[Freesurfer] How to maximize the number of subjects on a machine?

Dear Freesurfers, I am currently running 4 subjects, each on a separate x11 window. With 19 subjects at hand and subsequent manual editing, I can't resist the temptation to open more x11 terminals and to submit more jobs. However, how do I know that I max out the machine's computing power? Hard d

[Freesurfer] cerebellum

Dear all, it is just a simple question. How reliable are the cerebellum WM and cortex volumes? There is any kind of manual editing for this structure? Thank you so much, Clelia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

Re: [Freesurfer] How to maximize the number of subjects on a machine?

Hi Ye, if you have 4 cores, then it will not speed anything up to run more than 4 at one time (it will actually slow things down to run more at once). doug On 7/4/13 7:41 AM, ye tian wrote: Dear Freesurfers, I am currently running 4 subjects, each on a separate x11 window. With 19 subje

Re: [Freesurfer] How to maximize the number of subjects on a machine?

Hi Ye you have 4 cores, so running more than that won't help (the others will just slow down). You might start running out of ram with more than 4 in any case, but I think 4 should fit (Nick can correct me if I'm wrong) cheers Bruce On Thu, 4 Jul 2013, ye tian wrote: Dear Freesurfers, I

Re: [Freesurfer] cerebellum

Hi Clelia the relaibility of the cerebellar segmentations depends critically on your coil and landmarking. If you landmark too high then the cerebellum can be noisy as it is far from isocenter. The other problem with the cerebellum is that many of the foliations cannot be resolved at 1mm (or ev

Re: [Freesurfer] cerebellum

Hi, thank you so much. C. Il giorno 04/lug/2013 14:44, "Bruce Fischl" ha scritto: > Hi Clelia > > the relaibility of the cerebellar segmentations depends critically on your > coil and landmarking. If you landmark too high then the cerebellum can be > noisy as it is far from isocenter. The other

Re: [Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3

Hi Sal, not sure why the nu correction is crashing for you. can you check how the FS/RZ_1484_POST_FS.long.RZ_1484_Base/mri/orig.mgz and rawavg.mgz look? Also make sure the talariach.xfm is correct in the template (base). Next time please send the recon-all.log file (from the subject's scripts

Re: [Freesurfer] How to maximize the number of subjects on a machine?

Dear Doug and Bruce, Thank you very much! Sincerely, Ye On Thu, Jul 4, 2013 at 8:42 AM, Bruce Fischl wrote: > Hi Ye > > you have 4 cores, so running more than that won't help (the others will > just slow down). You might start running out of ram with more than 4 in any > case, but I think 4 sho

[Freesurfer] Contrast matrix for per-vertex regressor

Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting for age and gender that worked perfectly. However, when I tried to make a between groups comparison, I ran into an error

Re: [Freesurfer] Painting voxels vs. adding control points

1) The right panel shows the aseg voxels. The surfaces are the same in L and R panels. 2) What do the surrounding slices look like? It may be that the WM surface "fills in" more as you go along. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-bo

Re: [Freesurfer] Painting voxels vs. adding control points

Hi Ye one is surface-based and the other is voxel-based. It's impossible to tell which is correct from just a single slice. If you upload the entire subject directory to our ftp server and give us the voxel coords of that point we will take a look cheers Bruce On Thu, 4 Jul 2013, ye tian wro

Re: [Freesurfer] Contrast matrix for per-vertex regressor

Hi Elisa, can you send the command line and full terminal output? doug On 7/4/13 11:50 AM, Elisa Scariati wrote: Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting fo

Re: [Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3

Thank you Martin. Turns out that our cluster had crashed and killed the task due to hard drive space limitations. Its all fixed now and have been able to go through the tutorial at http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial for a single subject with 3 time points. One qu

[Freesurfer] Software Engineering positions in NGS, Novartis, Cambridge, MA {Disarmed}

The Novartis Institutes for BioMedical Research is the global pharmaceutical research organization for Novartis. For our new Next Generation Diagnostics (NGDx) group being launched at our global headquarters in Cambridge, MA, we are seeking two Software Engineers. Sr. Software Engineer, Sequenc

[Freesurfer] Software Engineering positions in NGS, Novartis, Cambridge, MA

The Novartis Institutes for BioMedical Research is the global pharmaceutical research organization for Novartis. For our new Next Generation Diagnostics (NGDx) group being launched at our global headquarters in Cambridge, MA, we are seeking two Software Engineers. Sr. Software Engineer, Sequenc

Re: [Freesurfer] Painting voxels vs. adding control points

Dear Bruce and Freesurfers, I am sorry that I am asking you this question, but I have trouble uploading my directory to freesurfer's ftp. I have tried the following 1. put /Path_to_subject/subjectDirectory > local: not a plain file 2. put -r /Path_to_subject/subjectDirectory