Freesurfer

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30133 discussions

Multiple Frames
by Alfred Ochs 22 Jan '14

22 Jan '14

Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia

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bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 22 Jan '14

22 Jan '14

Hi everybody, I'm trying to run trac all -prep on my data but I'm getting this error "bvecs and bvals don't have the same number of entries". I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. The other 2 bvals and bvecs in DTI folder are the one saved by trac-all in the dmri directory. I'm attaching also my configuration file "dmrirc.tutorial". Francesco Baldacchini

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Fwd: Applying two registration matrices
by Sebastian Moeller 21 Jan '14

21 Jan '14

Dear list, I notice I took this off-list for no apparent reason…. Maybe it can be useful.. best Sebastian Begin forwarded message: > From: Sebastian Moeller <sebastian.moeller1(a)rwth-aachen.de> > Subject: Re: [Freesurfer] Applying two registration matrices > Date: January 20, 2014 15:09:45 GMT+01:00 > To: "Caspar M. Schwiedrzik" <cschwiedrz(a)mail.rockefeller.edu> > > > On Jan 20, 2014, at 14:36 , "Caspar M. Schwiedrzik" <cschwiedrz(a)mail.rockefeller.edu> wrote: > >> Hi Freesurfer Experts, >> I was wondering what the best way to apply two registration matrices to the same data set would be, ideally without re-slicing after the first registration? > > Just multiply the matrices and apply the result? > > From http://en.wikipedia.org/wiki/Transformation_matrix > > Composing and inverting transformations[edit] > > One of the main motivations for using matrices to represent linear transformations is that transformations can then be easily composed (combined) and inverted. > Composition is accomplished by matrix multiplication. If A and B are the matrices of two linear transformations, then the effect of applying first A and then B to a vector x is given by: > > (This is called the associative property.) In other words, the matrix of the combined transformation A followed by B is simply the product of the individual matrices. Note that the multiplication is done in the opposite order from the English sentence: the matrix of "A followed by B" is BA, not AB. > A consequence of the ability to compose transformations by multiplying their matrices is that transformations can also be inverted by simply inverting their matrices. So, A−1 represents the transformation that "undoes" A. > > > > You could use the attached m files to read and write free surfer registration matrices and do the multiplication in matlab. (You probably could also apply the matrix in matlab or feed the matrix into tkregister2 or whatever script/binary was supposed to work on the original registration matrices…) > > best > Sebastian > > > > >> Thanks, Caspar >> >> _______________________________________________ >> 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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Applying two registration matrices
by Caspar M. Schwiedrzik 21 Jan '14

21 Jan '14

Hi Freesurfer Experts, I was wondering what the best way to apply two registration matrices to the same data set would be, ideally without re-slicing after the first registration? Thanks, Caspar

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Re: [Freesurfer] About Resampling FSAVERAGE_SYM
by Douglas N Greve 21 Jan '14

21 Jan '14

No, sorry, not easily On 01/21/2014 08:32 AM, 左西年 wrote: > Dear Dr. Greve and the List, > > In the new release of the FS, a new symmetric fsaverage model is included. Is there anyway we can resample the fsaverage_sym to another resolution space (e.g., fsaverage5_sym)? Thanks for your time and help! > > Best Regards, > -- > Xi-Nian Zuo, Ph.D. of Applied Mathematics > Distinguished Research Professor, Institute of Psychology > Deputy Director, MRI Research Center, Institute of Psychology > Chinese Academy of Sciences > No. 16 Lincui Road, Beijing, 100101, China > Email: zuoxn(a)psych.ac.cn > Tel: +86-10-64853798 (Office) > http://lfcd.psych.ac.cn/index.html > http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en > > > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Subcortical volume stream
by Gabor Perlaki 21 Jan '14

21 Jan '14

Dear all, Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.html) Which is the most time-efficient way to get subcortical segmentation with Freesurfer? Thanks, Gabor

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Problem with the Monte Carlo simulation
by Sophie Maingault 21 Jan '14

21 Jan '14

Dear FreeSurfer experts, We are running group analyses in 430 young healthy volunteers using Qdec interface and FreeSurfer 5.3. FDR correction seems to be not enough restrictive and on the contrary use a Bonferroni correction with the total number of vertices would be too much restrictive. In this context we would like to use the Monte Carlo simulation but we built our specific template and as you may know this is not possible in this case, this error message being displayed: " Erreur in Monte Carlo simulation: This function only works when using fsaverage as the common-space subject ". Thus I have two questions: 1) is it possible to adapt the Monte Carlo simulation to our template using some command line or something else? 2) If not what advice can you give to us? Thanks a lot, Best regards, Sophie Maingault

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Changing primary slice direction
by Arash Jalalian 20 Jan '14

20 Jan '14

Hi Freesurfer Community, I am using matlab to do a histogram segmentation on a FLAIR volume. The algorithm I am using best works with axial direction. Is there any way to change the primary slice direction from sagittal to axial? I have tried mri_convert with --out_orientation set to LIA but that produces coronal. Regards, Arash

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Join my network on LinkedIn
by Rosalia Dacosta Aguayo via LinkedIn 19 Jan '14

19 Jan '14

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Fwd: Control point failure - CA Normalize
by Mark Plantz 17 Jan '14

17 Jan '14

Hi Bruce, The nu.mgz file looks OK to me (I also attached a picture). When I opened the talairach with "tkregister2" everything looked ok, except I couldn't get the green lines from the original surface to show (even after pressing 's' in the viewing window). Anyways, since these two files seem to be OK, do you think it is an atlas issue? Thank you! - MP On Thu, Jan 16, 2014 at 7:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > does the input to mri_ca_normalize look ok (the nu.mgz)? Is the > talairach.xfm ok? > > Bruce > > On Thu, 16 Jan 2014, Mark Plantz wrote: > > Hello freesurfers, >> >> I am running into a problem during the "CA Normalize" sequence of >> autorecon-2. It looks like freesurfer is having a hard time creating >> control >> points based off the atlas I am using. The output is as follows: >> >> "finding control points in <Left_Cerebral_White_Matter>...found 0 >> control >> points" >> >> This repeated for the other various regions included in the atlas. >> The >> only control points found were "168 control points" in the >> "Right_Cerebral_White_Matter". Could this possibly be an alignment issue? >> If >> so, is there an easy way to check the alignment? >> >> Thank you, >> >> >> Mark >> >> >> >> >> >> >> > > 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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