Re: [Freesurfer] multi-slice timing correction
External Email - Use Caution Okay, I looked through the source code itself and I think I worked it out. preproc-sess calls on stc-sess, passing it both the sdf and the ngroups flags. stc-sess calls on stc.fsl, passing it both the sdf and the ngroups flags. stc.fsl calls on slicetimer. It uses the sdf flag if it has been set to a file name, otherwise it uses the other flags including ngroups to call on slicedelay to generate an sdf file which it then passes on to slicetimer. So in other words, if an sdf file is provided, then the ngroups flag is ignored and does not need to be set. Am I correct? I’d like to make sure I’m doing this right. Thanks again for this amazing toolset! Joe > On Jun 11, 2019, at 15:55, Joseph Dien wrote: > > External Email - Use Caution > > > looking further into the archives, I see that the -sdf flag can be used. I’m > still uncertain about the -ngroups flag. I see at least a couple other users > have asked about this but I don’t see a response. In the present case, if > there are 60 slices and they are accelerated by a factor of 6, does one > specify -ngroups 6 or -ngroups 10? > > Joe > >> On Jun 2, 2019, at 19:46, Joseph Dien > <mailto:jdie...@mac.com>> wrote: >> >> External Email - Use Caution >> >> >> Hi Doug, >>I’m happy to see that FreeSurfer6 provides enhanced support for slice >> timing. I’m trying to run it on some multi-slice data. May I ask you for >> some guidance on how to use the new preproc-sess options? As I understand >> it, I would specify “-ngroups 10” because the data were collected in ten >> groups of six slices at a time? I’m not sure how to specify “-sliceorder”. >> Slice times are below. Thanks for any help you can provide. >> >> Joe >> >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> 0 >> 877.5000 >> 502.5000 >> 125 >> 1005 >> 627.5000 >> 252.5000 >> 1130 >> 752.5000 >> 377.5000 >> >> >> >> Joseph Dien, PhD >> Senior Research Scientist >> Department of Human Development and Quantitative Methodology >> University of Maryland, College Park >> http://joedien.com <http://joedien.com/> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > Joseph Dien, PhD > Senior Research Scientist > Department of Human Development and Quantitative Methodology > University of Maryland, College Park > http://joedien.com <http://joedien.com/> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] multi-slice timing correction
External Email - Use Caution looking further into the archives, I see that the -sdf flag can be used. I’m still uncertain about the -ngroups flag. I see at least a couple other users have asked about this but I don’t see a response. In the present case, if there are 60 slices and they are accelerated by a factor of 6, does one specify -ngroups 6 or -ngroups 10? Joe > On Jun 2, 2019, at 19:46, Joseph Dien wrote: > > External Email - Use Caution > > > Hi Doug, >I’m happy to see that FreeSurfer6 provides enhanced support for slice > timing. I’m trying to run it on some multi-slice data. May I ask you for > some guidance on how to use the new preproc-sess options? As I understand > it, I would specify “-ngroups 10” because the data were collected in ten > groups of six slices at a time? I’m not sure how to specify “-sliceorder”. > Slice times are below. Thanks for any help you can provide. > > Joe > > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > 0 > 877.5000 > 502.5000 > 125 > 1005 > 627.5000 > 252.5000 > 1130 > 752.5000 > 377.5000 > > > > Joseph Dien, PhD > Senior Research Scientist > Department of Human Development and Quantitative Methodology > University of Maryland, College Park > http://joedien.com <http://joedien.com/> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer V6 installation: ubuntu virtual machine
External Email - Use Caution I have successfully run freesurfer 6.0 recon-all under Ubuntu in the OS X Parallels VM, as a workaround for the OS X recon-all CachedArray.cc <http://cachedarray.cc/> crash bug. Joe > On May 31, 2019, at 18:39, fsbuild wrote: > > External Email - Use Caution > > > Hello Steve, > > We have run the freesurfer 6.0.0 release on Ubuntu 16 and 18 which should > also work in a VM. > > You may have to install some packages in order to run freesurfer, especially > for the freeview program which uses various graphics packages, etc. After > downloading the freesurfer 6.0.0 binaries from, > > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz> > > - I would first try to run the freeview binary as that is a good test to help > determine what packages may be missing. > > I needed to both build and run freesurfer on Ubuntu, so I will list below the > packages I installed for both purposes. You should not need for example the > gcc compiler packages just to run the 6.0.0 release binaries, but I have not > tried to identify a set of packages to only run the binaries. > > You will likely also need sudo privileges to install packages. > > - R. > > $ sudo apt-get install build-essential > $ sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev > $ sudo apt-get install libblas-dev liblapack-dev > $ sudo apt-get install ocl-icd-opencl-dev > $ sudo apt-get install libxmu-dev libxi-dev > $ sudo apt-get install libopencv-dev > > Ubuntu 16: $ sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9 > Ubuntu 18: $ sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 > > $ sudo apt-get install xorg xorg-dev libx11-dev > $ sudo apt-get install tcl tcl-dev tk tk-dev > $ sudo apt-get install qt5-default qtcreator > $ sudo apt-get install libqt5x11extras5-dev > $ sudo apt-get install git-annex > $ sudo apt-get install python3-dev > > … you will need a libpng, which I got from the archives, > > > http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb > > <http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb> > > $ curl -O > http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb > >- then install the gdebi tool, > > $ sudo apt install gdebi > > - change directories to where you downloaded the libpng12 package, and > use gdebi to install it, > > $ sudo gdebi libpng12-0_1.2.54-1ubuntu1_amd64.deb > > > >> On May 31, 2019, at 02:57, Steve Petersen wrote: >> >> External Email - Use Caution >> >> >> Dear Freesurfer experts, >> >> >> Just a simple question, is possible to install the Freesurfer (Version 6) in >> a virtual machine of ubuntu? >> >> Thanks in advance, >> >> >> Best regards, >> >> Steve >> ___ >> 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 Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] multi-slice timing correction
External Email - Use Caution Hi Doug, I’m happy to see that FreeSurfer6 provides enhanced support for slice timing. I’m trying to run it on some multi-slice data. May I ask you for some guidance on how to use the new preproc-sess options? As I understand it, I would specify “-ngroups 10” because the data were collected in ten groups of six slices at a time? I’m not sure how to specify “-sliceorder”. Slice times are below. Thanks for any help you can provide. Joe 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 0 877.5000 502.5000 125 1005 627.5000 252.5000 1130 752.5000 377.5000 Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] request for corrected p-values for mni305 space
Hi, just a user request for corrected p-values for the mni305 space analyses (i.e., sig.voxel.nii.gz files). Thanks! Joe Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com ___ 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] mkanalysis-sess stimulusdelay parameter
I’m taking a look at the effects of stimulus delay settings in one of my datasets so I was surprised to notice that the default setting of mkanalysis-sess is a delay of -TR/2 seconds. What is the reasoning for this? If, as I expect, it was just empirically found that it worked better than without, my question is whether this decision was made on the basis of all the event-related options or just some subset of them? I’m worried that this might be an optimization that isn’t appropriate for my particular parameter choices (FS 5.3, spmhrf0). Any comments would be appreciated. Cheers! Joe Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park http://joedien.com ___ 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] ERROR running mkcontrast
Hi, I ran into an odd problem which I was able to fix but wanted to let others know about. This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3. I got the following error when I ran mkcontrast using batch files that previously worked fine: /private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn8gn/T/Cleanup At Startup/sh.h4SI0w: No such file or directory. ERROR running mkcontrast Looking into the directories in question, I found that while there was no directory named 'Cleanup At Startup’ inside the T directory, there was such a directory inside ‘vj5q34fs20x50sh_6rcrtkn8gn’. I’m guessing some version update changed the location of this directory. I went into T and performed the following command: mkdir 'Cleanup At Startup' after doing so, everything worked again. Cheers! Joe Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com ___ 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] FSFAST mkcontrast-sess with spmhrf 2 question
Doug, I see now what your concern was with just adjusting the beta weights. Since FSFAST is using a pseudo-mixed effects model, there is also a need to pass the cesvar statistics up to the second level. How that might accommodate the derivative boost computation is not straightforward to me. I need to understand better what fsfast is doing. I was wondering if you could answer a couple questions about how cesvar is computed; 1) The cesvar computations in the fast_fratio.m function provided a good guide. According to it: cescvm = inv(C*inv(X'*X)*X'*Sn*X*inv(X'*X)*C’); where Sn is the covariance matrix of the noise after the whitening (which is on by default). cesvar=rvar./cescvm. How is Sn computed? 2) I need to understand what fsfast is doing conceptually but I couldn’t reconcile the Thirion et al (2007) Equation #5 and the equations above, specifically the inclusion of the rvar term. Can you throw some light on this? I greatly appreciate your helpful tips and this amazing software that you have written. Respectfully, Joe > On Mar 17, 2016, at 15:48, Joseph Dien <jdie...@mac.com> wrote: > > I did more digging around and came up with a procedure. Please let me know > if it would cause any problems. > Looking at the contents of the X.mat files (which contain the predictors), it > appears that the betas are indeed arranged as c1 d1 c2 d2… > I also found that isxconcat-sess requires the contrast output of > mkcontrast-sess so I can’t just bypass it. > > So my thought is: > > 1) run mkanalysis-sess with -spmhrf 1 > 2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas > without bothering with the contrasts > 3) run mkanalysis-sess with -spmhrf 0 > 4) run selxavg3-sess again but with the contrasts to get everything set up > 5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative > boost with the beta values in mri.vol > 6) use these values to compute the desired contrasts. From my examination of > a sample ces.nii.gz file, a simple linear combination based on the contrast > weights is all that is needed. > 7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ > mri.vol with these new values > 8) write out the new ces.nii.gz files. > 9) proceed with the analysis stream, using isxconcat-sess to set up the > second level analysis > > So the question is, would this work? Am I neglecting files other than > ces.nii.gz that would need to be modified? or other fields in the mri data > structure? > When you referred to writing “out a new volume” is this what you meant? > > Thanks again for this help! > > Joe > > >> On Mar 15, 2016, at 17:32, Joseph Dien <jdie...@mac.com >> <mailto:jdie...@mac.com>> wrote: >> >> oh duh! Sorry, wasn’t thinking clearly. >> Okay, I see how to generate the betas now. I don’t even need to mess with >> the mkcontrast-sess command. >> I just run selxavg3-sess with the -no-con-ok flag. >> With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. >> With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. >> With 12 conditions, 12 more betas is exactly right. >> So how do I know which of the betas is which? >> I looked through the files and couldn’t find any labels. >> I’m guessing the first twelve are the condition betas for "spmhrf 0". >> If so, for "spmhrf 1", is it arranged as: >> >> 1) c1 c2 c3…d1 d2 d3... >> >> or >> >> 2) c1 d1 c2 d2... >> >> (where d is the first derivative term) >> >> also, when I asked you earlier about implementing this procedure, I had >> suggested reading the betas, computing the Calhoun, then generating new >> beta.nii.gz files with the new betas replacing the original spmhrf0 betas >> and then continuing with the regular analysis stream but you said it would >> result in invalid p-values. Instead, you suggested: >> >> "I was just thinking you could load the beta into matlab, make the >> Calhoun computations on each condition, then compute the contrasts, then >> write out the new volume” >> >> can you expand on how one might “compute the contrasts” and “write out the >> new volume”? >> >> Thanks again for this help! >> >> Joe >> >> >>> On Mar 15, 2016, at 12:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess) >>> >>> On 03/13/2016 10:29 PM, Joseph Dien wrote: >>>> After a long break, back to this… >>>&g
Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
I did more digging around and came up with a procedure. Please let me know if it would cause any problems. Looking at the contents of the X.mat files (which contain the predictors), it appears that the betas are indeed arranged as c1 d1 c2 d2… I also found that isxconcat-sess requires the contrast output of mkcontrast-sess so I can’t just bypass it. So my thought is: 1) run mkanalysis-sess with -spmhrf 1 2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas without bothering with the contrasts 3) run mkanalysis-sess with -spmhrf 0 4) run selxavg3-sess again but with the contrasts to get everything set up 5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative boost with the beta values in mri.vol 6) use these values to compute the desired contrasts. From my examination of a sample ces.nii.gz file, a simple linear combination based on the contrast weights is all that is needed. 7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ mri.vol with these new values 8) write out the new ces.nii.gz files. 9) proceed with the analysis stream, using isxconcat-sess to set up the second level analysis So the question is, would this work? Am I neglecting files other than ces.nii.gz that would need to be modified? or other fields in the mri data structure? When you referred to writing “out a new volume” is this what you meant? Thanks again for this help! Joe > On Mar 15, 2016, at 17:32, Joseph Dien <jdie...@mac.com> wrote: > > oh duh! Sorry, wasn’t thinking clearly. > Okay, I see how to generate the betas now. I don’t even need to mess with > the mkcontrast-sess command. > I just run selxavg3-sess with the -no-con-ok flag. > With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. > With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. > With 12 conditions, 12 more betas is exactly right. > So how do I know which of the betas is which? > I looked through the files and couldn’t find any labels. > I’m guessing the first twelve are the condition betas for "spmhrf 0". > If so, for "spmhrf 1", is it arranged as: > > 1) c1 c2 c3…d1 d2 d3... > > or > > 2) c1 d1 c2 d2... > > (where d is the first derivative term) > > also, when I asked you earlier about implementing this procedure, I had > suggested reading the betas, computing the Calhoun, then generating new > beta.nii.gz files with the new betas replacing the original spmhrf0 betas and > then continuing with the regular analysis stream but you said it would result > in invalid p-values. Instead, you suggested: > > "I was just thinking you could load the beta into matlab, make the > Calhoun computations on each condition, then compute the contrasts, then > write out the new volume” > > can you expand on how one might “compute the contrasts” and “write out the > new volume”? > > Thanks again for this help! > > Joe > > >> On Mar 15, 2016, at 12:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess) >> >> On 03/13/2016 10:29 PM, Joseph Dien wrote: >>> After a long break, back to this… >>> >>> My goal is still to get the betas for the first and maybe second spm >>> hrf so I can calculate a Calhoun derivative boost measure. >>> >>> As a first step I ran: >>> >>> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh >>> -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf >>> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg >>> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc >>> >>> to use the SPM HRF with one derivative. >>> >>> Then: >>> >>> selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh >>> >>> I got the following error: >>> >>> ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch >>> This condition has 2 regressors, but evrm has 1 >>> Struct contents reference from a non-struct array object. >>> >>> Error in flac_conmat (line 37) >>> if(nthcon > length(flac.con)) >>> >>> Error in flac_customize (line 369) >>> flacnew = flac_conmat(flacnew,nthcon); >>> >>> Error in fast_selxavg3 (line 65) >>> flac0 = flac_customize(flac0); >>> >>>>> -- >>> ERROR: fast_selxavg3() failed\n >>> >>> This ran fine with spmhrf 0 >>> >>> based on your prior response below that: >>
Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
oh duh! Sorry, wasn’t thinking clearly. Okay, I see how to generate the betas now. I don’t even need to mess with the mkcontrast-sess command. I just run selxavg3-sess with the -no-con-ok flag. With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex. With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex. With 12 conditions, 12 more betas is exactly right. So how do I know which of the betas is which? I looked through the files and couldn’t find any labels. I’m guessing the first twelve are the condition betas for "spmhrf 0". If so, for "spmhrf 1", is it arranged as: 1) c1 c2 c3…d1 d2 d3... or 2) c1 d1 c2 d2... (where d is the first derivative term) also, when I asked you earlier about implementing this procedure, I had suggested reading the betas, computing the Calhoun, then generating new beta.nii.gz files with the new betas replacing the original spmhrf0 betas and then continuing with the regular analysis stream but you said it would result in invalid p-values. Instead, you suggested: "I was just thinking you could load the beta into matlab, make the Calhoun computations on each condition, then compute the contrasts, then write out the new volume” can you expand on how one might “compute the contrasts” and “write out the new volume”? Thanks again for this help! Joe > On Mar 15, 2016, at 12:43, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess) > > On 03/13/2016 10:29 PM, Joseph Dien wrote: >> After a long break, back to this… >> >> My goal is still to get the betas for the first and maybe second spm >> hrf so I can calculate a Calhoun derivative boost measure. >> >> As a first step I ran: >> >> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh >> -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf >> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg >> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc >> >> to use the SPM HRF with one derivative. >> >> Then: >> >> selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh >> >> I got the following error: >> >> ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch >> This condition has 2 regressors, but evrm has 1 >> Struct contents reference from a non-struct array object. >> >> Error in flac_conmat (line 37) >> if(nthcon > length(flac.con)) >> >> Error in flac_customize (line 369) >> flacnew = flac_conmat(flacnew,nthcon); >> >> Error in fast_selxavg3 (line 65) >> flac0 = flac_customize(flac0); >> >>>> -- >> ERROR: fast_selxavg3() failed\n >> >> This ran fine with spmhrf 0 >> >> based on your prior response below that: >> >> "This is what happens. If you want to use the derivatives, >> then you need to spec -setwdelay. When you run the command, it will >> prompt you >> for 3 values to use. If you spec 1 0 0, then it will be the same as the >> default. If you want to test only the first derivative, then >> you would spec 0 1 0. Note that the 3rd regressor is the 2nd >> derivative wrt time, not the first derivative wrt the dispersion >> parameter. You >> cannot get the Calhoun 2004 value using a contrast (it is non-linear).” >> >> I tried: >> >> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh >> -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf >> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg >> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay >> >> but I just got the error: >> >> ERROR: Flag -setwdelay unrecognized. >> >> I also tried using the flag when setting up the contrasts but that >> didn’t work either. >> >> so not quite sure what I’m doing wrong. I had understood from your >> response below that the contrast weights didn’t need to be changed >> from the spmhrf 0 case but perhaps I misunderstood? >> >> any help would be welcome! >> >> Joe >> >>> On Jul 10, 2013, at 13:58, Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> >>> I was just thinking you could load the beta into matlab, make the >>> Calhoun computations on each condition, then compute the contrasts, then >>> write out the new volume >>> >>> >>> On 07/10/2013 0
Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
After a long break, back to this… My goal is still to get the betas for the first and maybe second spm hrf so I can calculate a Calhoun derivative boost measure. As a first step I ran: mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc to use the SPM HRF with one derivative. Then: selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh I got the following error: ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch This condition has 2 regressors, but evrm has 1 Struct contents reference from a non-struct array object. Error in flac_conmat (line 37) if(nthcon > length(flac.con)) Error in flac_customize (line 369) flacnew = flac_conmat(flacnew,nthcon); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n This ran fine with spmhrf 0 based on your prior response below that: "This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear).” I tried: mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm RPA1fix.par -nconditions 12 -spmhrf 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay but I just got the error: ERROR: Flag -setwdelay unrecognized. I also tried using the flag when setting up the contrasts but that didn’t work either. so not quite sure what I’m doing wrong. I had understood from your response below that the contrast weights didn’t need to be changed from the spmhrf 0 case but perhaps I misunderstood? any help would be welcome! Joe > On Jul 10, 2013, at 13:58, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > I was just thinking you could load the beta into matlab, make the > Calhoun computations on each condition, then compute the contrasts, then > write out the new volume > > > On 07/10/2013 01:40 PM, Joseph Dien wrote: >> Sounds good! >> >> Regarding creating a new volume and computing contrasts from it, what >> do you mean? I didn't follow that. >> >> Thanks! >> >> Joe >> >> >> On Jul 10, 2013, at 1:33 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >>> >>> On 07/10/2013 01:29 PM, Joseph Dien wrote: >>>> Sorry, not following what you are suggesting? >>>> >>>> I want the second derivative for calculating the Calhoun et al 2004 >>>> derivative boost measure. >>>> My understanding is that to the extent that the BOLD signal deviates >>>> from the canonical hrf, the amplitude of the primary regressor will be >>>> attenuated and the variance will instead end up in the first and >>>> second derivatives (to the extent that they are able to accommodate >>>> the divergence). By using a Calhoun measure that incorporates both >>>> the first and second derivatives, in principle I'll have a BOLD >>>> measure that is more robust to deviations from the canonical hrf. >>> Sorry, it had been a while since I read that paper. I did not know that >>> they had a formulation that included the 2nd derivative. >>>> >>>> However, if the way FSFAST is calculating the second derivative >>>> regressor is resulting in loss of statistical power due to shared >>>> variance with the primary regressor, then it would be best to just not >>>> include it at all in the estimation step. >>> I don't know how much it will hurt the power. You'd have to look at the >>> efficiency. >>> doug >>> >>>> >>>> >>>> On Jul 10, 2013, at 1:21 PM, Douglas N Greve >>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>>> wrote: >>
Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)
never mind! It turned out I was forgetting to run a script to move copies of the fixed fsgd files into their final locations. Once I did so the files I posted worked fine. Sorry for the false alarm and thanks for getting back to me! Joe > On Mar 3, 2016, at 12:18, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > I cannot replicate the error. What version of FS are you using? What > happens if you run > mri_glmfit --fsgd RPA-acc.fsgd > or > mri_glmfit --fsgd RPA-accGT.fsgd > > > > On 02/29/2016 09:38 PM, Joseph Dien wrote: >> Hi, >>I’m having an fsgd error that has totally stumped me. I’m trying to run >> the following command to compute the second level statistics: >> >> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz >> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C >> normAcc.mtx >> >> I get the error message: >> >> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white >> gdfReadHeader: reading RPA-accGT.fsgd >> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title >> >> I used the utility flip to make sure the file was in UNIX format (with >> linefeeds). >> I then double-checked by reading in the binary codes with Matlab’s fread and >> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). >> >> Here is the contents of the fsgd file. >> >> GroupDescriptorFile 1 >> Title RP1 >> Class Main >> Variables LogoAcc NormAcc OrthAcc PhonAcc >> InputRPA903 Main0.750.790.770.62 >> InputRPA906 Main0.810.810.830.74 >> InputRPA907 Main0.871 0.840.83 >> InputRPA908 Main0.910.930.950.89 >> InputRPA909 Main0.740.950.720.72 >> InputRPA910 Main0.850.960.810.79 >> InputRPA912 Main0.750.780.730.73 >> InputRPA914 Main0.7 0.850.830.81 >> InputRPA915 Main0.850.890.750.83 >> InputRPA916 Main0.840.920.870.72 >> InputRPA917 Main0.830.930.920.83 >> InputRPA918 Main0.870.910.790.85 >> InputRPA919 Main0.860.960.910.88 >> InputRPA920 Main0.840.920.870.84 >> InputRPA921 Main0.870.920.880.85 >> InputRPA922 Main0.8 0.9 0.9 0.72 >> >> What’s really driving me to distraction is that a previous version of this >> file (with a different set of participants) works fine. I’m attaching both. >> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s >> fread, the first 85 characters (first four lines) of both files are >> identical. >> >> I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. >> >> Any help would be greatly appreciated! >> >> Joe >> >> >> >> >> >> Joseph Dien, PhD >> Senior Research Scientist >> Maryland Neuroimaging Center >> University of Maryland, College Park >> E-mail: jdie...@mac.com >> Cell Phone: 202-297-8117 >> http://joedien.com >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to
Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)
Oops, never mind. User error. I’m too embarrassed to even explain what I did. :) Joe > On Feb 29, 2016, at 21:38, Joseph Dien <jdie...@mac.com> wrote: > > Hi, > I’m having an fsgd error that has totally stumped me. I’m trying to run > the following command to compute the second level statistics: > > mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz > --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C > normAcc.mtx > > I get the error message: > > Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white > gdfReadHeader: reading RPA-accGT.fsgd > FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title > > I used the utility flip to make sure the file was in UNIX format (with > linefeeds). > I then double-checked by reading in the binary codes with Matlab’s fread and > directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). > > Here is the contents of the fsgd file. > > GroupDescriptorFile 1 > Title RP1 > Class Main > Variables LogoAcc NormAcc OrthAcc PhonAcc > Input RPA903 Main0.750.790.770.62 > Input RPA906 Main0.810.810.830.74 > Input RPA907 Main0.871 0.840.83 > Input RPA908 Main0.910.930.950.89 > Input RPA909 Main0.740.950.720.72 > Input RPA910 Main0.850.960.810.79 > Input RPA912 Main0.750.780.730.73 > Input RPA914 Main0.7 0.850.830.81 > Input RPA915 Main0.850.890.750.83 > Input RPA916 Main0.840.920.870.72 > Input RPA917 Main0.830.930.920.83 > Input RPA918 Main0.870.910.790.85 > Input RPA919 Main0.860.960.910.88 > Input RPA920 Main0.840.920.870.84 > Input RPA921 Main0.870.920.880.85 > Input RPA922 Main0.8 0.9 0.9 0.72 > > What’s really driving me to distraction is that a previous version of this > file (with a different set of participants) works fine. I’m attaching both. > RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s > fread, the first 85 characters (first four lines) of both files are identical. > > I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. > > Any help would be greatly appreciated! > > Joe > > > > > Joseph Dien, PhD > Senior Research Scientist > Maryland Neuroimaging Center > University of Maryland, College Park > E-mail: jdie...@mac.com > Cell Phone: 202-297-8117 > http://joedien.com > > ___ > 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. Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com ___ 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] mysterious fsgd format error (not the end of line problem)
Hi, I’m having an fsgd error that has totally stumped me. I’m trying to run the following command to compute the second level statistics: mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C normAcc.mtx I get the error message: Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white gdfReadHeader: reading RPA-accGT.fsgd FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title I used the utility flip to make sure the file was in UNIX format (with linefeeds). I then double-checked by reading in the binary codes with Matlab’s fread and directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). Here is the contents of the fsgd file. GroupDescriptorFile 1 Title RP1 Class Main Variables LogoAcc NormAcc OrthAcc PhonAcc Input RPA903 Main0.750.790.770.62 Input RPA906 Main0.810.810.830.74 Input RPA907 Main0.871 0.840.83 Input RPA908 Main0.910.930.950.89 Input RPA909 Main0.740.950.720.72 Input RPA910 Main0.850.960.810.79 Input RPA912 Main0.750.780.730.73 Input RPA914 Main0.7 0.850.830.81 Input RPA915 Main0.850.890.750.83 Input RPA916 Main0.840.920.870.72 Input RPA917 Main0.830.930.920.83 Input RPA918 Main0.870.910.790.85 Input RPA919 Main0.860.960.910.88 Input RPA920 Main0.840.920.870.84 Input RPA921 Main0.870.920.880.85 Input RPA922 Main0.8 0.9 0.9 0.72 What’s really driving me to distraction is that a previous version of this file (with a different set of participants) works fine. I’m attaching both. RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s fread, the first 85 characters (first four lines) of both files are identical. I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. Any help would be greatly appreciated! Joe RPA-accGT.fsgd Description: Binary data RPA-acc.fsgd Description: Binary data Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com ___ 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] epidewarp.fsl for FSL 5.x
MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm fMRI/RPA003/bold/b0dcmap.nii.gz > On Feb 10, 2016, at 22:58, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > what is your command line? I think there is a rescaling in which it expcts > the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) > scanner. Could that be the problem? > > > On 2/10/16 10:40 PM, Joseph Dien wrote: >> I ran into the same issue: >> >> FSLVersion 5.0.4 >> FSLVerMaj 5 >> FSL Version is 5.0.4, must be 3.X or 4.X >> >> I downloaded the epidewarp.fsl script from the suggested ftp site and >> replaced the existing script. It did indeed fix the version incompatibility >> with FSL 5.x. >> >> I ran into a new problem where it was aborting. After some trouble shooting >> and looking over the documentation, I realized that —-epi is a required >> input without which the script crashes (or is it supposed to be optional but >> there is a bug in the script?). >> >> After including it, it ran much further but then aborted with the following >> error: >> >> ERROR: input phase image exceeds allowable phase range. >> Allowable range is 6.283 radians. Image range is: 12.5633 radians. >> >> This is consistent with the documentation. I’m not sure why the phase image >> exceeds the range though. >> >> It ran without problems with SPM’s FieldMap Toolbox and it is from a >> standard Siemen’s scanner sequence (two magnitude files and one phase >> difference file). >> >> Do I just divide the values by two with something like fslmaths since it >> seems to have exactly double the required range? >> >> Joe >> >>> On Nov 26, 2014, at 21:36, Douglas Greve < >>> <mailto:gr...@nmr.mgh.harvard.edu>gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> It is there again. I don't know what the status if it is in terms of the >>> version. Try it and let me know >>> doug >>> >>> On 11/25/14 4:34 PM, Morgan Hough wrote: >>>> Hi Doug, >>>> >>>> Could you put the epidewarp.fsl script back on your ftp site? I don’t see >>>> it at the link in the archives: >>>> >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl >>>> >>>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl> >>>> >>>> BTW, is the script updated in some way for 5.x or can I can the old script >>>> just be changed to accept 5.x version numbers. >>>> >>>> Cheers, >>>> >>>> -Morgan >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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 >>> <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. >> >> >> >> Joseph Dien, PhD >> Senior Research Scientist >> Maryland Neuroimaging Center >> University of Maryland, College Park >> E-mail: jdie...@mac.com <mailto:jdie...@mac.com> >> Cell Phone: 202-297-8117 >> http://joedien.com <http://joedien.com/> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer&g
Re: [Freesurfer] epidewarp.fsl for FSL 5.x
using spm_read_vols I confirmed that the min and max of the phase difference file is indeed -4096 and 4092 respectively. Further troubleshooting epidewarp.fsl indicates that the script is correctly branching to "# Input is phase difference and magnitude” It then executes the following commands: # Rescale the delta phase to be between -pi and pi. Starts out # at 0 - 4095. Make sure the phase is float precision with _32R set cmd = ($FSLToFloat $dph -sub 2047.5 -mul 0.00153435539 $tmpdir/dph $FSLToFloatFlag ) echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; what echoes to the screen is: fslmaths /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii -sub 2047.5 -mul 0.00153435539 fMRI/RPA003/bold/tmp-epidewarp.90814.fsl/dph -odt float it then aborts at the next section: cp $tmpdir/dph.$ext $tmpdir/dph.preprelude.$ext set dph = $tmpdir/dph if($#epimat) cp $epimat `dirname $dph`/`basename $dph .$ext`.mat # Copy matfile # Do the phase unwrapping (-f for 3D, -v for verbose) set cmd = (prelude -p $dph -a $mag -o $dph -f -v -m $head); echo $cmd |& tee -a $LF $cmd |& tee -a $LF if($status) exit 1; So apparently this rescaling command is not doing so correctly? The script comment says it expects the values to be between 0 and 4095 whereas the file goes to -4096 so perhaps that was a bit more negative than it was expecting? Joe > On Feb 11, 2016, at 11:12, Joseph Dien <jdie...@mac.com> wrote: > > MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag > /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii > --dph > /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii > --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm > fMRI/RPA003/bold/b0dcmap.nii.gz > > > >> On Feb 10, 2016, at 22:58, Douglas Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> what is your command line? I think there is a rescaling in which it expcts >> the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) >> scanner. Could that be the problem? >> >> >> On 2/10/16 10:40 PM, Joseph Dien wrote: >>> I ran into the same issue: >>> >>> FSLVersion 5.0.4 >>> FSLVerMaj 5 >>> FSL Version is 5.0.4, must be 3.X or 4.X >>> >>> I downloaded the epidewarp.fsl script from the suggested ftp site and >>> replaced the existing script. It did indeed fix the version >>> incompatibility with FSL 5.x. >>> >>> I ran into a new problem where it was aborting. After some trouble >>> shooting and looking over the documentation, I realized that —-epi is a >>> required input without which the script crashes (or is it supposed to be >>> optional but there is a bug in the script?). >>> >>> After including it, it ran much further but then aborted with the following >>> error: >>> >>> ERROR: input phase image exceeds allowable phase range. >>> Allowable range is 6.283 radians. Image range is: 12.5633 radians. >>> >>> This is consistent with the documentation. I’m not sure why the phase >>> image exceeds the range though. >>> >>> It ran without problems with SPM’s FieldMap Toolbox and it is from a >>> standard Siemen’s scanner sequence (two magnitude files and one phase >>> difference file). >>> >>> Do I just divide the values by two with something like fslmaths since it >>> seems to have exactly double the required range? >>> >>> Joe >>> >>>> On Nov 26, 2014, at 21:36, Douglas Greve < >>>> <mailto:gr...@nmr.mgh.harvard.edu>gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>> >>>> >>>> It is there again. I don't know what the status if it is in terms of the >>>> version. Try it and let me know >>>> doug >>>> >>>> On 11/25/14 4:34 PM, Morgan Hough wrote: >>>>> Hi Doug, >>>>> >>>>> Could you put the epidewarp.fsl script back on your ftp site? I don’t see >>>>> it at the link in the archives: >>>>> >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl >>>>> >>>>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl> >>>>> >>>>> BTW, is the script updated in some way for 5.x or can I can the old >>>>>
Re: [Freesurfer] epidewarp.fsl for FSL 5.x
I ran into the same issue: FSLVersion 5.0.4 FSLVerMaj 5 FSL Version is 5.0.4, must be 3.X or 4.X I downloaded the epidewarp.fsl script from the suggested ftp site and replaced the existing script. It did indeed fix the version incompatibility with FSL 5.x. I ran into a new problem where it was aborting. After some trouble shooting and looking over the documentation, I realized that —-epi is a required input without which the script crashes (or is it supposed to be optional but there is a bug in the script?). After including it, it ran much further but then aborted with the following error: ERROR: input phase image exceeds allowable phase range. Allowable range is 6.283 radians. Image range is: 12.5633 radians. This is consistent with the documentation. I’m not sure why the phase image exceeds the range though. It ran without problems with SPM’s FieldMap Toolbox and it is from a standard Siemen’s scanner sequence (two magnitude files and one phase difference file). Do I just divide the values by two with something like fslmaths since it seems to have exactly double the required range? Joe > On Nov 26, 2014, at 21:36, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > It is there again. I don't know what the status if it is in terms of the > version. Try it and let me know > doug > > On 11/25/14 4:34 PM, Morgan Hough wrote: >> Hi Doug, >> >> Could you put the epidewarp.fsl script back on your ftp site? I don’t see it >> at the link in the archives: >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl> >> >> BTW, is the script updated in some way for 5.x or can I can the old script >> just be changed to accept 5.x version numbers. >> >> Cheers, >> >> -Morgan > > ___ > 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. Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdie...@mac.com Cell Phone: 202-297-8117 http://joedien.com ___ 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] question about how to calculate COV for MNE
Hi, I have a question about how to calculate the COV for the MNE software. As I understand it from Section 4.17 of the 2.7.3 MNE manual, if one is averaging together COV matrices, one weights them by the number of observations going into each one. I also see from Section 4.17.2 that these are technically not covariance matrices so much as sum-of-squares matrices where the epochs going into each variable has been baseline corrected. Assuming my understanding so far is correct, my question is about how to proceed when making linear combinations of COV matrices, as in a difference wave, as discussed in Section 6.3. Would the following be the correct procedure? Compute the COV separately for the two conditions (say standard and rare oddballs). Subtract the two COV matrices to obtain C0. Then calculate C by dividing by Leff, which in turn is calculated as Leff= (L1*L2)/(L1+L2) where L1 is the number of observations in the first COV matrix and L2 is for the second. But if done in this way, the two COV matrices would not be weighted by their relative sample sizes. So would I also weight them by L1 and L2 during the subtraction, as done for averaging per 4.17? But then what is the purpose of the Leff calculation? Or is the idea that one would calculate a single COV based on both conditions and then one would modify COV by Leff to reflect that the signal-to-noise ratio has been reduced by combining two averages with differing sample sizes? But in the case where both samples equal, say, 10, Leff would end up equalling 100/20=5. Dividing C by 5 seems like too much. Anyway, very confused. Any guidance would be appreciated. Respectfully, Joe Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com ___ 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] missing codecs for mne_make_movie
Hi, I tried to use mne_make_movie but got the following error: Movie production selected (from data)... Scanning /Applications/MNE-2.7.3-3268-MacOSX-i386/lib for plugins Found lqt_mjpeg.so...Getting codec info from module Trying to load /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so... dlopen failed for /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so: dlopen(/Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so, 2): Library not loaded: /opt/local/lib/libjpeg.62.dylib Referenced from: /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so Reason: image not found ERROR: lqt_find_video_codec failed to find codecs! The command was: mne_make_movie --inv RPforMNE-eeg-inv.fif --meas RPforMNE.fif --tmin 0 --tmax 250 --tstep 10 --stc RPforMNE --view lat --mov RPforMNE I’m using MNE 2.7.3 under OS X 10.9.2. Any help would be appreciated. Joe Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com ___ 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] beta weights from FS-Fast analysis
I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr
Re: [Freesurfer] beta weights from FS-Fast analysis
then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way
Re: [Freesurfer] beta weights from FS-Fast analysis
It's a boxcar design so 20.265. mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 17, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you ran mkanalysis-sess, what did you set --refeventdur to? On 07/17/2013 02:50 PM, Joseph Dien wrote: then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files
Re: [Freesurfer] beta weights from FS-Fast analysis
It's a little complicated. Basically there were eight runs, comprising four conditions (me, we, you1, you2) each with two adjoining runs. For the analysis, I merged each of the pairs into a single run and added a nuisance regressor to account for the difference in run means. There were a total of four different kinds of boxcars (AR, CS, EM, MP). So 4x4=16 conditions. There was also a covariate of non-interest to mark the switch point for each boxcar, one for each run, so 20 total. The 7 nuisance regressors are six movement covariates plus one to account for merging eight runs into four (it consists of 1 for the first half and -1 for the second, so the difference in the run means). I'm using the movement covariates from a prior SPM run since ARTdetect (for detecting bad volumes) isn't set up for AFNI style data. From all published accounts the different movement detection routines yield similar enough results that it shouldn't be a problem (consistent with what I found when I compared them for this dataset). You're thinking that collinearity could have reduced the effect sizes? When I correlate the X.X regressor matrix, the 20 predictors don't correlate by more than about .2 at worst. I do see greater correlations with some of the nuisance regressors (as high as the .4 range). Are my betas unusually small for FSFAST analyses? They did come up clusterwise significant at least. Or should I not worry? I'm not sure what to expect from FSFAST analyses. Thanks! Joe On Jul 17, 2013, at 3:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: why do you have 20 conditions? And what are the 7 nuisance regressors? On 07/17/2013 03:54 PM, Joseph Dien wrote: It's a boxcar design so 20.265. mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 17, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: when you ran mkanalysis-sess, what did you set --refeventdur to? On 07/17/2013 02:50 PM, Joseph Dien wrote: then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses? On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The beta's have already been scaled. What do you get if you just beta/runmean ? On 07/17/2013 01:45 PM, Joseph Dien wrote: I implemented the ROI percent signal change formula following the MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too small (on the order of .0002%). Basically the formula is the (beta * peak absolute value of the canonical HRF regressor * 100)/(run mean). No derivatives in this case as it is a boxcar design. I took the mean across all the runs since FSFAST uses the same regressor across the entire experiment (unlike SPM). I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you suggested (where m equals the condition+1). Is it possible that I'm missing something in the scaling here? Especially with a boxcar design, the signal change should be much larger than this for a significant cluster, I think. For example, the peak HRF value for one of the conditions is 0.0092. If the betas are already scaled according to the peak value, then it would come out as .02%, which is more reasonable, although still too small. Thanks for your help with this! Joe On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Oh, right, it is probably not there for subcortical. I don't know what I would have to do to write it out. It won't be something that happens before I get back from HBM. Can you remind me after HBM? doug On 05/31/2013 04:44 PM, Joseph Dien wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly
[Freesurfer] fsfast read_surf bug
I've been trying to use the read_surf.m Matlab function included in the Matlab
folder of 5.3.0 on a Mac under Matlab 2013a.
[vertex_coords, faces] = read_surf('fmcpr.sm5.fsaverage.lh.nii');
Undefined function or variable vertex_coords.
Error in read_surf (line 77)
vertex_coords = reshape(vertex_coords, 3, vnum)' ;
It looks as though the reason is that the magic number evaluates as:
6029568
which does not match either of the numbers it is looking for (which denote
triangle and quad files).
Does that mean that current surface files have a different format and this
function needs to be updated accordingly?
Anyway, is there some way I can load surface files into Matlab?
I looked through the fsfast Matlab functions but it wasn't clear to me if one
of them would do.
The best candidate seemed to be fast_read_curv.m but it yielded too many
numbers so I'm thinking a curvature file is something different.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com//
___
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] FSFAST funcroi-sess problem
/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --trgsubject fsaverage --regmethod surface srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label/lh.cluster-001.label srcsubject = CPA003 trgsubject = fsaverage trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/Volumes/Data/CP1/freesurfer FREESURFER_HOME /Applications/freesurfer Loading source label. Found 952 points in source label. Starting surface-based mapping Reading source registration /Volumes/Data/CP1/freesurfer/CPA003/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white Reading target registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 952 nlabel points Performing mapping from target back to the source label 163842 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label 1367 mri_label2label: Done mri_label2label --hemi lh --srclabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label --outmask /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz --regmethod surface --trglabel /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label --s fsaverage srclabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/target.label srcsubject = fsaverage trgsubject = fsaverage trglabel = /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/Volumes/Data/CP1/freesurfer FREESURFER_HOME /Applications/freesurfer Loading source label. Found 1311 points in source label. Starting surface-based mapping Reading source registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.white Reading target registration /Volumes/Data/CP1/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1311 nlabel points Performing mapping from target back to the source label 163842 Number of reverse mapping hits = 0 Checking for and removing duplicates Creating output /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz Writing label file /Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/junk.label 1311 mri_label2label: Done Ended at Fri Jul 12 18:23:48 EDT 2013 funcroi-sess completed Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] FSFAST funcroi-sess problem
I followed the tutorial:
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh
-fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7
-tpexclude tpexclude.dat
On Jul 12, 2013, at 7:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am
running this ROI follow-up with 5.2.0, could that be a problem? From
the release notes, it didn't look like it would be an issue)
No, that is fine.
Anyway, I've run the following set of commands:
funcroi-config -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-annot
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
cluster-001 -analysis CPA.sm05.lh
funcroi-sess -roi
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/roi.AR-v-CS_HC.HC.th2.neg.cluster1.roicfg
-s CPA003 -d .
I get the following output.
When I checked the results with:
tksurfer fsaverage lh inflated -overlay
roi.AR-v-CS_HC.HC.th2.neg.cluster1.nii.gz -fthresh .5
sure enough, it didn't look right. Instead of the cluster, I got
speckles all over the surface.
I used the Matlab command:
[vertex_coords, faces] = read_surf('lh.white');
and found sure enough that the size of the vertex array was only
143827 whereas mri_info indicates that the ocn file has 163842
When you made the analysis (mkanalysis-sess), do you specify the subject
as self or fsaverage?
doug
Any suggestions what I might be doing wrong?
Thanks!
Joe
---
/Volumes/Data/CP1/fsfast/CPA003
Fri Jul 12 18:23:28 EDT 2013
mri_annotation2label --subject CPA003 --hemi lh --annotation
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
--outdir
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
subject = CPA003
annotation =
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
hemi = lh
outdir =
/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/tmp.funcroi-sess.roi.AR-v-CS_HC.HC.th2.neg.cluster1/label
surface = white
Reading surface
/Volumes/Data/CP1/freesurfer/CPA003/surf/lh.white
Loading annotations from
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143827
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143828
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143829
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143830
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143831
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143832
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 143833
i=, in_array_size=143827
…
MRISreadAnnotationIntoArray: vertex index out of range: 163838
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163839
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163840
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20.neg.sig.ocn.annot
MRISreadAnnotationIntoArray: vertex index out of range: 163841
i=, in_array_size=143827
annot file:
/Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/AR-v-CS/AR-v-CS_HC.wls/HC/cache.th20
[Freesurfer] minor fsfast bug report
In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g., cache.th20.pos.sig.ocn.annot), the names of the clusters take the form: cluster0 cluster-001 cluster-002 … but the last one is of the form cluster6 which is to say, no dash and no zero-padding. I assume they are meant to have a consistent format. Not a big deal, but consistency would be helpful for scripts. Cheers! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] FSFAST mkcontrast-sess with spmhrf 2 question
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks! Joe On Jul 10, 2013, at 12:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea doug On 07/09/2013 10:26 PM, Joseph Dien wrote: It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights? Joe On Jul 9, 2013, at 5:08 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: I tried correlations and the 2nd derivative is definitely not orthogonal. corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) ans = 1. -0. -0.5427 -0.1. -0.0298 -0.5427 -0.02981. I looked at the regressors that SPM generates for the same data: ans = 1.0.04360.1740 0.04361. -0.0226 0.1740 -0.02261. The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power? Thanks for the help! Joe On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
Sorry, not following what you are suggesting? I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf. However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step. On Jul 10, 2013, at 1:21 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless. As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative? doug On 07/10/2013 12:47 PM, Joseph Dien wrote: I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks! Joe On Jul 10, 2013, at 12:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea doug On 07/09/2013 10:26 PM, Joseph Dien wrote: It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights? Joe On Jul 9, 2013, at 5:08 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: I tried correlations and the 2nd derivative is definitely not orthogonal. corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) ans = 1. -0. -0.5427 -0.1. -0.0298 -0.5427 -0.02981. I looked at the regressors that SPM generates for the same data: ans = 1.0.04360.1740 0.04361. -0.0226 0.1740 -0.02261. The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power? Thanks for the help! Joe On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2
Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
Sounds good! Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that. Thanks! Joe On Jul 10, 2013, at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:29 PM, Joseph Dien wrote: Sorry, not following what you are suggesting? I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf. Sorry, it had been a while since I read that paper. I did not know that they had a formulation that included the 2nd derivative. However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step. I don't know how much it will hurt the power. You'd have to look at the efficiency. doug On Jul 10, 2013, at 1:21 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless. As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative? doug On 07/10/2013 12:47 PM, Joseph Dien wrote: I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks! Joe On Jul 10, 2013, at 12:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea doug On 07/09/2013 10:26 PM, Joseph Dien wrote: It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights? Joe On Jul 9, 2013, at 5:08 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: I tried correlations and the 2nd derivative is definitely not orthogonal. corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) ans = 1. -0. -0.5427 -0.1. -0.0298 -0.5427 -0.02981. I looked at the regressors that SPM generates for the same data: ans = 1.0.04360.1740 0.04361. -0.0226 0.1740 -0.02261. The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power? Thanks for the help! Joe On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com mailto:jdie...@mac.com wrote: Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three
[Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] FSFAST mkcontrast-sess with spmhrf 2 question
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: 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/ ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] FSFAST mkcontrast-sess with spmhrf 2 question
I tried correlations and the 2nd derivative is definitely not orthogonal. corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) ans = 1. -0. -0.5427 -0.1. -0.0298 -0.5427 -0.02981. I looked at the regressors that SPM generates for the same data: ans = 1.0.04360.1740 0.04361. -0.0226 0.1740 -0.02261. The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power? Thanks for the help! Joe On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com wrote: Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: 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/ ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ Freesurfer mailing list Freesurfer
Re: [Freesurfer] FSFAST ocn vs. cluster outputs
Ah never mind, I figured it out. tksurfer was automatically setting the range to go from 2-5 so cluster 1 was not getting displayed. So please convert this question to a user suggestion to automatically set the threshold setting to the full range when displaying ocn and cluster overlays (as the default threshold was also the reason the suparmarginal gyrus cluster was not being displayed). Cheers! Joe On Jun 15, 2013, at 12:07 AM, Joseph Dien jdie...@mac.com wrote: I'm getting some puzzling discrepancies when comparing the ocn and the cluster outputs. The summary file indicates there should be five significant clusters (see below). The cluster file only shows four of the clusters, although I'm guessing that the supramarginal one is not being displayed because it did not pass the three-space Bonferroni (so the cluster file only includes clusters that pass that additional correction)? What is really confusing me is that the ocn file does display the supramarginal cluster but does not show the rostral anterior cingulate cluster. How does this work? See attached images below. This is with Freesurfer 5.20 on OS X 10.8.3. Cheers! Joe tksurfer fsaverage lh inflated -aparc -overlay CPA.sm05.lh/CS-v-OTHERS/CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.ocn.nii.gz tksurfer fsaverage lh inflated -aparc -overlay CPA.sm05.lh/CS-v-OTHERS/CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.cluster.nii.gz # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ # CreationTime 2013/05/26-22:53:59-GMT # cmdline mri_surfcluster --in CS-v-OTHERS.wls/osgm/sig.nii.gz --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/pos/th20/mc-z.csd --mask CS-v-OTHERS.wls/mask.nii.gz --cwsig CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.cluster.nii.gz --vwsig CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.voxel.nii.gz --sum CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.cluster.summary --ocn CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.ocn.nii.gz --oannot CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.ocn.annot --annot aparc --csdpdf CS-v-OTHERS.wls/osgm/cache.th20.pos.pdf.dat --cwpvalthresh .05 --o CS-v-OTHERS.wls/osgm/cache.th20.pos.sig.masked.nii.gz --no-fixmni --bonferroni 3 --surf white # cwd /Volumes/Data/CP1/fsfast/secondLevel/CPA.sm05.lh/CS-v-OTHERS # sysname Darwin # hostname megajoe.home # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input CS-v-OTHERS.wls/osgm/sig.nii.gz # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /Applications/freesurfer/subjects # SearchSpace_mm2 65416.6 # SearchSpace_vtx 148649 # Bonferroni 3 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signpos # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 5.96965 at vertex 140670 # Overall min -3.06064 at vertex 162717 # NClusters 5 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 15.970 140670 2209.93 -5.9 40.9 -0.0 0.00030 0.0 0.00060 4223 rostralanteriorcingulate 24.146 49359 1566.01 -4.0 -19.8 35.8 0.00030 0.0 0.00060 3668 posteriorcingulate 33.860 111375446.35-44.6 -37.3 25.1 0.02558 0.02204 0.02911 1037 supramarginal 43.711 128614652.01-24.4 -26.8 -24.3 0.00150 0.00060 0.00240 1539 parahippocampal 53.647 25172 1334.99-48.7 -50.3 17.3 0.00030 0.0 0.00060 2700 inferiorparietal question5.jpg On May 31, 2013, at 4:44 PM, Joseph Dien jdie...@mac.com wrote: It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you
Re: [Freesurfer] beta weights from FS-Fast analysis
On May 31, 2013, at 12:09 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 05/30/2013 04:37 PM, Joseph Dien wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. I don't understand. If you don't have a cluster for a contrast, how are you defining the cluster? From another contrast? Well, what the reviewer told me to do is if I present a figure with a significant cluster for one condition, I should use that as an ROI to calculate the %age signal change for all four conditions and present it as a bar chart as part of the figure. I think she wanted to be able to get a more qualitative sense of the data patterns. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? What do you mean? The cluster p-value is corrected, why do you need the max p and why does it need to be corrected? Well, as I understand it, the drawback of clusterwise statistics is that while it assures you that the cluster passes muster as not being due to random chance (at 95% confidence), it doesn't provide any assurances at the voxel level (or in this case the vertex level) as it is likely that a cluster is composed of both signal and noise and you don't know which part is which. So if a cluster covers both BA44 and BA45 (for example), you can't be sure whether the activation involves BA44, BA45, or both. A voxelwise correction is more conservative but if it provides significance, it does allow for this kind of interpretation. I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? Same as the sign of gamma.mgh Ah, great! I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Some of the BA labels are in FS, but not nearly all of them doug No problem! I worked out that I can use the talairach.nii file made available by the Talairach Daemon folks. Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent
Re: [Freesurfer] beta weights from FS-Fast analysis
On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Only if you specified it when you ran
Re: [Freesurfer] beta weights from FS-Fast analysis
It looks like the corrected vertex p-values (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh and rh spaces. For the subcortical volume-based analysis I don't see the corresponding corrected voxel p-values being available? On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com wrote: On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 05/31/2013 01:49 AM, Joseph Dien wrote: I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug Excellent! Thanks! :) Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com mailto:jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz
Re: [Freesurfer] beta weights from FS-Fast analysis
Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Only if you specified it when you ran isxconcat-sess. Note that the non-scaled values are actually scaled to percent of grand mean intensity. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) Perfect! :) Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer
[Freesurfer] MRIread generating one dimensional vector
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
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] MRIread generating one dimensional vector
Oh duh. Okay, thanks!
Joe
On May 30, 2013, at 5:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
That is a surface file. Each of the 163842 values corresponds to a vertex in
the surface. If you want xyz, you need to load in the surface. You can also
analyze the data in the native space if that would make it easier (but you
can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com mailto:jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
--
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: 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/
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.
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
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] beta weights from FS-Fast analysis
I was able to make more progress so I'm mostly good at this point but I have a remaining question: I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com wrote: Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things: 1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest. The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that. So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest. Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram? This would suffice to give me the %age signal change? I would be doing these computations in Matlab using MRIread. 2) A results table with the headings: Cluster p (FWE corrected) Cluster size Peak Voxel p (FWE corrected) Peak Voxel T Peak Voxel Coords BA Anatomical Landmark I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis. I can get the peak voxel coordinates from the summary files as well. I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information? I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic? I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?). Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up. Cheers! Joe On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/29/13 10:42 PM, Joseph Dien wrote: On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the simple contrast (ces) and as a percent of the baseline at the voxel (cespct, cesvarpct). 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Only if you specified it when you ran isxconcat-sess. Note that the non-scaled values are actually scaled to percent of grand mean intensity. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1
Re: [Freesurfer] beta weights from FS-Fast analysis
On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Joe, On 05/29/2013 01:00 AM, Joseph Dien wrote: I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? For the first level analysis, the first N beta weights correspond to the N conditions in the paradigm file. The rest are nuisance variables. Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. Is that from a group analysis? Yes, that's right. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. If this is from a group analysis, then there should already be a file there (something.y.ocn.dat) that has a value for each subject in the rows and a value for each cluster in the columns. I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? try this plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) Perfect! :) Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: 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/ ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ 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] SUMA and FSFAST
I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ 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] beta weights from FS-Fast analysis
I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? Sorry for all the questions! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ 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] v5.2.0 preproc-sess failing on 3dvolreg.afni
.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com// ___ 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] mkbrainmask-sess
I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesurfer 5.2.0. Is there some way to set up Freesurfer so it'll look in the correct directory? For now I'm copying the critical files to /bin but am hoping there is a better solution. Thanks! Joe It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. doug On 3/25/12 7:05 AM, Kiley Seymour wrote: Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K *From:* Kiley Seymour kiley_seym...@yahoo.com.au *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find/media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # -- Using FSL's BET to Extract Brain-- # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o/tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min0.01 max+infinity binval1 binvalnot 0 ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com
