[Freesurfer] FREESURFER SUBJECT DIR

Hi, I have changed the path for subject directory. It causes the error.Following is my SetUpFreeSurfer.csh What mistake did I made in? #!/bin/tcsh -ef # # SetUpFreeSurfer.csh # # This is a sample SetUpFreeSurfer.csh file. # Edit as needed for your specific setup. # The defaults should wor

[Freesurfer] Open positions @ CASIA

Dear all, Open positions @ Brainntome Center. http://brainnetome.org/en/recruitment.html *Job 1: PhD Positions in Neuroimaging and Neuroscience, Beijing, China Brainnetome Center* *Applications Deadline: March 15 , 2015. * *Brainnetome Center* Brainnetome Center ( www.brainnetome.org) at

[Freesurfer] Please advise about the cause of Error

Wed Feb 4 11:53:21 KST 2015 /media/sf_F_DRIVE/ADHD200/Classification/Processed/TDC-51 /home/naveed-centos/freesurfer/bin/recon-all -i /media/sf_F_DRIVE/ADHD200/Classification/Original_selected/TDC/7407032/Pekin g_7407032/Peking_7407032_1/scans/anat_1-anat/resources/NIfTI/files/rest.nii -subject

Re: [Freesurfer] Cortical Thickness under iEEG leads

sure, just draw an ROI in the volume (in e.g. freeview) and save it as a .label file, then load it into tksurfer and it will get sampled onto the surface (then save it) On Tue, 3 Feb 2015, rwlod...@uic.edu wrote: > Hello! > I was just wondering what the best way to find the cortical thickness

[Freesurfer] Use applyMorph on Coordinate list Using CVS register Warp

Hi all, I'm using mri_cvs_register to warp a T1 (already in orig space) to the CVS MNI152 template. The warped volume and surface look good, but my goal is to get the equivalent of a list of voxel coordinates from the patient's native orig volume in the template MNI152 space via the non-linear war

[Freesurfer] Cortical Thickness under iEEG leads

Hello! I was just wondering what the best way to find the cortical thickness under specific intracranial EEG leads is. Is this even possible? I know freesurfer doesn't allow you to place leads onto the 3D model it generates, but if I knew exactly where the lead was is there some way to determine t

Re: [Freesurfer] tksurfer

Is it world readable? You might also change its name to license.txt On 2/3/15 12:13 PM, André Schmidt wrote: Dear experts, I like to see the obtained annotation files using tksurfer. However, I already got the following error message if I use tksurfer HC001 lh inflated in the terminal: Fr

[Freesurfer] unsubscribe

De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprak

[Freesurfer] tksurfer

Dear experts, I like to see the obtained annotation files using tksurfer. However, I already got the following error message if I use tksurfer HC001 lh inflated in the terminal: FreeSurfer license file /Applications/freesurfer/.license not found But there is a .license file in that folder. Ca

Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

Thanks, Doug. On Tue, Feb 3, 2015 at 10:37 AM, Douglas Greve wrote: > Hi Corinna, > > In each iteration, the mc-full replaces your data (--y) with white > gaussian noise, smoothes it, then computes the GLM and p-values from the t > or F-test. The mc-z ignores your data entirely and creates a si

Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

Hi Corinna, In each iteration, the mc-full replaces your data (--y) with white gaussian noise, smoothes it, then computes the GLM and p-values from the t or F-test. The mc-z ignores your data entirely and creates a single frame of WGN in each iteration, smoothes it, rescales it back to a z, t

Re: [Freesurfer] defining ROIs/clusters

Just run mris_preproc on your healthy group, then run mri_segstats using the cluster annotation from your first analysis and the HC stack as the input. Does that make sense? doug On 2/3/15 9:18 AM, maaike rive wrote: Hi all, Does anyone know how to extract average (thickness/area/GI) value

Re: [Freesurfer] vertexwise statistical modeling

On 2/3/15 4:21 AM, Schweren, LJS (med) wrote: Thank you Doug! One more question for clarification: “You would remove the quadratic term from the FSGD file, then create an image of quadradic values for each veretx and pass that with --pvr to glmfit”. My quadratic value (age-squared) is a c

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

There is not a way to do it from the command line. You can do it in matlab, something like sig = MRIread('sig.mgh'); sigmat = fast_vol2mat(sig); p = 10^-abs(sigmat); fdr = .05; pthresh = fast_fdrthresh(p,fdr); ind = find(p < pthresh); % This will be a list of ROI indices that survive FDR do

[Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

Hi all, I am wondering what the specific reasons might be for choosing to run the mc-z simulation compared to mc-full? What are the pros and cons for each method for looking at group morphometry differences? Thanks Corinna ___ Freesurfer mailing list Fr

[Freesurfer] defining ROIs/clusters

Hi all, Does anyone know how to extract average (thickness/area/GI) values of a cluster A for subjects in a group which was NOT included in the model where this cluster A emerged? For example: in a t-test for diagnosis1>dagnosis2 there is an effect in an insulacluster (found with mri_glmfit

Re: [Freesurfer] average values per cluster

Hi Doug, Sorry, the statistician doesn't understand it yet; we're currently building freesurfer and SPSS models step by step to find out what's going on, but it's a litte time consuming... so, to be continued! Maaike From: r_maaike@hotmail.comTo: freesur...@nmr.mgh.harvard.eduDate: Fri, 30

[Freesurfer] Group differences of functional connectivity differ in SPM and FSL

Dear users, I writhe in the hope somebody encountered a similar problem. I have individual normalized maps of intrinisc brain networks from a dual regression. This maps are projected back into individual subject space and further into individual surface space. Finally I normalize this maps into

Re: [Freesurfer] vertexwise statistical modeling

Thank you Doug! One more question for clarification: "You would remove the quadratic term from the FSGD file, then create an image of quadradic values for each veretx and pass that with --pvr to glmfit". My quadratic value (age-squared) is a constant per participant. Do you mean I should creat

Re: [Freesurfer] subsampling procedure for fsaverages (Douglas Greve)

Hello! Thanks. I realized that vertices are added at the end when increasing resolution, what I was asking about is more about the details of the subsampling procedure, eg. what's the vertex number of the new vertex created on the edge between vertices n and m when doing a icosahedral subdivisi