[Freesurfer] Repost: Make liberal ROI masks

Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overla

[Freesurfer] Supratentorial Volume Versus Sum of Parts

Hello, We're trying to make multiple comparisons between FreeSurfer outputs on severely atrophied brains and controls. Some of the comparisons are regions of interest, like hippocampal volume or the volumes of regions in the frontal lobe, but we've also been making comparisons with supratentorialn

[Freesurfer] Correction with white-matter-points

Dear FreeSurfer Team! We have a question concerning corrections with white-matter-points. We are currently working on a T1 data set. After performing Freesurfer-Segmentations several days ago, we corrected the intensity normalization in small regions (e.g. Gyrus temporalis superior) with WM-po

Re: [Freesurfer] Correction with white-matter-points

Hi Pawel does this happen in both versions? If so, upload a bad subject and we will take a look cheers Bruce On Tue, 14 Jul 2015, Wrobel, Pawel wrote: > Dear FreeSurfer Team! > > We have a question concerning corrections with white-matter-points. > > We are currently working on a T1 data set. A

Re: [Freesurfer] Supratentorial Volume Versus Sum of Parts

Hi Chris, I would generate some scatterplots of some of the various "summary" type measures available in aseg.stats.  That will quickly show you if you indeed have some pronounced outliers that don't fall near the regression line. e.g., compute a 4 x 4 panel scatterplot of CortexVol, SubCo

[Freesurfer] Dynamic causal modeling

Hi list, I'm performing the functional connectivity analysis by FAST.Next, I'd like to perform spectral dynamic causal model analysis (SPM, Friston et al. 2015; Crone et al. 2015) on FS-FAST output.Have you any suggestion in this matter?Thanks, Stefano __

Re: [Freesurfer] Dynamic causal modeling

I've never done DCM so I don't know how one would proceed. Maybe someone else on the list can make a suggestion. doug On 07/14/2015 12:13 PM, std...@virgilio.it wrote: > Hi list, > > I'm performing the functional connectivity analysis by FAST. > Next, I'd like to perform spectral dynamic causal m

Re: [Freesurfer] Repost: Make liberal ROI masks

There is not an easy way to do that, though Thomas might want to chime in. I would probably use the code that generates the wmparc (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels On 07/14/2015 08:18 AM

Re: [Freesurfer] Fwd: [FreeSurfer] aparc+aseg.mgz unkown voxels

Are they "Unknown" or "ctx-?h-unknown" ? On 07/13/2015 07:22 PM, joseph veliz wrote: > Hello, > > Just checking if this email thread was still being tracked. > > Thanks so much > > Joseph > -- Forwarded message -- > From: *joseph veliz* > > Date: Th

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Hi, I'm getting a new error mri_tessellate: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Linux dws-9 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u1 x86_64 GNU/Linux For this particular library for Debian, there is *.so.5 and *.so.7

Re: [Freesurfer] Supratentorial Volume Versus Sum of Parts

For a given subject, if you sum up the parts that go into the supratentoria do you get the volume reported for the supratentoria? On 07/14/2015 12:12 PM, Harms, Michael wrote: > > Hi Chris, > I would generate some scatterplots of some of the various "summary" > type measures available in aseg.st

Re: [Freesurfer] fast_selxavg3.m

not sure what to tell you. Is there a critical number that causes it to fail? Eg, 400? Or a particular contrast name? I assume that none of the contrast names have a space in them. On 07/09/2015 10:06 AM, Xiaomin Yue wrote: > Hi, > > I am using v5.3 fsfast to analyze a function data. The sexlav

[Freesurfer] mri_vol2vol

Hi Freesurfer experts I am always a little confused with the registration matrices from tracula output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon space, do we use the matrix anatorig2diff.bbr.dat? mri_vol2vol --mov //dmri/dtifit_MD.nii.gz --targ //mri/brainmask.mgz --reg /

Re: [Freesurfer] fast_selxavg3.m

Thanks for responding.  There is no contrast name with space in them.  I will test if there is a critical number causing fail.    Xiaomin _ From: Douglas N Greve Sent: Tuesday, July 14, 2015 1:15 PM Subject: Re: [Freesurfer] fast_selxavg3.m To:

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

I will have to investigate why this error is occurring as it shouldn't be happening. But regardless a quick fix should be to symlink to the *.so.7 as that is more likely to be backwards compatible: $> cd /usr/lib64 $> sudo ln -s libnetcdf.so.7 libnetcdf.so.6 -Zeke On 07/14/2015 12:59 PM, Ione

Re: [Freesurfer] mri_vol2vol

Anastasia would know better but she is away for a week or two. But looking at it, I would say that your command line is correct. The registration does map the anat to the diffusion space, but mri_vol2vol understands this and simply inverts the matrix. You should just verify it for yourself by l

[Freesurfer] Registering Myelin Water Fraction Images to Freesurfer Longitudinal Template

Hello, We are looking to use the the Freesurfer longitudinal pipeline automatic parcellation to assist with automatic ROI segmentation for our Myelin Water Fraction (MWF) analysis. Typically, we use a combination of FSL commands to register the first echo of the T2 sequence to the brain anatom

Re: [Freesurfer] Registering Myelin Water Fraction Images to Freesurfer Longitudinal Template

Hi, your commands look right. It could be that your second image (WMI_J01_MWFmap.nii) is not in the same space as the first (WMI_J01_WIP_T2W_GRASE_scratch_SENSE_4_1x1A.nii). In that case applying the transform from step 1 will map it somewhere but not at all close to the target. If that is the

Re: [Freesurfer] Registering Myelin Water Fraction Images to Freesurfer Longitudinal Template

Also, for the second step you cannot use the standard robust register (as that is mono-modal). So for that you should really use bbregister. You can try the x-modal robust register tool, by passing --cost NMI or --cost robent (which will be very slow), but since your target is a fully process