Re: [Freesurfer] REPOST: registering longitudinal data to template

So, because mris_preproc does not already try to fit the data we use that for LMEs because that's where different model fits are then specified. Thanks a lot! - Ursprüngliche Mail - Von: "mreuter" An: "Freesurfer support list" Gesendet: Donnerstag, 24. März 2016 18:18:58 Betreff: Re: [

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

Hi Martin, When doing cross-sectional analysis on a longitudinal data set and the qdec table is ordered as followed: fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 Why does the presmoothing not have to be: recon-all -s d115a.long.d115_base -qcache recon-all -s d120a

[Freesurfer] binary mask for the gm wm and csf

Dear Freesurfer experts, I am wondering if the gm/wm/csf binary masks (with of course the cerebellum) could be extracted from the recon-all freesurfer results. Any idea/suggestion will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien d

Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

Hi Tilak this one (attached) worked pretty well on one of the datasets you sent me. Run recon-all with -expert xopts.txt and the usual other args. I would be very cautious about interpreting results though. For example there is very little gray/white contrast in multiple regions such as periro

[Freesurfer] Visualising regional values on the surface

Hi, I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to. It seems

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

Hi Kasper, because that is the way it is designed. Whenever recon-all runs on longitudinal data, it needs to know where the cross and base are (just in case that this info is needed somewhere). So the correct call is the one with the -long telling it that this is a longituidnal run (and not j

Re: [Freesurfer] REPOST: registering longitudinal data to template

Yes, exactly. On 03/29/2016 04:36 AM, Clara Kühn wrote: > So, because mris_preproc does not already try to fit the data we use that for > LMEs because that's where different model fits are then specified. > Thanks a lot! > > - Ursprüngliche Mail - > Von: "mreuter" > An: "Freesurfer suppo

Re: [Freesurfer] Visualising regional values on the surface

Hi Kirstie, You could write your own CLUT file with the color corresponding to the correlation you want to show? Just open up the file and play with the values in the color columns. Then simply load the color table in Freeview and use it to visualize the annotation. There are of course other ways

Re: [Freesurfer] Visualising regional values on the surface

Hi Kirstie, Here's an example of how to do this in PySurfer: http://pysurfer.github.io/examples/plot_parc_values.html Hope that helps, Michael On Tue, Mar 29, 2016 at 8:08 AM, dgw wrote: > Hi Kirstie, > > You could write your own CLUT file with the color corresponding to the > correlation you

[Freesurfer] Cognitive & Brain Sciences PhD opening call, University of Trento, Italy

Dear All, We are pleased to announce the opening of a call for 14 fellowships for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing in November 2016 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields

Re: [Freesurfer] Visualising regional values on the surface

Thank you Michael! I <3 Pysurfer. (and freesurfer of course!) The *real* goal is to integrate the code that I've written as a wrapper around pysurfer to show regional values (exactly as you suggest) with BrainNet which can show the network nicely on top of fr

Re: [Freesurfer] Visualising regional values on the surface

Hi Kirstie, Nibabel has a write_annot function that should work: http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot Best, Michael On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker wrote: > Thank you Michael! I <3 Pysurfer. > > (and freesurfer of cour

Re: [Freesurfer] Visualising regional values on the surface

Brilliant - I think that's probably my friend! Thanks again everyone for all the help! Kx On 29 March 2016 at 16:50, Michael Waskom wrote: > Hi Kirstie, > > Nibabel has a write_annot function that should work: > http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#

Re: [Freesurfer] Surface area of an fsaverage label

what is your command line? On 03/28/2016 05:50 PM, Jaiashre Sridhar wrote: > Hello, > > I have used label_area to compute the surface area of a desikan label > on fsaverage. Is the correction factor taken into account during > computation with this function? > > Thanks, > Jaiashre. > > > ___

Re: [Freesurfer] Left right flip surfaces

hmmm, we don't have a caudate surface. How did you make it? mris_reverse just changes the sign on the x coordinate. This might not show up "properly" in freeview; it does not surprise me that it could appear to be 1 voxel off. This was not the intended use of this program. xhemireg will not hel

Re: [Freesurfer] DODS vs DOSS for correlation analysis

Hi Cassie, DOSS has a bug in QDEC so please do not use it. I thought we disabled it. What version are you using? If you want to compare DODS vs DOSS, then you'll have to use the command-line stream (mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim) doug On 03/28/2016 08:10

Re: [Freesurfer] Left right flip surfaces

Hi Doug, I used the caudate surface I created as an example as I was testing the command out. I do not plan to use this command for the caudate. It just happened to show the same issue as the earlier post ( https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Fre

Re: [Freesurfer] Left right flip surfaces

You should use xhemireg. Just changing the sign of the x coordinate will not be meaningful. On 03/29/2016 12:49 PM, Ajay Kurani wrote: > Hi Doug, >I used the caudate surface I created as an example as I was testing > the command out. I do not plan to use this command for the caudate. > It

Re: [Freesurfer] Surface area of an fsaverage label

Douglas, This is my command line: label_area lh fsaverage lh.temporalpole Output: bash-3.2$ label_area lh fsaverage lh.temporalpole reading /Volumes/project/fsaverage/surf/lh.smoothwm... adjusting for group surface area 1.31 (82220 / 62822) fsaverage: lh.temporalpole - 512.352 square mm Thanks,

Re: [Freesurfer] Surface area of an fsaverage label

Hi Jaiashre, please include previous correspondences so I know the context thanks doug On 03/29/2016 02:37 PM, Jaiashre Sridhar wrote: > Douglas, > > This is my command line: > label_area lh fsaverage lh.temporalpole > > Output: > bash-3.2$ label_area lh fsaverage lh.temporalpole > reading /Volume

Re: [Freesurfer] Surface area of an fsaverage label

, Jaiashre. Re: [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46383.html> 2016-03-29<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20160329&o=newest&f=1> Thread<https://

Re: [Freesurfer] Surface area of an fsaverage label

yes, it looks like it is correcting then. Bruce On Tue, 29 Mar 2016, Jaiashre Sridhar wrote: Douglas, This is my command line: label_area lh fsaverage lh.temporalpole     Output: bash-3.2$ label_area lh fsaverage lh.temporalpole reading /Volumes/project/fsaverage/surf/lh.smoothwm... adjusti

[Freesurfer] Tracula problems (creating symbolic link)

Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am u

Re: [Freesurfer] Tracula problems (creating symbolic link)

Hi Efrat - This appears to be a virtual machine problem: https://communities.vmware.com/thread/312591?tstart=0 There are some solutions suggested in that thread. I'm wondering if using a relative instead of an absolute path for the symlink works, i.e., ln -sf dwi.nii.gz /mnt/hgfs/linux_share