[Freesurfer] recommende pc and cuda
Hi I am in the process of acquiring a new computer to run freesurfer on. I am currently think about buying a PC with a geforce 4X0 and a Tesla card along with a two screen setup running either Ubuntu or Redhat Linux enterprise 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte of ram. What kind of tesla card is recommend for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0. Knut J ___ Freesurfer mailing list 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.
Re: [Freesurfer] recommende pc and cuda
Maybe a NVidia GTX590 (it's a dual GPU) On Mon, Apr 4, 2011 at 08:13, Knut J Bjuland wrote: > Hi > > I am in the process of acquiring a new computer to run freesurfer on. I am > currently think about buying a PC with a geforce 4X0 and a Tesla card along > with a two screen setup running either Ubuntu or Redhat Linux enterprise > 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte > of ram. What kind of tesla card is recommend for using with Freesurfer? Will > Freesurfer 5.1 also support cuda 4.0. > > Knut J > > ___ > Freesurfer mailing list > 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recommende pc and cuda
On Mon, 2011-04-04 at 13:13 +0200, Knut J Bjuland wrote: > I am in the process of acquiring a new computer to run freesurfer on. > I am currently think about buying a PC with a geforce 4X0 and a Tesla > card along with a two screen setup running either Ubuntu or Redhat > Linux enterprise 6.0. I think the PC should be a core i7 with 6 core > and above 12 gigs byte of ram. What kind of tesla card is recommend > for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0. If your budget can withstand a Tesla C2050, by all means go for it. I've not checked in detail how much GPU RAM FreeSurfer requires, so it might be possible to run on a 'lesser' GeForce card. There's not enough double precision stuff to be significant in the GeForce vs Tesla choice. And I don't do overlapping transfers, which would be another factor. The main thing to do is make sure you have a 'Fermi' GPU - that's a Tesla 20 series, or GeForce GTX 400 or 500 series. Large speed ups depend on the Fermi card. As for the CPU... just make sure it's Nehalem class. FreeSurfer on both the CPU and GPU likes fast RAM access. As for CUDA 4.0 support that will depend on NVIDIA not breaking backwards compatibility (not an absolute given - they are not IBM). I don't expect any trouble, but until we upgrade to CUDA 4.0 here (and 3.2 just broke binary compatibility), I wouldn't want to promise anything. HTH, Richard ___ Freesurfer mailing list 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.
Re: [Freesurfer] help with CT scaling
Hi Andy can you run mri_info on the volume and see what it thinks the voxel dimensions are? Then also run it on the dicom series? cheers Bruce On Fri, 1 Apr 2011, Andrew R. Dykstra wrote: > Hi all, > > I'm having problems either or converting a series of dicoms from a CT scan > obtained at MGH main. When viewing them in the standard hospital viewer, > they appear normal, but when viewing them in TKMEDIT (either the original > dicom series or converted mgz file), the scaling changes. Are there any > options in mri_convert I can use to overcome this problem? See attached > view of the mgz file. > > Cheers, > Andy > ___ Freesurfer mailing list 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.
[Freesurfer] mri_ca_register error
Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.00, rms=0.657 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Mon Apr 4 07:57:30 EDT 2011 /home/virtualuser/apps/freesurfer/subjects/flo/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s flo exited with ERRORS at Mon Apr 4 07:57:30 EDT 2011 The recon-all.log indicates that mri_ca_register couldn’t write the talairach.m3z file. The brainmask.mgz file is skull-stripped and the cerebellum is attached. There is enough disc space. Does anyone know what this could possibly mean and how to avoid it? Thanks in advance for your advice. Thomas Hagen ___ Freesurfer mailing list 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.
Re: [Freesurfer] LGI error in make_outer_surface at 31
Dear List
I have recently come up agains the same problem as described below, namely
the error when I compute lGI reads
>>reading filled volume...
closing volume...
??? Undefined function or method 'fspecial' for input arguments of
type 'char'.
Error in ==> make_outer_surface at 31
Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file
I have tried re-running the subject (as recommended below), as well as
looking at any output from the mris_compute_lgi -debug flag directly, but
the error is the same (Note I am trying to process subjects on a linux
computer, and have verified that the same subject runs successfully on a
Mac).
I'd appreciate any suggestions you might have,
Thanks in advance,
Lisa
On Wed, Sep 24, 2008 at 7:18 PM, Martin Kavec wrote:
> Hi Jenifer,
>
> I don't know what the error exactly means, but sometimes just re-running
> the
> analysis helps.
>
> Best,
>
> Martin
>
> On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote:
> > Hi,
> > Encountering some difficulties with LGI on a RHEL4 box (64bit) with
> MATLAB
> > v7.6.0.324 (R2008a) installed. Subject was processed under fsv405.
> Specific
> > error is pasted below:
> >
> > Any suggestions to correct my error?
> >
> > Thanks,
> > Jenifer
> >
> > >> reading filled volume...
> >
> > closing volume...
> > ??? Undefined function or method 'fspecial' for input arguments of type
> > 'char'.
> >
> > Error in ==> make_outer_surface at 31
> > Gaussian = fspecial('gaussian',[2 2],1);
> >
> >
> > ERROR: make_outer_surface did not create output file
> > 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain
> > 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64
> > GNU/Linux
> >
> > recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008
> >
> > [jjuranek@localhost jjuranek_fsv405]$
> >
> >
> > ___
> > Freesurfer mailing list
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Re: [Freesurfer] LGI error in make_outer_surface at 31
Hi Lisa
Are you able to see the paths traced from the 'intermediate' files - you can
find them in a tmp folder within the subject's surf directory
Lena
On 04/04/2011 16:24, "Lisa Ronan" wrote:
Dear List
I have recently come up agains the same problem as described below, namely the
error when I compute lGI reads
>>reading filled volume...
closing volume...
??? Undefined function or method 'fspecial' for input arguments of type 'char'.
Error in ==> make_outer_surface at 31
Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file
I have tried re-running the subject (as recommended below), as well as looking
at any output from the mris_compute_lgi -debug flag directly, but the error is
the same (Note I am trying to process subjects on a linux computer, and have
verified that the same subject runs successfully on a Mac).
I'd appreciate any suggestions you might have,
Thanks in advance,
Lisa
On Wed, Sep 24, 2008 at 7:18 PM, Martin Kavec wrote:
Hi Jenifer,
I don't know what the error exactly means, but sometimes just re-running the
analysis helps.
Best,
Martin
On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote:
> Hi,
> Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB
> v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific
> error is pasted below:
>
> Any suggestions to correct my error?
>
> Thanks,
> Jenifer
>
> >> reading filled volume...
>
> closing volume...
> ??? Undefined function or method 'fspecial' for input arguments of type
> 'char'.
>
> Error in ==> make_outer_surface at 31
> Gaussian = fspecial('gaussian',[2 2],1);
>
>
> ERROR: make_outer_surface did not create output file
> 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain
> 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64
> GNU/Linux
>
> recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008
>
> [jjuranek@localhost jjuranek_fsv405]$
>
>
> ___
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[Freesurfer] Converting an FSL label to Freesurfer space
Hi, I'm trying to convert the individual FS parcelations to individual space in FSL. I'm not sure how to proceed. I've made a label from the individual subject's parcelation, and have saved it. How would I then convert the label to use it as a mask in the subject's structural space in FSL? Would mri_label2vol suffice? What would be my --reg? Thanks, Massih ___ Freesurfer mailing list 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.
Re: [Freesurfer] Pial surface correction failure after adding control points
Hi Min, It's difficult to tell what may be going wrong based on that one slice. Could you upload the subject and send it to Khoa so she can investigate? She's an expert in exactly these kinds of problems. Allison On Mon, 4 Apr 2011, Min Liu wrote: > Dear Freesurfer users, > > Thank you Dr.Stevens for suggestions. I reran -autorecon2 but still it > didn't fix the pial surface. I edited wm.mgz again by adding more control > points AND more white matter voxels using the 'edit voxel brush' but still, > after reran the whole second recon step, pial surface failed to include the > added wm voxels in. Pls see the attachment. Does anyone encounter the same > thing before? Thank you for advice! > > Min > > On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens < > astev...@nmr.mgh.harvard.edu> wrote: > >> Hi Min, >> We've learned that -autorecon2-cp might not be doing what was intended. Try >> runing -autorecon2 and see if it fixes everything. >> Allison >> >> >> On Thu, 31 Mar 2011, Min Liu wrote: >> >> Dear Freesurfer users, >>> >>> My first run of recon1&2 left some white and grey matter at temporal pole >>> region excluded. So I edited the wm.mgz by adding a bunch of control >>> points >>> intending to get more white matter and expand the pial surface (please see >>> the coronal slice in the attachment where the control points were placed). >>> Then I ran the command 'recon-all -autorecon2-cp -subjid XX' WITHOUT >>> '-autorecon3'. From my understanding, Freesurfer would recalculate the >>> wm.mgz as well as the white matter and pial surfaces in temporal pole >>> according to the control points. However, I got wm.mgz corrected and pial >>> surface wrong (as the attached graph indicated). >>> >>> Did I do something wrong? Why wm.mgz got fixed while pial surface not? >>> Thanks for help in advanced! >>> >>> Veronica >>> >>> >> >> 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with CT scaling
Hi Bruce, Here is the output from mri_info on both the mgz volume and dicom series. Cheers, Andy On Mon, Apr 4, 2011 at 11:08 AM, Bruce Fischl wrote: > Hi Andy > > can you run mri_info on the volume and see what it thinks the voxel > dimensions are? Then also run it on the dicom series? > > cheers > Bruce > > > > On Fri, 1 Apr 2011, Andrew R. Dykstra wrote: > > Hi all, >> >> I'm having problems either or converting a series of dicoms from a CT scan >> obtained at MGH main. When viewing them in the standard hospital viewer, >> they appear normal, but when viewing them in TKMEDIT (either the original >> dicom series or converted mgz file), the scaling changes. Are there any >> options in mri_convert I can use to overcome this problem? See attached >> view of the mgz file. >> >> Cheers, >> Andy >> >> > > 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. > > -- Andrew R. Dykstra PhD Candidate Harvard-MIT Division of Health Sciences and Technology Program in Speech and Hearing Bioscience and Technology "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov [huygens:Cashlab] (nmr-std-env) mri_info iEEG/MG45_SURFER_OUTPUT/ct/ct.mgz Volume information for iEEG/MG45_SURFER_OUTPUT/ct/ct.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 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., y_r = 0., z_r = 0., c_r =16.1619 : x_a = 0., y_a = 0., z_a = 1., c_a =-5.1820 : x_s = -0., y_s = -1., z_s = -0., c_s =55.6768 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 144.1619 0. 0. 1. -133.1820 -0. -1. -0. 183.6768 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 144.1619 0. 0. -1. 183.6768 0. 1. 0. 133.1820 0. 0. 0. 1. [huygens:Cashlab] (nmr-std-env) mri_info iEEG/MG45_SURFER_OUTPUT/ct/1.2.840.113619.2.80.973217100.26943.1289361217.3.dcm Starting DICOMRead2() dcmfile = iEEG/MG45_SURFER_OUTPUT/ct/1.2.840.113619.2.80.973217100.26943.1289361217.3.dcm dcmdir = iEEG/MG45_SURFER_OUTPUT/ct Ref Series No = 301 Found 83 files, checking for dicoms Found 79 dicom files in series. First Sorting Computing Slice Direction Vs: -105.559 33.8442 0.644257 Vs: -0.952237 0.305304 0.00581175 Second Sorting Counting frames nframes = 1 nslices = 79 ndcmfiles = 79 PE Dir = UNKNOWN (dicom read) Segmentation fault [huygens:Cashlab] (nmr-std-env) ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_ca_register error
Hi Thomas, usually that means the partition you are trying to write to is full, cheers Bruce On Mon, 4 Apr 2011, T. Hagen wrote: Hello all, I got this error message while running one of my subjects (freesurfer version 5.0.0): gcamFindOptimalTimeStep: Complete in 23335.062 ms 0388: dt=0.00, rms=0.657 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Mon Apr 4 07:57:30 EDT 2011 /home/virtualuser/apps/freesurfer/subjects/flo/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s flo exited with ERRORS at Mon Apr 4 07:57:30 EDT 2011 The recon-all.log indicates that mri_ca_register couldnÿÿt write the talairach.m3z file. The brainmask.mgz file is skull-stripped and the cerebellum is attached. There is enough disc space. Does anyone know what this could possibly mean and how to avoid it? Thanks in advance for your advice. Thomas Hagen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
[Freesurfer] {Disarmed} Re: Questions about GLM, Random and Fixed Effects Analysis in FsFast
Thank you, your reply was very helpful.
I have one more specific question. How is the variance of the "group-level
contrast map" estimated in the RFX and WRFX cases (to be used for a t-test
or F-test)? Is it simply the sample variance of the lower level contrast
maps stored in "ces.nii" files?
Thanks,
Gabriel
On Mon, Mar 14, 2011 at 10:19 AM, Douglas N Greve wrote:
>
> Hi Gabriel,
>
> for mri_glmfit, W = diag(sqrt(1./yffxvar)), ie, it is a diagonal matrix
> where each element is the square root of the inverse of the variance from
> the lower level. This changes the equation from a simple ordinary least
> squares into a weighted least squares (though not quite a true mixed-effects
> analysis).
>
> There are not explicitly nuisance regressors in the B matrix. The B is the
> matrix of regression coefficients ("betas") based on the solution to the
> forward model y=X*B (B=inv(X'*X)*X'*y). So the frames in B depend on the
> design matrix which depend on how you've set up your FSGD (or if you've
> entered the X matrix explicitly).
>
> I don't have another manuscript, but there is a lot of detail in the
> tutorial slides ftp://spdb.set_trace()
>
> urfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt
>
> doug
>
>
>
> Gabriel A. Tobon wrote:
>
>> Hello Freesurfers
>>
>> I would like to run a specialized group GLM analysis on the volume using
>> estimates from the individual subject analysis in Freesurfer as summary
>> statistics. I would like to learn a little more about how this estimation
>> is done before doing so. I have looked at the documentation for
>> "mri_glmfit" and the following tutorial:
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
>> I also have your 1999/2003 manuscripts on "Signal Processing and
>> Statistical Analysis for Event-Related fMRI" and "fMRI Analysis 101 -
>> Univariate Analysis," but I am not sure if the method has been updated since
>> then.
>>
>> * I noticed there is a weight matrix (W) described for "mri_glmfit"
>> command. How is this derived and used? I can't find more information about
>> it in the documentation/mailing list.
>> * How are the nuisance regressors organized in the B matrix? I assume the
>> conditions are first? What are the following regressors?
>> * Do you have a similar manuscript that describes just how group analysis
>> is implemented in FsFast?
>>
>> Thank you for your time and help!
>> Gabriel
>>
>>
>> ___
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>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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
>
>
>
> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Converting an FSL label to Freesurfer space
Hi Massih, Try looking at http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 4/4/11 2:38 PM, mmoayedi wrote: > Hi, > > I'm trying to convert the individual FS parcelations to individual > space in FSL. I'm not sure how to proceed. I've made a label from the > individual subject's parcelation, and have saved it. How would I then > convert the label to use it as a mask in the subject's structural space > in FSL? Would mri_label2vol suffice? What would be my --reg? > Thanks, > Massih > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain
He Lena, here's a paper that uses this method ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tom.2007.science.LossAversion.pdf doug On 4/3/11 7:52 AM, Lena Palaniyappan wrote: Doug Do you have any citations where people have done this before -- it is relevant for a VBM + SBM analysis I am currently doing, Cheers Lena On 31/03/2011 22:51, "Douglas N Greve" wrote: Hi Scott, no there is not another space I would recommend. The cortical surfaces across subjects don't line up at all with a 12DOF transform. If you look at your activation in the volume along with surface lines, you may see that your surfaces intersect some of the activation but not others. I guess if the surface is showing your important activation, then it's probably ok. I've seen people do this before. doug Scott Burns wrote: > Doug -- > > >> After you've gone into MNI space with all of your subjects, then >> visualizing the results on the surface are of questionable value. >> > > All of our first-level and second-level statistical maps in MNI space and we wish to overlay them onto fsaverage, is there another space I could map these spmT images into that when overlayed would be more reliable/publication worthy? If this wouldn't work, what would you suggest? > > Scott > > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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. ___ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH *Ph: 0115 82 30407 * This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list 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.
Re: [Freesurfer] resampling vol to surface
Hi Greg, mri_vol2surf will take a --regheader option which tells it to assume that the movable is in the anatomical space. doug On 4/1/11 4:11 PM, GREGORY R KIRK wrote: > Hi guys, > > i am using the freesurfer-fsl integration to use labels from the freesurfer > cortical surface as seeds for probtrackx > probabilistic diffusion tractography. when the output of probtrackx is > generated it is already in the freesurfer > conformed space. I want to resample the output of probtrackx onto the > cortical surface. I have the transformations > from the diffusion data to freesurfer conformed space generated using > bbregister to do the tractography but > to use mri_vol2surf i need to first tranfrorm the output of probtrackx back > into the epi space with the > inverse of the bbregister tranform ( output in the fsl format) and resample > it to the lower resolution epi resolution. > > i.e. there is not an option for mri_vol2surf to assume the data to be > resampled onto the cortical surface > is already in freesurfer conformed space. i suppose i could compute > transformations from freesurfer > conformed space to say brain.mgz, which would essentially be the identity > transformation. > > mriconvert -it mgz -ot nii brain.mgz brain.nii > i.e. bbregister --mov brain.nii --t1 -s subject -init-fsl --reg register.dat > > or i could make a fake identity transform like > > 1.0 > 1.0 > ? don't know what this number is > 1 0 0 0 > 0 1 0 0 > 0 0 1 0 > 0 0 0 0 > round ? what should i use here. > > whats the best way to go here > > thanks > > greg > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] help with CT scaling
Looks like we can't read the dicom fully. Is this a standard ct produced by the scanner? I guess I would try some other conversion utility like mricro to convert to nifti On Apr 4, 2011, at 5:16 PM, "Andrew R. Dykstra" wrote: > Hi Bruce, > > Here is the output from mri_info on both the mgz volume and dicom series. > > Cheers, > Andy > > > > On Mon, Apr 4, 2011 at 11:08 AM, Bruce Fischl > wrote: > Hi Andy > > can you run mri_info on the volume and see what it thinks the voxel > dimensions are? Then also run it on the dicom series? > > cheers > Bruce > > > > On Fri, 1 Apr 2011, Andrew R. Dykstra wrote: > > Hi all, > > I'm having problems either or converting a series of dicoms from a CT scan > obtained at MGH main. When viewing them in the standard hospital viewer, > they appear normal, but when viewing them in TKMEDIT (either the original > dicom series or converted mgz file), the scaling changes. Are there any > options in mri_convert I can use to overcome this problem? See attached > view of the mgz file. > > Cheers, > Andy > > > > 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. > > > > > -- > Andrew R. Dykstra > PhD Candidate > Harvard-MIT Division of Health Sciences and Technology > Program in Speech and Hearing Bioscience and Technology > > "How small the cosmos. How paltry and puny compared to human consciousness . > . . to a single individual recollection." - Vladimir Nabokov > ___ Freesurfer mailing list 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.
[Freesurfer] preproc-sess
Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message: Session: /home/fsl/structural/LD08 Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural I put the retinotopic and structural data into the structural directory. In addition, I have the subjectname file that contains LD08 in this case. Any help would be most appreciated. I am attaching the output, in case it is helpful. Thanks. Michelle ing Douglas N Greve : I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt doug 1. Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like: stimtype polar direction pos 2. Run preprocessing preproc-sess -surface self lhrh -fwhm 5 3. Create analysis (30 sec period, 'rtopy.par' is the name of the paradigm file from above): mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par 4. Run analysis selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ... 5. View results a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign [fsl@localhost structural]$ preproc-sess -force -surface self lhrh -fwhm 5 -s LD08 -- preproc-sess logfile is log/preproc-sess.log -- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ fsl setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /home/fsl/structural Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /home/fsl/structural /usr/local/freesurfer/fsfast/bin/preproc-sess -force -surface self lhrh -fwhm 5 -s LD08 Tue Apr 5 07:38:35 BST 2011 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain LD08 Template - mktemplate-sess -s LD08 -d /home/fsl/structural -fsd bold Session: /home/fsl/structural/LD08 Tue Apr 5 07:38:35 BST 2011 Detected input format at nii /home/fsl/structural mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/template.nii --frame 0 mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/template.nii --frame 0 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/fsl/structural/LD08/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999754, 0.00122074, 0.0221564) j_ras = (0.00198375, 0.999446, 0.0332345) k_ras = (0.0221035, -0.0332703, 0.999202) keeping frame 0 writing to /home/fsl/structural/LD08/bold/template.nii... Run: 001 Tue Apr 5 07:38:36 BST 2011 /home/fsl/structural mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/001/template.nii --mid-frame mri_convert /home/fsl/structural/LD08/bold/001/f.nii /home/fsl/structural/LD08/bold/001/template.nii --mid-frame $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/fsl/structural/LD08/bold/001/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999754, 0.00122074, 0.0221564) j_ras = (0.00198375, 0.999446, 0.0332345) k_ras = (0.0221035, -0.0332703, 0.999202) keeping frame 74 writing to /home/fsl/structural/LD08/bold/001/template.nii... Run: 002 Tue Apr 5 07:38:37 BST 2011 /home/fsl/structural mri_convert /home/fsl/structural/LD08/bold/002/f.nii /home/fsl/structural/LD08/bold/002/template.nii --mid-frame mri_convert /home/fsl/structural/LD08/bold/002/f.nii /home/fsl/structural/LD08/bold/002/template.nii --mid-frame $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/fsl/structural/LD08/bold/002/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999754, 0.00122074, 0.0221564) j_ras = (0.00198375, 0.999446, 0.0332345) k_ras = (0.0221035, -0.0332703, 0.999202) keeping frame 74 writing to /home/fsl/structural/LD08/bold/002/template.nii... Tue Apr 5 07:38:38 BST 2011
