo Baggio 25 Jul '12

25 Jul '12

Dear all, I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct me if I'm wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise correction to this (should I expect clusters at smoother areas to be bigger?)? 2. Does FS perform some sort of correction to this non-stationarity or are images assumed to be stationary at statistical analyses? Thanks a lot for your help! Hugo

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MRIread on matlab
by Kevin Chen 25 Jul '12

25 Jul '12

Hi all, I am a beginner to FreeSurfer, and have been experimenting with the MRIread function on MATLAB. I am able to load .nii files using MRIread, but is there a way to display a particular slice from a nifti file on MATLAB using MRIread and its related functions? Thanks in advance, Kevin

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Re: [Freesurfer] Freesurfer Question
by Alexandra Tanner 25 Jul '12

25 Jul '12

Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex > Hi Alexandra, what structure are you looking to analyze? Ie, the volume > of what? The volume of cortex? > doug > ps. In the future, please post such questions to the freesurfer list as > it gives others the opportunity to answer and to learn. thanks! > > On 07/23/2012 12:03 PM, Alexandra Tanner wrote: >> Hi Mr. Greve, >> >> My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain >> Genomics Lab. I had a question regarding conducting volume analyses. On >> the freesurfer wiki there are commands that show how to conduct Paired >> Analyses to look at average surface, and I was curious if it was >> possible >> to do a paired analysis looking at volume instead. >> Any information you have would be very helpful. >> >> Thanks so much! >> >> Best, >> >> Alexandra Tanner >> Clinical Research Coordinator >> Laboratory for Brain Genomics >> Division of Psychiatric Neuroimaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA 02129 >> (p) 617.643.3215 >> >> > > -- > 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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Recon-all -qcache curvature error & recon-all make -all
by Gibbard, Clare 25 Jul '12

25 Jul '12

Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points. I re-ran them to incorporate the edits using recon-all -s subject_no -make all -xopts-use. This worked well. I then ran recon-all -s subject_no -qcache ready for doing a group analysis. I got an error reading the curvature file in those subjects I had edited. I can see from the mailing list that others have had this error previously and ran recon-all -s subject_no -make all to fix it. I tried this, but I got a message saying that there was nothing to be done for all. Are you able to advise me on what I can try now? Do I need to go back a step? Thank you very much, Clare

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Paired t-test with independent samples
by Jürgen Hänggi 24 Jul '12

24 Jul '12

Dear statistic experts We have done statistics between two independent groups using an independent t-test. One group consistent of 13 male patients and the other group consistent of 13 male control subjects who were matched to the patients with respect to age and education (in years). The reviewer proposed that it might be more appropriate to use a paired t-test. However, we can imaging a design where such an approach is adequate e.g. monozygotic twins reared in shared environments who are discordant for a particular trait. In our opinion, the matching of only age and education is not sufficient in order to apply a paired t-test. In addition, the paired t-test is more anti-conservative than the independent t-test and therefore advantages our hypothesis and this might be identified as a statistical "trick" by other reviewers. Any comment about whether or not the suggested paired t-test is appropriate in our study is highly appreciated. Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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tracula RAM memory ?...
by Gonzalo Rojas Costa 24 Jul '12

24 Jul '12

Hi: How much memory needs tracula to process a DTI study ?... Because my PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in trac-preproc... There exist any tip & trick in such a case?... 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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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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Freesurfer July 2012