Re: [Freesurfer] FW: FW: Functional group analysis

Hi Bruce, I will. Thanks! Best, Silas Date: Sun, 28 Jun 2015 13:20:30 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Functional group analysis Hi Silas Doug (who normally answers this kind of question) is on vacation. Can you repost

Re: [Freesurfer] Preproc-sess failed

Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the suffix i686 instead of i386, so try   sudo yum remove libXp.i686 By removing the 32-bit version you essential ensure only the 64-bit version is available when the application tries to load libXp. Hope that works. My

[Freesurfer] 2D sphere co-ordinates

Hi Freesurfer Experts! I'm looking to find the 2D co-ordinates for a vertex in the fsaverage surface I can find their 3D volume co-ordinates using read_surf but I'd like the 2D coordinates. I'll explain: I would like to study properties of the inflated STS. For each of the vertices I can find the 3

Re: [Freesurfer] 2D sphere co-ordinates

Hi Jonathan sure. The sphere.reg acts as a lookup table for this. For the vertex you want, just compute it's spherical coordinates from the sphere.reg file and you should be all set. cheers Bruce On Mon, 29 Jun 2015, jonathan oron wrote: Hi Freesurfer Experts!I'm looking to find the 2D co-

[Freesurfer] Fwd: Recon-all different execution time for same subjects

Dear freesurfer experts, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capabi

[Freesurfer] Recon-all error

Hi,I keep getting an error when I run recon-all and can’t figure out what is wrong. I would really appreciate your help. I’ve attached the log file.Thank you so much,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General Hospit

Re: [Freesurfer] finding local extrema in surface data

Not the fastest approach, but for each vertex, you could find the neighbors and then test if the vertex is the maximum. There are matlab functions for getting the list of neighboring vertices. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurolo

Re: [Freesurfer] too much white matter

Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2)

[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)

Dear FS experts I extracted the vertex indices of several subjects. But unfortunately I did not extract the corresponding Vertex RAS values. Is there a command to translate the Vertex Index into a Vertex RAS so that I do not have to scroll through all the subjects again? I would like to script

Re: [Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)

Hi Christopher mris_info --v will print out the surface RAS coords of the vertex (plus some other stuff that you probably don't care about) Bruce On Mon, 29 Jun 2015, Milde, Christopher wrote: Dear FS experts   I extracted the vertex indices of several subjects. But unfortunately I

Re: [Freesurfer] FW: FW: Functional group analysis

How have your processed the fMRI data? If you have beta maps in the native functional space, then you'll need to run bbregister on a template from the native space, then run mri_vol2surf, the mri_concat, then mri_glmfit doug On 6/28/15 1:17 PM, Silas wrote: Dear all, Can anyone help me with

[Freesurfer] SMS3 pre-processing

Hi all, We are currently using SMS3 scans for our resting state data. In order to preprocess this scan, we are using the preproc-sess command which includes slice-time correction. Since SMS3 is a multi-slice sequence that is interleaved, do we need to use a different slice-time correction speci

Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it w

Re: [Freesurfer] help on mris_preproc

Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: > > Hi Doug, > > Thanks. > > I can see that the “mris_preproc” command reads the header information > in “register.dat”. > > I set the “.” as the $SUBJECTS_DIR, and thus it seems that > “mris_preproc” cannot locate

Re: [Freesurfer] Timecourses In freesurfer

you can do something like this mri_vol2surf --mov func.nii.gz --hemi lh --reg register.dat --projfrac 0.5 --o func.lh.mgh tksurfer subject lh inflated -t func.lh.mgh doug On 06/13/2015 03:27 AM, jonathan oron wrote: > Hi, > In tksurfer I would like to be able to see the timecourse (Percent >

Re: [Freesurfer] Retinotopic mapping

Hi try starting out on this web page http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis On 06/16/2015 02:04 PM, lucas hosse wrote: > > Hi FreeSurfer experts, > > I have to construct the retinotopic mapping of angle and eccentricity. > > I have created with FreeSurfer the

Re: [Freesurfer] SMS3 pre-processing

I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might not need it for 1.15s TR. How long are your stimuli? On 06/29/2015 04:41 PM, Rodriguez-Thompson, Anais wrote: > Hi all, > > We are currently using SMS3 scans for our resting state data. In order to > preprocess this scan, w

Re: [Freesurfer] Functional group analysis

I'm not sure what you mean. Why not use isxconcat-sess? Is your data already on the surface in fsfast? On 06/19/2015 08:26 AM, Silas wrote: > Dear FreeSurfer team, > > I'm currently doing a functional group analysis using FreeSurfer by > following your tutorial: > https://surfer.nmr.mgh.harvard

Re: [Freesurfer] Extracting values from GLM Clusters

You can probably use the csdbase.y.ocn.dat file. Run mri_glmfit-sim --help to get more info On 06/19/2015 10:18 AM, Andrew Schoen wrote: > Hi, > > I have run some analyses using the GLM and cluster wise correction for > multiple comparisons outlined here: > http://freesurfer.net/fswiki/FsTutori

Re: [Freesurfer] mni152reg

What version of mni152reg are you using? On 06/22/2015 05:17 AM, OKADA NAOHIRO wrote: > Hello Freesurfer Experts, > > I am trying to create a registration matrix from subject space to MNI152: > > mni152reg --s bert > > However, this error appeared: > > fslregister --mov > /usr/local/fsl/data/stan

Re: [Freesurfer] SMS3 pre-processing

Hi Doug, Thanks for your reply. It's for our resting scan, so we don't have any stimuli present. Best, Anais Sent from my iPhone > On Jun 29, 2015, at 6:46 PM, Douglas N Greve > wrote: > > I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might > not need it for 1.15s T

Re: [Freesurfer] SMS3 pre-processing

oh, then I certainly would not worry about it. FC is really slow, so STC won't make much of a difference On 06/29/2015 07:01 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > Thanks for your reply. It's for our resting scan, so we don't have any > stimuli present. > > Best, > Anais > > Sent fr