[Freesurfer] Skull as an Object

Good Morning Freesurfer experts, I am trying to get the brain and skull as separate objects for use in blender. Is there any way to retain the skull in freesurfer? If not, would it be possible to retain all the mapping from the skullstrip feature? Best, - Alex _

[Freesurfer] partial volume correction

Hi Freesurfers, We are trying to apply the PVC process to our PET images. We proceeded through step3 as indicated on fswiki, and obtained the files: - gtm.nii - nopvc.nii - mgx.gm.nii How can we obtain the corrected uptake values from these files? Can we obtain a corrected volume file for voxel bas

[Freesurfer] loading multiple saved points

External Email - Use Caution Hello Freesurfer experts, I am wondering if there is any way I can load up multiple points I saved in tkmedit, in either viewing software at the same time. Each time I defined a point, I changed the edit.dat file's name so it would save as individual

Re: [Freesurfer] loading multiple saved points

Not in tksurfer/tkmedit. You can create a point list to be used in freeview. On 07/16/2018 10:50 AM, Yagmur Ozdemir 19 wrote: > > External Email - Use Caution > > Hello Freesurfer experts, > > I am wondering if there is any way I can load up multiple points I > saved in tkmedit, in either

Re: [Freesurfer] loading multiple saved points

External Email - Use Caution Basically an edit.dat file with points in each row? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N. Greve [dgr...@mgh.harvard.edu] Sent: Monday, Jul

Re: [Freesurfer] loading multiple saved points

Yes, or like a control.dat file. You can also create them from scratch directly in freeview On 07/16/2018 11:22 AM, Yagmur Ozdemir 19 wrote: > External Email - Use Caution > > Basically an edit.dat file with points in each row? > > From: freesurfe

Re: [Freesurfer] across-subject overlap

You can also use mri_concat to compute the mean, eg, mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh On 07/13/2018 11:17 AM, Bruce Fischl wrote: > Hi Elisa > > if you only use --s fsaverage, then mri_surf2surf assumes you are > mapping within subject. If you want to map from o

Re: [Freesurfer] Euler number as quantitative quality measure

These numbers are output automatically in the aseg.stats file in v6, eg, # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 17, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 12, unitless # M

Re: [Freesurfer] glmfit-sim FWHM 34?

surface area will be very smooth because of the jacobian correction. For that reason, you do not need to smooth very much (certainly no where near 15mm) On 07/12/2018 04:46 AM, Backhausen, Lea wrote: > > > Hi Doug, thanks for your answer! > > This particular case is surface area. I thought I

Re: [Freesurfer] Petsurfer: Longitudinal GTM stats?

There is nothing special to do in terms of longitudnial for PET. For the MRI, you may want to use the longitudinal stream (depending upon how far apart your time points are and whether you are expecting atrophy or other changes), and then use the closest time point for the GTM and sampling on

Re: [Freesurfer] non-stationarity in CTh maps

By non-stationarity, I assume you are talking about variable smoothness across the cortical surface? We don't correct for it right now, which means that p-values for clusters in low-smoothness regions will be a little conservative and those in high-smoothness regions will be a little liberal.

Re: [Freesurfer] question about the GLM power

I'm not sure what you mean by this. power with clusterwise corrections is quite tricky. You'd have to do a simulation under non-null conditions to see what the true positive rate is On 07/10/2018 11:53 AM, Ting Li wrote: > External Email - Use Caution > > Hi Freesurfer Expert, > > How

Re: [Freesurfer] Exvivio stats?

This is something new in 6.0. The "thresh" version is the label thesholded such that the likelihood of a vertex being in the given label is at least 10%. On 07/10/2018 03:04 AM, Jason Bruggemann wrote: > > > Hello, > > > I ran a batch in order to tabulate the FreeSurfer stats from our data >

Re: [Freesurfer] Monte Carlo simulation - vertex wise threshold question

Yes, 3 is p<.001, which is converted to a z before thresholding the map. Note that we are trying to push people to use permutation instead of MC. On 07/09/2018 05:22 PM, Dincer, Aylin wrote: > > > Hi FreeSurfer experts, > > > I am trying to understand the Monte Carlo Z simulation in FreeSufer >

Re: [Freesurfer] question about the GLM power

External Email - Use Caution Hi Douglas, Thanks for your response. I did the monte carlo simulation. Could you give me any instructions about how to perform a simulation under non-null conditions? Thanks a lot! Best, Ting > On Jul 16, 2018, at 12:15 PM, Douglas N. Greve wrote

Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting

There is nothing to plug and play. I'm not even sure about the theory, but I'd guess you'd use something like a repeated measures anova or simply average the two controls together and do a simple paired test. Do you know what the theory would be behind your statitical test? On 07/09/2018 01:27

Re: [Freesurfer] Extract Value from pcc.nii.gz

what values do you want to extract? You can load the file into matlab with pcc = MRIread('PCC.nii.gz'); The group analysis is the same as for task-based analysis On 07/09/2018 10:00 AM, Wang, Zhuonan wrote: > Hi FS Experts, > > I am doing the FAST analysis. After I finished the isxconcat-sess

Re: [Freesurfer] After v.5.3 to v.6.0 update octave set up doesn't work

Oh, I see now. It never failed for me because matlab is defined in my path. I think the right logic is if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then ... I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 Can you try it out? On 07/06/2018 01:20 PM, Pat

Re: [Freesurfer] Monte Carlo threshold p-values

1.3 is not a z value, it is -log10(.05) On 07/06/2018 10:15 AM, Dincer, Aylin wrote: > > > Hello FreeSurfer experts, > > > In the FreeSurfer wiki page regarding multiple comparisons > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons > ) under "Simulation", it mentions

Re: [Freesurfer] fthresh documentation

The values are -log10(p). So if you want to view voxels with p<.01, then set the threshold = 2 On 07/05/2018 11:10 PM, srishti goel wrote: > > > Hello, > > I am trying to decide what fthresh values should I be using for > viewing my mkda maps on surface. Where could I find some theoretical >

Re: [Freesurfer] Visualization of surface based analysis results

You might not be doing anything wrong. Try going to those vertices on the surface and see if they are part of the cluster. Those vertices are the places that have the highest significance. You can have it report the centroid if you prefer. On 07/05/2018 03:20 PM, John Anderson wrote: > >   

Re: [Freesurfer] Multiple comparison - permutation

My guess is that something is going wrong with the backgrounding. Try running it without the --bg option. You can run it with a few (eg, 100) iterations just to see if it finishes. On 07/05/2018 12:34 PM, Ting Li wrote: > > External Email - Use Caution > > Dear Freesurfer Experts, > >

Re: [Freesurfer] recon-all -s 1 exited with ERRORS

can you send the /home/regal/Data/Subjects/test_old_version/mysubject1/mri/mri_nu_correct.mni.log file? On 07/05/2018 08:30 AM, Bernardo Regal wrote: > > External Email - Use Caution > > Hi Bruce, > > I attach the file recon-all.log. > > Thanks > > Mailtrack >

Re: [Freesurfer] Multiple comparison - permutation

External Email - Use Caution Hi Douglas, I just try your suggestion. It gives me information like the following. What does the design matrix stands for? Thanks. Ting ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to d

Re: [Freesurfer] fthresh documentation

External Email - Use Caution Thanks a lot Douglas. Does this stand for all commands in freesurfer where we put threshold value such as mri_binarize and mri_vol2surf? Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab U

Re: [Freesurfer] question about the GLM power

It is different than the MC simulations. When you run mri_glmfit, specify the --save-yhat option. This will create a file called yhat.mgh which will be used as the non-null basis of the simulation. You will have to add noise to this file and analyze through mri_glmfit and mri_glmfi-sim and see

Re: [Freesurfer] Multiple comparison - permutation

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm?highlight=%28permutation%29 On 07/16/2018 02:15 PM, Ting Li wrote: > > External Email - Use Caution > > Hi Douglas, > > I just try your suggestion. It gives me information like the > following. What does

Re: [Freesurfer] question about the GLM power

External Email - Use Caution Thanks for your detail information. I will try it now. Ting > On Jul 16, 2018, at 1:26 PM, Douglas N. Greve wrote: > > It is different than the MC simulations. When you run mri_glmfit, > specify the --save-yhat option. This will create a file calle

Re: [Freesurfer] Exvivio stats?

Correction: each label was thresholded to have the same area as the average area across ex vivo subjects. The thresholds are different based on how spread out the distribution is. On 07/16/2018 01:35 PM, Douglas N. Greve wrote: > > This is something new in 6.0. The "thresh" version is the label