[Freesurfer] Hippocampal volumes measured by Freesurfer 4.3.0 vs 4.5

Hi, I would like to merge two datasets containing volumetric data from two different versions of Freesurfer (4.3.0 and 4.5). I am only interested in looking at volumes of hippocampus, entorhinal cortex, and whole brain. A cursory look at the release notes for versions 4.4 and 4.5 suggests th

[Freesurfer] problem with selxavg3

Hi, I am encountering a memory allocation error with selxavg3-sess and I am not sure how to get around it: Here is the lines that I am running mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm allpara.par -designtype event-related -funcstem fmc -motioncor -runlistfile FHPDM_runlist.txt -inor

[Freesurfer] tkmedit: Extending white matter and pial surfaces

Hi Freesurfers, When looking at the surfaces in tkmedit, I noticed that quite a bit of the tip of the temporal lobe was not included in pial/wm surfaces. I need to extend both surfaces. In what order does one do the edits? Does one paint in wm voxels first or pial first? Thanks. Michelle

[Freesurfer] about correction of inhomogeneity

Hi All, I am now trying to do inhomogeneity correction for T1 images. I find that there are two commands: nu_correct and mri_nu_correct.mni in Freesurfer. I am not sure about the difference between these two commands. To me, they seem to be the same I would be glad if someone could answer my

Re: [Freesurfer] Freesursfer versions and Linux CentOS versions

you can use the centos4 build with centos5.6. its what we use in our center (the centos4 freesurfer build on our centos5.6 platforms). the centos5 build of freesurfer is not publicly distribution (that is, not listed on the download page) because the centos4 build works fine with centos4, and the

[Freesurfer] DTI and Fresurfer

Dear All, I would like to do DTI analysis on my subjects data. I finished the pre-processing using recon-all and also I used GLm for the group study. Can you please let me know how I can do DTI analysis using FSL in Freesurfer? What steps I need to follow? Many thanks, Antonella __

[Freesurfer] Freesursfer versions and Linux CentOS versions

I have a few questions related to Freesursfer versions and Linux CentOS versions. We have we processed some data (i.e. generated surfaces using -autorecon 1 -autorecon2, and then GM and WM surface-based volumes using mris_anatomical_stats and mris_wm_volume, respectively), using the build 'f

Re: [Freesurfer] Fw: fsaverage

Are you setting the cwp to .01? The cwp controls the threshold for cluster significance. The number after "--cache" controls the cluster-forming threshold Antonella Kis wrote: > Hi Doug, > > Since running mri_glmfit-sim will do a correction by multiple > comparison (I suppose is doing a Mont

Re: [Freesurfer] free surfer group analysis how to get cache-in thickness.fwhm10.fsaverage ?

Hi Xian, you need to run recon-all again with -qcache -measure thickness cheers Bruce cheers Bruce On Fri, 26 Aug 2011, xian zhang wrote: Dear Freesurfer: I am new in freesurfer. I have done recon-all for my subjects and the results are good. however in this tutorial the commands between r

Re: [Freesurfer] Fw: fsaverage

Hi Doug, Since running mri_glmfit-sim will do a correction by multiple comparison (I suppose is doing a  Monte Carlo to remove areas that are not statically significant) I wonder why I still get clusters with p>0.01? Do I need to apply FDR before -sim? Thank you for your time and help. Antone

[Freesurfer] free surfer group analysis how to get cache-in thickness.fwhm10.fsaverage ?

Dear Freesurfer: I am new in freesurfer. I have done recon-all for my subjects and the results are good. however in this tutorial the commands between recon-all the mirs-process are missing. Please advice what I have to after recon-all to have thickness.fshm10.fsaverage available? Appreciate yo

Re: [Freesurfer] Correlation cortical thickness and lgi

Hi You should take a look at the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. The next step is to design your correlation or group difference by switching tab and let qdec design contrast vector and fsgd files. The next step before you have finished the

[Freesurfer] Correlation cortical thickness and lgi

Dear freesurfer experts, I have finsihed my lgi analyzes with qdec. In the next step I want to make a correlation between lgi and cortical thickness. Is this possible with qdec and if it is how can I do that? Best regards and thanks a lot. Daniel Klein _

[Freesurfer] Reference for tracula and enable mpi in tracula?

Hi I am having trouble finding all reference to Tracula in the wiki. Could you please add them. I read in (Postelnicu, Zollei et al. 2009) that combined surface and volumetric algorithm could use MPI . Is the same true for tracula? Knut J Postelnicu, G., L. Zollei, et al. (2009). "Combi