Re: [Freesurfer] Error - Need help

Is there any way that after this change , the execution will start exactly where it failed . Or do I need to start all over again Regards - Original Message - Darshan, copy the fsaverage subject from $FREESURFER_HOME/subjects to your $SUBJECTS_DIR n. The information in this e-mail is

[Freesurfer] setting a cluster size and thresholding in tksurfer

Hi I am displaying the fMRI results in tksurfer. Is there a way in tksurfer to set a cluster size (for eg 50 vertices) and display only those activated regions which have bigger clusters than 50 ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] FreeSurfer Lab seeks Research Assistant

Please forward to anyone you think may be interested: Position involves working in a fast-paced Computational Neuroimaging Lab. The lab develops and maintains software for MR image analysis and works primarily in a UNIX environment. The lab is also responsible for several in vivo and ex vivo (h

Re: [Freesurfer] mri_compile_edits

Mike, Hi, what you describe is a bug in mri_compile_edits. I've posted a fixed version for linux here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/mri_compile_edits N. On Thu, 2012-02-02 at 14:51 -0600, Michael Harms wrote: > Hi Nick, > > Why does mri_compile_edit

[Freesurfer] Defects in freesurfer output

Hello, I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data view

Re: [Freesurfer] Reposting: Clusters by Multiple comparison

What I have listed as fa.nii.gz should be the same file that you passed to mri_glmfit with the --y option. doug Antonella Kis wrote: > Dear Doug, > > THANKS SO MUCH for your help. My last questions is: I suppose the --i > fa.nii.gz is an input file. What should be my input in thi scase if > for

Re: [Freesurfer] Question about ?h.sulc and ?h.curv

Thanks, Bruce and Matt. bestJingDate: Wed, 8 Feb 2012 11:53:44 -0500 From: fis...@nmr.mgh.harvard.edu To: m...@ma-tea.com CC: freesurfer@nmr.mgh.harvard.edu; mj_com...@hotmail.com Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv oops, thanks Matt Bruce On Wed, 8 Feb 2012, Matt Glasse

Re: [Freesurfer] Reposting: Clusters by Multiple comparison

Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary The fa.avg.dat will have a table of data. Each row will be

Re: [Freesurfer] Reposting: Clusters by Multiple comparison

Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \  

Re: [Freesurfer] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark

Hi Mark, I talked to Allison and you should be able to rerun 5.1 on top of 5.0 but do NOT use the -clean flag (as it will delete your edits). Just make sure you make a backup copy of your data before doing this. Another thing: manual edits to the brainmask are treated differently from most manual

Re: [Freesurfer] Question about ?h.sulc and ?h.curv

oops, thanks Matt Bruce On Wed, 8 Feb 2012, Matt Glasser wrote: I think Bruce meant: "the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation." Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:frees

Re: [Freesurfer] Question about ?h.sulc and ?h.curv

I think Bruce meant: "the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation." Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent:

Re: [Freesurfer] Question about ?h.sulc and ?h.curv

They are computed from the ?h.white surface. The ?h.curv is the spatially smoothed mean curvature, and the ?h.curv is the integrated dot product of the movement vector with the surface normal during inflation. Therefore the curv is a local differential measure that will highlight small scale st

Re: [Freesurfer] Reposting: Clusters by Multiple comparison

Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to

[Freesurfer] Reposting: Question regarding DTI group analysis

Dear Experts, I completed my FA group analysis and I expect my FA to be larger in controls versus patients (based on the uncorrected results). I corrected by multiple comparisons using: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign pos \ --cwpv

[Freesurfer] Reposting: Clusters by Multiple comparison

Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh  with the clusters summary so as you recommended I am running the mri_volcluster --in G

Re: [Freesurfer] volume smoothing

Holger, you might also play with the fill threshold (--fillthresh) option. In the end, it can't be any smoother than your voxel size of course. doug Bruce Fischl wrote: > Hi Holger > you can try dilating and eroding the label (a morphological close) > > cheers > Bruce > > On Wed, 8 Feb 2012, Klei

Re: [Freesurfer] volume smoothing

Hi Holger you can try dilating and eroding the label (a morphological close) cheers Bruce On Wed, 8 Feb 2012, Klein, Holger wrote: Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to amelior

Re: [Freesurfer] Verifying ICV in FS5

Hi Jeff it looks pretty far off. Typically you want the surfaces to match the general shape of the brain cheers Bruce On Tue, 7 Feb 2012, Jeff Sadino wrote: Thank you Martin and Nick for the clarification about how to verify the talairach transformation in the newer FreeSurfers.  I think I

Re: [Freesurfer] mris_divide_parcellation

Thank you Bruce, the parcellation looks good, as you say, I think that it doesn't affect me. yolanda 2012/2/7 Bruce Fischl > Hi Yolanda > > does the resulting parcellation look ok? I think that's a small bug that > may not have any effect on you (there will just be extra, unused color > table e

[Freesurfer] volume smoothing

Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to ameliorate the smoothness of my volume but could not find a solution. Could anyone give me an advice to cope with that problem? Any help is gre

Re: [Freesurfer] autmatic image with panel of hemisphere made by script

Hi Thanks. Python was the first programing languages that I learned along with Java. Cheers Knut Jørgen On 08. feb. 2012 06:42, Michael Waskom wrote: Hi, On the off chance that you are comfortable with Python, you may find that PySurfer provides a more pleasant