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30099 discussions

glm specification in longitudinal analyses for one group
by Sandra Preissler 22 Jan '14

22 Jan '14

Dear freesurfer experts and users At the moment our group is working on longitudinal analyses for two different time points in one group. Our analyses worked well and we tried to calculate the effects of six different covariates and one fix moderator variable (we had two different MRI Scanner and tried to consider this effect) with the function mri_glmfit. We did pre-processing with mri_preproc: mris_preproc --fsgd extra_komplett.fsgd --cache-in long.thickness-rate.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.extra_komplett.thickness.10.mgh With the fsgd-File designed like the following example: GroupDescriptorFile 1 Title G1V2 Class Scannertyp-Main Variables z1 z2 z3 z4 z5 z6 Input P01 Scannertyp-Main T3 z11 z21 z31 z41 z51 z61 Because of the consideration of the variable Scanner we designed the design matrix on our own. Before calculating the effect of the covariates we calculated the main effect (for the assumed underlying regression model please refer to equation number 1 in the attached pdf). For doing this we built a contrast file (please refer to equation 2). In a longer discussion we decided to delete different covariates and get the regression model shown in equation 3 (and the contrast file for the main effect in equation 4). Surprisingly both main effects not even were similar. Therefore we tried two different models (please refer to equation 5 and 7 for the two regression models). If the underlying model is a normal linear model the first three Contrasts and regression models should gave the same results. In our analyses we have really different results, therefore we have problems in interpreting and understanding the underlying general linear model. There seems to be still an influence of the covariates even if there are modeled with 0 (which in our understanding means they were mathematically not included in the model). Is the probability dependent on the distribution of the covariates even if they are modeled with no influence? If so, how is the belonging regression model? The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this theoretical problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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FreeSurfer installation
by Neda Mohammadi 22 Jan '14

22 Jan '14

Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda

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surface repositioning tool documentation
by Jason Tourville 22 Jan '14

22 Jan '14

Hi, Is there documentation for the use of freeview's surface repositioning tool? Including the recon-all steps that should be rerun to ensure that the surface edits are reflected in the surface stats? Are edits made with this tool applied to future runs through the recon-all process (like pial and wm edits)? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Re: [Freesurfer] Multiple Frames
by Bruce Fischl 22 Jan '14

22 Jan '14

that's what I wondered. AFI = "Actual Flip angle Imaging" usually On Wed, 22 Jan 2014, Glasser, Matthew wrote: > AFI is a bias transmit scan, not an MPRAGE. Look for T1w. > > On 1/22/14 11:44 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Al, >> >> can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not >> familiar with their naming convention. I'll cc Matt Glasser who can >> probably help. >> >> cheers >> Bruce >> On Wed, 22 Jan 2014, Alfred Ochs wrote: >> >>> 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 >>> >>> >> >> >> 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. > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > >

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Cortical Flat Mapping Crash
by Sherryse Corrow 22 Jan '14

22 Jan '14

We are doing some cortical flat mapping in FreeSurfer. We are following these instructions: http://openwetware.org/wiki/Beauchamp:FreeSurfer#Creating_Flat_Maps. We are able to create the flat map without a problem. However, just before we are able to do the last step "Save the patch by clicking File->Patch->Save Patch As" the process crashes and the flat map is lost. In the terminal, we see this error: surfer: filling (ctrl-c to cancel)...... done, 154370 vertices filled #Filling the uncut area was successful. surfer: ripped 12057 vertices tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort (core dumped) So, the uncut area is filled and before we have time to click File, Save As, etc. . . the process crashes and we have to start the process over again. Any suggestions? Thanks for your time. -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

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Re: [Freesurfer] Multiple Frames
by Bruce Fischl 22 Jan '14

22 Jan '14

p.s. thanks Matt Bruce On Wed, 22 Jan 2014, Glasser, Matthew wrote: > AFI is a bias transmit scan, not an MPRAGE. Look for T1w. > > On 1/22/14 11:44 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Al, >> >> can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not >> familiar with their naming convention. I'll cc Matt Glasser who can >> probably help. >> >> cheers >> Bruce >> On Wed, 22 Jan 2014, Alfred Ochs wrote: >> >>> 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 >>> >>> >> >> >> 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. > > > ________________________________ > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > >

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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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