Re: [Freesurfer] dt_recon error

Thanks Doug, In the dt_recon help, > The bvalues are in a simple text file, one for each direction > (including b=0). The bvectors (gradient directions) are also in a > simple text file with three components on each row. These also include > the b=0 values. There must be as many rows in the bval

Re: [Freesurfer] dt_recon error

Doug, Never mind. I think I just figured it out!0 Yuko On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote: > Thanks Doug, > > In the dt_recon help, > >> The bvalues are in a simple text file, one for each direction >> (including b=0). The bvectors (gradient directions) are also in a >> simple

Re: [Freesurfer] run preproc-sess with -nomc

Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and o

Re: [Freesurfer] mri_ca_register from virtual box

*No.. it doesn't work. The RAM is not enough. We abandoned that machine.. Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 GHz with 8 GB of RAM. And.. IT WORKS! We completed the autorecon1, autorecon2 and autorecon3 stages with succes!! We use a virtual box under Windows 7 ba

Re: [Freesurfer] mri_ca_register from virtual box

Ops.. I'm sorry.. the selecting bar of our virtual box changes from green to red at 5.4 GB (not 4 GB.. i was wrong!) but if i allocate more than 3.5 GB it does not start! Thanks! L. Busti 2011/12/12 Lorenzo Busti > *No.. it doesn't work. The RAM is not enough. > > We abandoned that machine..

[Freesurfer] Converting thickness maps to vtk

Hello, I was wondering if there is a command like mris_convert to create a thickness map in vtk format (either on the white or pial surface) ? Thanks, -- Navid Shiee Ph.D. Candidate Laboratory of MEDical Image Computing (MEDIC) Image Analysis and Communication Laboratory (IACL) Johns Hopkins Un

Re: [Freesurfer] tracula and snow leopard: can't allocate region / memory error

Hi Scott - Sending to the list is always good so that others can find it in the archives when they have similar problems. Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have the right dimensions/frames? a.y On Mon, 12 Dec 2011, Scott Hayes wrote: Thanks for the prom

[Freesurfer] tracula failed to find header file for -t

Hi, I have received the following error message (copied from trac-all.log file). fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri

[Freesurfer] FA interpretation from cvs registration for group analysis

Dear Lilla, I will appreciate a lot if you can help me understand what is the meaning of the results after running after running mri_cvs_register and the GLM group analysis. More exactly, I followed all the instructions from the webpage: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diff

Re: [Freesurfer] tracula failed to find header file for -t

Hi Scott - Which version of FSL are you using? I cannot replicate this behavior of fslstats on our data. Thanks, a.y On Mon, 12 Dec 2011, Scott Hayes wrote: > Hi, > I have received the following error message (copied from trac-all.log file). > > fslstats -t /Volumes/RAID_4TB/futhink/nc331_reco

Re: [Freesurfer] tracula failed to find header file for -t

Hi, I'm using FSL 4.1.4 On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki wrote: > > Hi Scott - Which version of FSL are you using? I cannot replicate this > behavior of fslstats on our data. > > Thanks, > a.y > > > On Mon, 12 Dec 2011, Scott Hayes wrote: > >> Hi, >> I have received the followi

Re: [Freesurfer] tracula failed to find header file for -t

Ok, I just checked the 4.1.4 version of fslstats, and indeed it doesn't have the -t option. We're using version 4.1.5. On Mon, 12 Dec 2011, Scott Hayes wrote: Hi, I'm using FSL 4.1.4 On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki wrote: Hi Scott - Which version of FSL are you using?

Re: [Freesurfer] Converting thickness maps to vtk

Navid, Are you needing to convert the thickness.mgh file or a surface (e.g., ?h.pial, ?h.white, etc) file to .vtk? We've used mris_convert many times to create .vtk files from FS surfaces. The command is fairly straightforward. mris_convert /?h. /?h..vtk I'm not sure you can convert the th

Re: [Freesurfer] Converting thickness maps to vtk

What I need is basically both. I used the mris_convert command similar to your suggestion to get the inner and pial surfaces before. Now what I need, is the thickness values on each coordinate of the surface in vtk format. Do you know how to create this? Thanks, On Mon, Dec 12, 2011 at 3:47 PM,

Re: [Freesurfer] Cluster-wise correction for multiple comparisons: customized Zstats data

If you have a full-width half-max (FWHM) for your analysis, you can convert your z into a sig (-log10(p)*sign(z)), then run mri_surfcluster. You should give it a CSD file that corresponds to your FWHM, the sign of the contrast you are interested in, and the voxel-wise threshold. The CSD files a

Re: [Freesurfer] convert surface label on to functional image

Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz file for this. This file has cortical labels already in the volume, you just need to map them to your functional space, something like mri_label2vol --aparc+aseg --temp functemplate.nii --reg register.dat --o aparc+aseg.fmri.nii do

Re: [Freesurfer] run preproc-sess with -nomc

Hi Evelina, why don't you do the whole analysis in SPM then map the results to the surface? doug Thunell Evelina wrote: > > Hi Douglas, > > I do most of my analysis in matlab and SPM. For this one part of my > experiment - it's a retinotopic mapping that I will use to ensure that > my ROIs are

Re: [Freesurfer] multiple overlay - tksurfer

Hi Vin, why do you say it's a 50% threshold? What is the 1.nii data? What colors do you want? doug vin . wrote: > Dear FreeSurfer list, > Greetings! > > a newbie to freesurfer. > -- would like to overlay tracking group results (Sum from all > subjects)-(from FSL ) in the inflated lh & rh. -- > >

[Freesurfer] problem using an older environment...

Hello folks, I'm trying to reanalyze some old data that was originially analyzed in freesurfer version 4. Because the code I was using was from 4.0, I set the environment to 4 before starting, then made a new analysis and a few new contrasts. When I tried to run selxavg3-sess with the following

Re: [Freesurfer] Cluster-wise correction for multiple comparisons: customized Zstats data

Thank you, Doug! Found the CSD file. Just want to make sure that I picked up the correct one: mult-comp-cor/fsaverage/lh/cortex/fwhm08/abs/th23/mc-z.csd corresponding to a FWHM=8, voxel-wise z-thr=2.3, the sign is both pos and neg? Actually, the zstats were converted from pearson correlations, whic

Re: [Freesurfer] problem using an older environment...

The version 4 analysis from mkanalysis-sess is not compatible with version 5. You will have to run mkanalysis-sess again. doug On 12/12/11 6:48 PM, Joe Andreano wrote: Hello folks, I'm trying to reanalyze some old data that was originially analyzed in freesurfer version 4. Because the code I