Re: [Freesurfer] per voxel regressor in LME toolbox?

Hi Jorge, Thanks for your reply. Actually I don’t want to have different numbers of columns in the design matrix for different vertices. Instead I want to add an extra column to the design matrix, the value of which varies across vertices. It looks like I can just add an extra column in the des

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

Hi all, Looking forward someone can help me. Thanks. All the best. Rujing Zha 2014-05-02 charujing123 发件人："charujing123" 发送时间：2014-05-01 11:38 主题：[Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask 收件人："freesurfer@nmr.mg

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

Hi Josh, the method fits a statistical atlas of the hippocampal subfields to the image data. It is assumed that all subfields other than the fimbria have the same distribution of intensities - because they are all assumed to be gray matter. Therefore, most of the internal boundaries of the hippo

Re: [Freesurfer] Plot Histograms

you can also histogram surface overlays in tksurfer (and I think in freeview too now) Bruce On Thu, 1 May 2014, Douglas N Greve wrote: There is no such function from the command line. You can load the data in matlab (MRIread.m) and do it there. You can load the cortical label into matlab as w

Re: [Freesurfer] Plot Histograms

There is no such function from the command line. You can load the data in matlab (MRIread.m) and do it there. You can load the cortical label into matlab as well with read_label.m On 05/01/2014 10:27 AM, Dídac Vidal wrote: > Hi! > > I would like to plot an histogram with values from sig.mgh acr

Re: [Freesurfer] Constraining fMRI data with a surface label generates a bfloat file?

Thank you Doug! > > On 5/1/14 3:59 PM, jaco...@nmr.mgh.harvard.edu wrote: >> Hello Freesurfer Experts, >> >> Using func2roi (in stable3), we constrained our functional data with >> specific surface labels and t thresholds, and over-threshold masks were >> outputted as .bfloat files. Does this mean

Re: [Freesurfer] Rendering in 3ds Max?

Hi, Have a look at Anderson's blog here http://brainder.org/2014/01/08/splitting-cortical-surface-into-independent-regions/ All the best, Arman Sent from a mobile device, please excuse my brevity/misspellings. > On May 2, 2014, at 1:04 AM, Sourena Soheili-Nezhad > wrote: > > Hi Dorian, > >

Re: [Freesurfer] Rendering in 3ds Max?

Hi Dorian, I have tried exporting in .STL with success. 3d max can import this format. If I recall corretly the command was mris_convert ?h.pial ?h_pial.stl Cheers, Sourena On 4/29/14, Dorian P. wrote: > Hi list, > > Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D > s

Re: [Freesurfer] Constraining fMRI data with a surface label generates a bfloat file?

On 5/1/14 3:59 PM, jaco...@nmr.mgh.harvard.edu wrote: > Hello Freesurfer Experts, > > Using func2roi (in stable3), we constrained our functional data with > specific surface labels and t thresholds, and over-threshold masks were > outputted as .bfloat files. Does this mean these masks are in volum

[Freesurfer] Constraining fMRI data with a surface label generates a bfloat file?

Hello Freesurfer Experts, Using func2roi (in stable3), we constrained our functional data with specific surface labels and t thresholds, and over-threshold masks were outputted as .bfloat files. Does this mean these masks are in volume format and that the volumetric functional data was mapped to t

[Freesurfer] cortical thickness limit

Hello, I have done some comparative cortical thickness analyses in children using FreeSurfer and noticed that the maximum regional thickness value is 5.0. I was wondering if there is an explanation for this limit. Perhaps this is because FreeSurfer was designed for adults? Thank you, Hayyah __

Re: [Freesurfer] cortical thickness limit

Hi Hayyah that's to prevent outliers corrupting the thickness data. You can rerun mris_thickness with -max N to change 5 to whatever N you want cheers Bruce On Thu, 1 May 2014, Hayyah Clairman wrote: Hello, I have done some comparative cortical thickness analyses in children using FreeSu

[Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

Posted on behalf of the CPB: Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Institute of Mental Health (NIMH) Division of Intramural Research Programs (DIRP) Section on Childhood Neuropsychiatric Disorders (SCND) Child Psychiatry Branch (CPB) Staff Sc

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

Thanks for the clarification Eugenio. Would saying that it relies on shape instead of surface be more accurate? I would like to understand better. Also, it is good news that there are plans to model the SLRM. Josh - Joshua Lee Doctoral Candidate Department of Psychology & Center for Mind and Brain

Re: [Freesurfer] installing freesurfer on mac

Hi Charmaine, Sounds like you just need to change the folder permissions for, /Applications/freesurfer/ before attempting to copy the .license file to that location. -Louis On Thu, 1 May 2014, Demanuele, Charmaine wrote: > Hi, > > I am trying to install freesurfer on my mac, and I got a licens

Re: [Freesurfer] per voxel regressor in LME toolbox?

The lme toolbox allows you to have different regression models across locations. If there is a missed data value at some location (vertex/voxel) for a given time-point for a given subject then you can exclude the corresponding row of the full design matrix at that location using the parameter Xr

[Freesurfer] installing freesurfer on mac

Hi, I am trying to install freesurfer on my mac, and I got a license key, which I need to save as ".license" file. However, the mac is not allowing me to do so. I tried saving the file in linux and importing to the mac but this failed too. I also tried saving it as freesurfer.license instead of

[Freesurfer] Plot Histograms

Hi! I would like to plot an histogram with values from sig.mgh across all cortical mantle (as represented in qdec or in tksurfer-overlay options). Which function would allow me to obtain/create histograms from *mgh files? I also would like to obtain a similar histogram, but restricted to a cortic