Re: [Freesurfer] downsampling 4D volume

2012-01-09 Thread Zhen Zonglei
I use FEAT from FSL to do the fMRI analysis. But the data were unpacked with the Freesurfer unpacksdcmdir. Zonglei Zhen On Tue, Jan 10, 2012 at 1:49 PM, Douglas Greve wrote: > what software package are you using to do the fMRI analysis? > doug > > > On 1/9/12 9:19 PM, Zhen Zonglei wrote: >

[Freesurfer] About ROI edit

2012-01-09 Thread zhang mingxia
Hi, every one, I have a question about ROI edit. Is there a way with which we can define spherical ROIs with exact radius. Now, I just know the manual method. But I want to define a ROI with exact Talairach Coordinate and radius. Are there bottons when I input Talairach Coordinate and radius in t

Re: [Freesurfer] mri_glmfit-sim error

2012-01-09 Thread zhang mingxia
Thank you very much!! On Wed, Jan 4, 2012 at 11:55 PM, zhang mingxia wrote: > Hi, every one, > > I just run the flag mri_glmfit-sim for Surface-based Correction for > Multiple Comparisons as below: > > mri_glmfit-sim \ > --glmdir lh.Chinese_fastreading_thickness.glmdir \ > --cache neg 1.3 \ > --c

Re: [Freesurfer] downsampling 4D volume

2012-01-09 Thread Douglas Greve
what software package are you using to do the fMRI analysis? doug On 1/9/12 9:19 PM, Zhen Zonglei wrote: Thank you very much, Doug. In my case, the fMRI data is in LPS orientation, but the MNI152 in FSL are in LAS orientation. To overlay our fMRI results to MNI152 template, I wonder I shoul

Re: [Freesurfer] downsampling 4D volume

2012-01-09 Thread Zhen Zonglei
Thank you very much, Doug. In my case, the fMRI data is in LPS orientation, but the MNI152 in FSL are in LAS orientation. To overlay our fMRI results to MNI152 template, I wonder I should reorient the fMRI data to LAS orientation, am I right? When I use mri_convert to do the task, it only conve

[Freesurfer] trac-all update

2012-01-09 Thread Anastasia Yendiki
Hi all - There is an updated version of trac-all here that's recommended for all users: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/trac-all This version switches on an option in the implementation that had not been fully tested at the time of the release las

Re: [Freesurfer] GLM design question

2012-01-09 Thread Douglas N Greve
Hi Martijn, yes, that is a good thing to do! doug Martijn Steenwijk wrote: > Hi Doug, > > Thanks for your reply again. It's getting more and more clear now. > > I've however one question remaining, which is regarding the correction > for sex. What I did not tell (my fault ;-) ), is that 75% of t

Re: [Freesurfer] mri_glmfit-sim error

2012-01-09 Thread Douglas N Greve
Hi Mingxia, use --cache 1.3 neg you have it the other way around doug zhang mingxia wrote: > Hi, every one, > > I just run the flag mri_glmfit-sim for Surface-based Correction for > Multiple Comparisons as below: > > mri_glmfit-sim \ > --glmdir lh.Chinese_fastreading_thickness.glmdir \ >

Re: [Freesurfer] How to export non spatial normalization fMRI images?

2012-01-09 Thread Douglas N Greve
You can take fmcpr.up.sm4.fsaverage.lh.nii.gz and export it back to the native functional space with mri_surf2vol, something like mri_surf2vol --surfval fmcpr.up.sm4.fsaverage.lh.nii.gz --hemi lh --fillribbon --reg register.dof6.dat --template template.nii.gz --o fmri.surf.nii.gz and mri_surf2vo

Re: [Freesurfer] downsampling 4D volume

2012-01-09 Thread Douglas N Greve
Hi Zonglei, it should be fixed for version 5. Note that you should not use --out_orientation unless the orientation information is actually wrong. I think FSL has some tools to re-orient. doug Zhen Zonglei wrote: > Hi, Doug; > > Is the bug still in FS5.0. > > When I used mri_convert to re

Re: [Freesurfer] Building from source without GUIs

2012-01-09 Thread Malcolm Tobias
Nick, While configure now works, I'm getting a build-time error. It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide: https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide Is this a new depe

Re: [Freesurfer] Building from source without GUIs

2012-01-09 Thread Malcolm Tobias
Nick, With the new configure.in, --disable-all-apps works as advertised. Thanks! Malcolm On Monday 09 January 2012 13:36:37 Nick Schmansky wrote: > malcolm, > > can you try using the attached configure.in? you will need to > run ./setup_configure, which will create a new configure script. >

[Freesurfer] Non_FA Group Analysis study

2012-01-09 Thread Antonella Kis
Dear FS team, I wonder if I can use my results from the mri_cvs_register to do a non_FA group analysis, more exactly I am interested on the mean diffusivity (adc.nii from dt_recon). I hope I don't need to run again the registration again. Since from the significant map I can only find/ tells

Re: [Freesurfer] Building from source without GUIs

2012-01-09 Thread Nick Schmansky
try addong --disable-tcltk-apps to your configure command line. --disable-all-apps appears to be broken. send me your config.log file if it still doesnt work. n. On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote: > Nick, > > Tcl/Tk is installed on the system under /usr/bin so I can't e

Re: [Freesurfer] Building from source without GUIs

2012-01-09 Thread Malcolm Tobias
Nick, Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path. Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a c