Re: [Freesurfer] .license file on Mac

Hi Serena It means you don't have write permissions in the directory. You should invoke pico like sudo pico /Applications/freesurfer/.license ..it'll ask for your password and save successfully, provided you have permissions. -Krish On Aug 1, 2010, at 8:32 AM, sere f wrote: Hi All,

Re: [Freesurfer] Error when doing Talairach transformation

Hi Feng, have you looked at the talairach transform (talairach.xfm) to see if it is indeed incorrect? If so, you should correct it manually using tkregister2 (there is a tutorial for this on our wiki) cheers Bruce On Mon, 2 Aug 2010, Xue, Feng wrote: Dear Freesurfer experts, I'm

Re: [Freesurfer] Non-linear correlations

There is nothing to fit nonlinear parameters. You can do some simpling things. Eg, if you believe that thickness is changing exponentially with time, th = exp(-a/t), then you can take the log of the thickness so that log(th) = -a/t, then fit for a. doug mmoayedi wrote: Hi Everyone, I was

Re: [Freesurfer] Comparing results of independent experiments

This is with FSFAST? You can run isxconcat-sess on both analyses. For version4.X, this will create output files like lh.ces.mgh. If you keep the subject order the same for both analyses, then you can use mris_calc to take the difference between them (ie, a paired analysis). You will then have

Re: [Freesurfer] Freesurfer and AFNI - 3dmaskave problems

The freesurfer results are going to be in the anatomical space (256^3, 1mm^3). Your functional results will be in a different space (eg, 64x64x30 or whatever), so you'll need to put the functionals into the anatomical space or the other way around. You'll need a registration matrix between the

[Freesurfer] Errors with the Cut Plane feature in tksurfer

I've been trying to implement the cut plane feature to get an occipital patch but every time my tksurfer crashes and I get this message: % tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr-stride' failed. Abort I can't figure out if I am doing something

[Freesurfer] Question re: Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction

Hi, My question is in reference to the recommended high res structural scans (T1) for optimal FS reconstruction. Within the Documentation section of the FS wiki, the page titled Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction http://martinos.org/~andre/ lists two MPRAGE

Re: [Freesurfer] Question re: Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction

Hi Andrea, what receive coil are you using? Bruce On Mon, 2 Aug 2010, Andrea L. Gold wrote: Hi, My question is in reference to the recommended high res structural scans (T1) for optimal FS reconstruction. Within the Documentation section of the FS wiki, the page titled Suggested Morphometry

[Freesurfer] preproc-sess error

Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find

Re: [Freesurfer] preproc-sess error

which version are you using? swood...@nmr.mgh.harvard.edu wrote: Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout

Re: [Freesurfer] preproc-sess error

Additional info: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 NMR Center info (/space/freesurfer exists): Does this give you the info

Re: [Freesurfer] preproc-sess error

If you're going to continue to use stable3 then you will need to have an old version of FSL (the ip program is an FSL program from several versions ago). Can you start using the new version of FSFAST? doug swood...@nmr.mgh.harvard.edu wrote: Additional info: FREESURFER_HOME:

[Freesurfer] Undefined Variable

Hi! I may be missing something basic but when I enter: recon-all -s bert -autorecon1 I get: FREESURFER_HOME: Undefined variable. But I have already ran: setenv FREESURFER_HOME /Applications/freesurfer so that FREESURFER_HOME should be defined, right? I'm not sure if I'm missing something

Re: [Freesurfer] .license file on Mac (Krish Subramaniam)

Hi Krish, thank you for your advicenow it works!!! Serena. -- Message: 7 Date: Mon, 2 Aug 2010 03:16:09 -0400 From: Krish Subramaniam kr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] .license file on Mac To: sere f serena...@gmail.com Cc:

[Freesurfer] intracranial volume in qdec

Hi experts, I was wondering it is possible to account for total intracranial volume in qdec statistical calculations, and if so, where do I find that under the 'general stats data tables' Thanks, Philip York UCDenver Radiology ___ Freesurfer mailing

[Freesurfer] ROI-questions

Hi All, I use QDEC to compare two groups differences, find some regions with significant differences. Considering this regions as ROI, i want to extract the mean thickness of ROIs for every subject, then compute the correlation between mean thickness and some scales . My questions is :