Re: [Freesurfer] Cortical gray matter surface area

That is the surface area of the cortical GM where it has its junction with the WM. Or do you want the surface area of the pial surface? On 9/2/14 12:22 AM, will brown wrote: Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray

Re: [Freesurfer] problemi with mri_glmfit-sim

The final FWHM is larger than the maximum that the correction has been computed for. This often happens with lGI because lGI naturally has a large amount of spatial correlation. Did you smooth it prior to running mri_glmfit? If so, try it without smoothing. doug On 9/2/14 11:47 AM,

[Freesurfer] prefrontal gyrification

Dear list, how would I get gyrification for the prefrotnal cortex? there is no annotation for this structure? Do I need to make my own? and if so, how? best, Melly ___ Freesurfer mailing list

[Freesurfer] mkanalysis-sess blocked design

Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for

Re: [Freesurfer] mkanalysis-sess blocked design

I solved the problem. I figured out that the event-related flag also refers to blocked-designs Best wishes Chris Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Milde, Christopher Gesendet: Mittwoch, 3. September 2014 14:12 An:

Re: [Freesurfer] prefrontal gyrification

HI Melly: I assume that you have run your brains through the FreeSurfer recons. Once you have done this and made corrections to the surfaces, run your brains through a post processing step as below: recon-all -s subj -localGI This will give you gyrification indices for all lobes across the

[Freesurfer] Functional connectivity

Dear Freesurfer experts, We are trying to perform a resting state functional connectivity analysis (seed based, seed = PCC) in a single patient. How can we visualize the map of the (expected) DMN of this single patient in freeview? We tried an overlay with subjectname/mri/orig.mgz and

[Freesurfer] Vertex space

Dear Freesurfer users, I was wondering if it is possible to transform functional connectivity images (.img format) derived e.g. from an ICA of resting state fMRI data into vertex space reflecting cortical thickness (derived from the Freesurfer pipeline on anatomical data). We have been trying

Re: [Freesurfer] Nframes greater than 1...

Hi: I don't know it is an mprage got in our center using a Siemens Avanto equipment freesurfer specify that the images has two nframes and for that reason freesurfer could not process it... Sincerely Gonzalo Rojas Costa Hi Gonzalo what is in the two frames? Bruce On Tue, 2 Sep 2014,

Re: [Freesurfer] Vertex space

Hi Lorenzo we need more information if we are going to be able to help you. What is not working? You should be able to use bbregister on the fMRI data to register it to the surface, then mri_vol2surf to sample it onto the vertex mesh. Note that you should avoid .img format! Use nifti

Re: [Freesurfer] Nframes greater than 1...

Hi Gonzalo is it multi-echo? Phase and mag? You need to find out before you can process it properly. You can extract the frames via: mri_convert -nth frame # input dicom output.mgz cheers Bruce On Wed, 3 Sep 2014, Gonzalo Rojas Costa wrote: Hi: I don't know it is an mprage got in

[Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However,

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele, You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b/ and trac-all output to

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Barbara, I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, You would have

[Freesurfer] Question about mri_convert

Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file. *mri_convert

[Freesurfer] how generate a head model?

Hi Experts I have been studying how to generate a head model, and is said to FreeSurfer software allows better tissue segmentation. I've driven German Gomez Herrero tutorial: http://www.germangh.com/tutorials/dipoles/head_model.htm I have installed freesurfer and matlab. I have verified that

[Freesurfer] Tracula

Hello, I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex. When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area

[Freesurfer] Average myelination within ROI

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele, Yes, tracula would have complained at the very first call, if the dwi data was not there. So here is the problem, you write: setenv /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b in the very first line in your

[Freesurfer] From bedpostX and recon-all to tracula

Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they