Re: [Freesurfer] dura flag in fsv5.0.0

Hi Jenifer, did you try giving it to mris_make_surfaces directly? Bruce On Fri, 8 Oct 2010, Juranek, Jenifer wrote: > Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 > echoes) be passed to the latest version of FS? > > Many Thanks, > Jenifer > _

[Freesurfer] Upscaling Functional Data

Using jip-align, we have successfully registered functional data to templates we created from high resolution anatomical scans. To create the templates though, we had to downsample the original scans and lose resolution. Ideally we would like to maintain the resolution of the anatomicals, and ups

[Freesurfer] FW: Extracting coordinates of segmented volume

Hello there, I am just getting started with learning the ways of FreeSurfer. I am hoping you can help explain how (and if) FreeSurfer can give me the information I need. I want to use FS's segmentation to better label optical properties in the head for optical reconstructions. Does FS outp

[Freesurfer] mri_convert with flash - FS 4.5.0 vs 5.0

Hi, We're having trouble using mri_convert as wrapped within mne_flash_bem to create the bem surfaces from our FLASH volumes. The script runs but the inner_skull and outer_skull surfaces that it outputs seem to be rotated, for example if we display the surfaces on the T1 coronal, we see what looks

Re: [Freesurfer] converting IMA files

Hi Doug, I have plenty of disk space available. I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0. Best, Lisa On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve wrote: > Are you running out of disk space? What version of FS are you using? > > doug > > Lisa F. Akiyama wrot

[Freesurfer] error loading averaged brain in QDEC (2)

sorry - on further inspection i changed "Common-Space Subject" to the new averaged subject folder. However, when trying to run analyses, i get an error message: Error in Analyze: Couldn't open file /usr/local/FS5/subjects/FS080920cr/surf/lh.thickness.fwhm10.avgsubject.mgh (where"avgsubject" was t

Re: [Freesurfer] converting IMA files

Are you running out of disk space? What version of FS are you using? doug Lisa F. Akiyama wrote: > Hello, > > I am a Freesurfer newbie trying to use the mri_convert command to > convert IMA format files to either nii or nifti1 format files. > Whenever I run the command I get an error at the very

[Freesurfer] converting IMA files

Hello, I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any hel

Re: [Freesurfer] Creating Brainmaps for Significant Regression

Hi Adam, there is an example of this on the FreeSurfer wiki. Search for FSGD and look for the One Group, One Covariate in the FSGD Example page. doug Adam Nitenson wrote: > Hi Doug, > > Ok this makes sense, I just am unsure as to how I should create my > contrast (.mtx) file. If I have 1 class a

[Freesurfer] error loading averaged brain in QDEC

Hi there, i ran "make_average_subject", and then tried to load the averaged brain to QDEC 1.4. I get this error message: ERROR: MRISread: file '/usr/local/FS5/subjects/avgsubject/surf/lh.avg_thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Wha

[Freesurfer] dura flag in fsv5.0.0

Since the -dura flag is not recognized in FSv5.0.0, how should mempr data (4 echoes) be passed to the latest version of FS? Many Thanks, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

Re: [Freesurfer] motion correction and registration of fMRI data with only one resampling

Sorry, I don't have any code to do this. doug Imri Sofer wrote: > Hello, > please correct me if I am wrong, but when one processes fMRI data he > usually does two spatial processing that required resampling. First he > resamples the functional volume to correct for motion, and then he > takes

[Freesurfer] motion correction and registration of fMRI data with only one resampling

Hello, please correct me if I am wrong, but when one processes fMRI data he usually does two spatial processing that required resampling. First he resamples the functional volume to correct for motion, and then he takes the resampled volume and resample it again to register it to the anatomical sca

Re: [Freesurfer] Creating Brainmaps for Significant Regression

Hi Doug, Ok this makes sense, I just am unsure as to how I should create my contrast (.mtx) file. If I have 1 class and 3 levels of 1 continuous variable (3 allele loads: 0,1,2) how would I structure the contrast file to answer the question, "Is there a significant linear relationship between alle

[Freesurfer] Lab Coordinator Position Available

*_Lab Coordinator Position Available_* Project on Language and Spatial Development (PLSD) and Developmental Cognitive Neuroscience (DCN) Laboratory, Florida International University (Miami, FL) *_Job Description:_* The Project on Language and Spatial Development (directed by Dr. Shannon Pr

Re: [Freesurfer] multiecho MPRAGE (MEMPR)

Hi Mike, not sure, I'd have to look at it. The code wouldn't work as-is, since it uses the ratio of the echoes to get a rough estimate of T2*. cheers Bruce On Fri, 8 Oct 2010, Michael Harms wrote: > > Hello, > Deniz mentioned "T2-SPACE" rather than the multi-echo MPRAGE (memprage). > Can you

Re: [Freesurfer] multiecho MPRAGE (MEMPR)

Hello, Deniz mentioned "T2-SPACE" rather than the multi-echo MPRAGE (memprage). Can you do something similar using the 3D T2-SPACE? cheers, -MH > Hi Deniz, > > yes, it should be in the mris_make_surfaces of that version. You need to > run it with -dura memprage_echo%d.mgz 4 > > where 4 is the