[Freesurfer] Recon-all and CT/SPECT images

Hi, I try to use the command "recon-all" with my CT and SPECT images, like my IRM, but I have this error message: talaraich failure detection: ERROR talarach_afd: talarach transform ... thanks marie ___ Freesu

Re: [Freesurfer] problem of correction for multiple comparisons in surface based analyses

I'd like to make a correction on my statement below. FDR is not biased by having dependence in the data (though it may make it more variable). Thanks to Mike Harms and Tom Nichols for pointing this out. doug Douglas Greve wrote: > Hi Petra, if the data are independent, then large amounts of smo

Re: [Freesurfer] ROI-based fixed effect analysis

Hi Qi Zhu, sorry for the delay (always a good idea to just repost if a few days go by). To answer your question, yes you can do a FFx analysis that way, ie, average the gamma and gammavar across the ROI, then t=gamma/sqrt(gammavar) and use the DOF from the dof.dat file in the mri_glmfit output

Re: [Freesurfer] reg-feat2anat problem

That would be the same as specifying highres.nii.gz as the intermediate registration (--int to bbregister). Is this what you tried? doug Cris Lanting wrote: > Dear all, > dear Doug, > > >> If you have a partial FOV, then it >> will probably fail. You can test this by running bbregister outsi

Re: [Freesurfer] Longitudinal comparison of thickness data

Hi Jonathan, sorry, missed your mail completely. Anyway, in 5.1 there will be tools to do all this automatically for you (also for more than 2 time points). Everything below is only for 2 time points. Also about your questions: Something is wrong with you data, you should have the ?h.shpere.reg

[Freesurfer] ROI-based fixed effect analysis

Hi, Sorry for posting again. I just want to get the average ces and cesvar values across subjects (fixed effect) for a specific ROI, and then run some statistics on them. Can I just average the gamma and gammavar that in the osgm folder after I ran the voxel-based ffx group analysis in my group da

Re: [Freesurfer] reg-feat2anat problem

Which version of freesurfer are you running? At one point, reg-feat2anat was dependent on the feat registration, but "now" it is not. I don't know whether you fall into the "now" category. If you have a partial FOV, then it will probably fail. You can test this by running bbregister outside of

[Freesurfer] reg-feat2anat problem

Dear all, I'm having a slight problem with reg-feat2anat to transform functional data (FSL) to anatomical (Freesurfer) in that the resulting transformation seems completely wrong. What I've done so far is the following: 1) run FEAT including the normal FEAT registration (which I know fails due to

Re: [Freesurfer] problem of correction for multiple comparisons in surface based analyses

Hi Petra, if the data are independent, then large amounts of smoothing does not affect the validity of the statistics (it helps cluster-wise correction). If the data are not independent, then the problem is that the voxel-wise p-values will be inaccurate (causing cluster

Re: [Freesurfer] Fwd: bbregister bug? with init-spm option--flips left and right

As Michael says, with spm8 you have to use nifti. When 4.5 was written, spm8 was not around (or not used much), so this was never a problem. One way you can get around it is to modify your copy of spmregister (in $FREESURFER_HOME/bin). There is a line in there that indicates the format to use

[Freesurfer] problems with set gaLinkedVars(vertexset)

Hello Freesurfers, I have a little problem using a tcl script with tksurfer. I want to load the pial surface to a cuted patch. So I used the following comandline: tksurfer fsaverage lh inflated -patch testpatch -tcl test.tcl test.tcl include the following lines: set gaLinkedVars(vertexset) 3

Re: [Freesurfer] Problem with Freesurfer

Hi Bruce, > thanks for your answer. In fact, I wrote: > -recon-all -i home/pmod/Bureau/freesurfer/subjects/Marie/image(n).nii -subjid > image(n) > in order to analyse my images. I created folders for each patient, but when I > try to open these (tkmedit) I can't recover ... I have new folders

[Freesurfer] [Re] Problem with freesurfer

Hi Bruce, > thanks for your answer. In fact, I wrote: > -recon-all -i home/pmod/Bureau/freesurfer/subjects/Marie/image(n).nii -subjid > image(n) > in order to analyse my images. I created folders for each patient, but when I > try to open these (tkmedit) I can't recover ... I have new folders

Re: [Freesurfer] Problem with freesurfer

Hi Marie what is the error? And what do you want to do with the PET and SPECCT images? You would only give recon-all the anatomical (T-weighted) images. The others you would probably want to register with bbregister. cheers Bruce On Mon, 28 Mar 2011, Marie ERESUE wrote: > > Hi, > I'd like to

[Freesurfer] problem of correction for multiple comparisons in surface based analyses

Hi, This is probably a question for Doug Greve, Which is to most preferably correction for multiple comparisons when investigating surface based cortical thickness changes between groups in smoothed data. Furthermore subjects between groups are related in other words not independent from each