Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a

[Freesurfer] Stats for Yeo and Choi Parcellations

Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I noticed that the Yeo 2011 annot files are a

Re: [Freesurfer] Extracting BOLD from a flattened surface

Hello Doug, Sorry for the confusing and long email, I am interested in extracting the raw BOLD signal from a processed 4D nifit file. After registering the functional to ${subject}/mri/orig.mgz and generating the registration file, I proceeded to convert the functional image to the same dimensions

Re: [Freesurfer] no recon button

Hi Sarah no, I don't think it is. The recon edit for example will set voxels to "1" not "0" when erase so that we can keep track of them. If you are editing as part of the recon-all stream you are better off using it than just plain voxel editing. cheers Bruce On Wed, 4 May 2016, Burke,Sarah E

[Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estima

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

I think I have a fix for this if you want to edit your version of fast_selxavg3.m Change this line: if(~isempty(analysis) & DoGLMFit & strcmp(flac.designtype,'event-related')) To: % Check to make sure that each task ev as the same number % of regressors before saving the h.dat file evtaskind =

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

On 05/04/2016 04:08 PM, S.V.Shepherd [work] wrote: > I can /also /confirm that it ran fine when the big matrix was changed > from taskreg to nuisreg, so we can probably consider the issue > resolved. I suspect the problem is with multi-column taskregs. If I > want to have the regressors track

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

I can *also *confirm that it ran fine when the big matrix was changed from taskreg to nuisreg, so we can probably consider the issue resolved. I suspect the problem is with multi-column taskregs. If I want to have the regressors tracked equivalently across runs, I'd need to add them as taskregs, o

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

I can confirm that having taskregs with a paradigm works. For example, I've run successfully analyzed the following: mkanalysis-sess -native -event-related -refeventdur 10 -paradigm aboutFace.para -nconditions 13 -TR 2. -rlf rlf_aboutFace_subjvid -funcstem fm2tas1 -mask brain -analysi

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

I don't think it is going to work to have both a -taskreg and a paradigm. You should be able to model it as a nuisance regressor. The fact that it may be the same across runs won't make much of a difference. doug On 05/04/2016 03:33 PM, S.V.Shepherd [work] wrote: > mkanalysis-sess -native -eve

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

mkanalysis-sess -native -event-related -refeventdur 10 -paradigm aboutFace.para -nconditions 13 -TR 2. -rlf rlf_aboutFace_subjvid -funcstem fm2tas1 -mask brain -analysis a_401_Av_s_task_fmov_bgrnd_icadenoise -taskreg taskreg_face__zmove.dat 1 -taskreg taskreg_face__bgrnd.dat 1 -taskr

Re: [Freesurfer] External ROI for fcseed

You actually need the ROI in the anatomical volume space (ie, the "conformed" space of 1mm3, 256^3). If you have a binary (ie, 0,1) mask of your ROI called roi.mgz, then use -seg roi.mgz -segid 1 On 04/28/2016 08:22 PM, Martin Juneja wrote: > Hi all, > > I am trying to perform step-3 from the

Re: [Freesurfer] Extracting BOLD from a flattened surface

Sorry, can you tell me what you are trying to do? You just want a number of time points -by- number of vertices file? Then mri_vol2surf should do that for you. Flattening is irrelevant for this as it only changes the xyz coordinate of the vertex and not the vertex identity. doug On 04/29/2016

Re: [Freesurfer] surface-based spatial smoothing model

Thank you! 2016-05-04 21:09 GMT+02:00 Douglas N Greve : > you can reference this one > http://www.ncbi.nlm.nih.gov/pubmed/17011792 > > > Smoothing and cluster thresholding for cortical surface-based group > analysis of fMRI data. > > Hagler DJ Jr > < > http://www.ncbi.nlm.nih.gov/pubmed/?term

Re: [Freesurfer] error in fast_selxavg3 (line 1248)

Can you send your mkanalysis-sess command? Can you also send one of the regressor files? And can you send the full selxavg3 terminal output? On 05/04/2016 02:46 PM, S.V.Shepherd [work] wrote: > I've modified an analysis to include a vector of noise time courses > estimated using ICA. Since IC ef

Re: [Freesurfer] Resting-state fcMRI analysis with GLM

We don't usually use mri_glmfit for this kind of thing. If you want to do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option). On 05/04/2016 10:17 AM, Eun Young Choi wrot

Re: [Freesurfer] surface-based spatial smoothing model

you can reference this one http://www.ncbi.nlm.nih.gov/pubmed/17011792 Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data. Hagler DJ Jr ^1 , Sayg

Re: [Freesurfer] Symmetric label on fsaverage

ive put a copy here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg On 05/03/2016 04:21 AM, Alexandre Routier wrote: > Hello Douglas, > > Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer > 5.3. Is there anything to do to solve this problem ? > >

[Freesurfer] error in fast_selxavg3 (line 1248)

I've modified an analysis to include a vector of noise time courses estimated using ICA. Since IC effects should be consistent across runs, I'm using taskregs instead of nuisregs. I can define the analysis and set up contrasts fine; however, when I run the analysis (selxavg3-sess), I get the follow

Re: [Freesurfer] no recon button

Douglas, can you please let me know if the voxel edit button is appropriate to use in place of the recon edit? Thanks, Sarah Sent from my iPhone > On May 3, 2016, at 3:04 PM, Burke,Sarah E wrote: > > > Is this information correct? > >> On May 2, 2016, at 3:55 PM, Burke,Sarah E wrote: >>

[Freesurfer] Resting-state fcMRI analysis with GLM

Hi all, I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an exampl

Re: [Freesurfer] downsample fsaverage5 - after and during recon-all

Hi Thomas mri_surf2surf will resample to whatever subject you specific (inludding fsaverage5). I'm not sure what using fsaverage5 in recon-all would mean as we don't really use fsaverage, but I suspect the answer to your question is "no". cheers Bruce On Wed, 4 May 2016, Wolfers, T. (Thoma

Re: [Freesurfer] Correcting defect

sure. Or you can load the ?h.inflated.nofix and look at it - it should be obvious if there is a huge defect (you can also load the file ?h.defect_labels as an overlay on that surface and it will show you the segmentation of the defects) cheers Bruce On Wed, 4 May 2016, Katarina Trojacanec wrot

[Freesurfer] downsample fsaverage5 - after and during recon-all

Is there an easy option to re-sample surface (area.pial and thickness) into fsaverage5 space? How is it possible to use fsaverage5 instead of fsaverage for recon-all? Many thanks for your answers Thomas Wolfers Donders Center for Cognitive Neuroimaging Kapittelweg 29 6525EN Nijmegen The Netherla

Re: [Freesurfer] Brainstem segmentation

Dear Haque, FreeSurfer 6 has not been released yet. But if you want to try the brainstem segmentation module, you can download the dev version; you will find it in there. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/

[Freesurfer] Correcting defect

Dear FreeSurfer Team, I have been trying to run creation of template with FreeSurfer. However, for two cases for one patient (case 1: template based on TP1 and TP4, case 2: template based on TP2 and TP4), the correcting defect step is running too long. According to the information in the mail