[Freesurfer] funcroi commands

Hi Freesurfers, I would like to make sure I am using the funcroi commands correctly for anatomical and functional ROI analyses (using the aseg to anatomically constrain), and I have some questions about the commands. If I want to extract the average percent signal change in the whole left amyg

Re: [Freesurfer] funcroi commands

the label file instead of seg? Thanks! Emily On Dec 12, 2013, at 11:36 AM, Douglas N Greve wrote: > > On 12/12/2013 10:08 AM, Emily Boeke wrote: >> Hi Freesurfers, >> >> I would like to make sure I am using the funcroi commands correctly for >> anatomical a

Re: [Freesurfer] funcroi commands

; > where ces.nii.gz is the output of isxconcat-sess for the analysis/contrast > you want to extract the data from > > doug > > On 12/12/2013 02:04 PM, Emily Boeke wrote: >> Hi Doug, >> >> Thanks for your response. >> >> I have another question rel

Re: [Freesurfer] funcroi commands

rage/mri/orig.mgz > > instead > doug > > On 12/13/2013 09:17 AM, Emily Boeke wrote: >> Hi Doug, >> >> I tried the mri_label2vol command but the mask created does not match the >> label. The mask is shifted so that it's posterior to the label (by ~15 >> sli

[Freesurfer] ROI analyses

Hi Freesurfers, I have some questions about ROI analyses. 1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I spec

Re: [Freesurfer] ROI analyses

--src subject fsaverage --trglabel ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod surface --hemi lh Thanks, Emily On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote: > > On 03/28/2014 08:51 AM, Emily Boeke wrote: >> Hi Freesurfers, >> >> I

Re: [Freesurfer] ROI analyses

it creating one segmentation out of my label and one out of the rest of the cortical surface? Also, could you please address the 3rd question from the email below? Thanks so much! Best, Emily On Mar 28, 2014, at 12:37 PM, Douglas N Greve wrote: > > On 03/28/2014 12:04 PM, Emily Boeke

[Freesurfer] convert MNI152 mask to label file

Hi all, I want to convert a mask I made in MNI152 space using the Harvard-Oxford Atlas into a (subcortical) label file so that I can run an ROI analysis using func2roi-sess. Does anyone know what commands I would need to do so? Thanks! Emily___ Free

[Freesurfer] Fwd: [All] freesurfer and centos6 updates!

Hi all, I would like to save copy of the CentOS5 release of Freesurfer in my group's work space as described in the email below. The link in the email that is supposed to explain this doesn't work; could someone please let me know how to do this or point me to another webpage that explains it?

[Freesurfer] Monte Carlo simulation: Talairach coordinates

Hi All, I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates

flowed can you send the file? On 06/25/2013 10:08 AM, Emily Boeke wrote: > Hi All, > > I'm running Monte Carlo simulations on functional data, and the coordinate > information outputted in the cluster.summary file isn't making sense. Usually > the coordinates for th

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates

Any thoughts on why this file turned out this way? Thanks! Emily On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote: > Sure, here it is: > > # Cluster Growing Summary (mri_volcluster) > # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ > # cwd > /autofs/c

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates

This was the command I ran: mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 1 2 HvL.SBQ.2.1.pos --stim-sign pos On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote: > Hi Emily, what is your mri_glmfit-sim command line? > doug > > > On 06/28/2013 02:40 PM, Em

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates

4.5 Emily On Jul 2, 2013, at 11:45 AM, Douglas N Greve wrote: > > Hi Emily, what version of FS are you using? > doug > > > On 07/02/2013 11:41 AM, Emily Boeke wrote: >> Hi Doug, >> >> Sorry to be overly persistent, but I just wanted to make sure y

[Freesurfer] Different results in surface and volume analyses

Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in t

Re: [Freesurfer] Different results in surface and volume analyses

ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer@nmr.mgh.harvard.edu Message-ID: <948e8fdf-

[Freesurfer] FDR in different hemispheres

Hi Freesurfers, I have a contrast that produces comparable activation in both hemispheres. But when I set the threshold using FDR in the Configure Overlay Display window, the threshold is set to 5.1 for left hemisphere and 3.3 for the right hemisphere, leaving significant clusters only in the

[Freesurfer] Paradigm files

Hi Freesurfers, I am doing some analyses for an experiment where paradigm files were automatically generated by Matlab during stimulus presentation. The script was designed to make paradigm files for an older version of freesurfer, so the files only have 2 columns. I am going to adjust these fi