Re: [Freesurfer] problem fast_selxavg3b

I don't think they are using the compiled version of selxavg. Rather, the matlab script makes a unix call to run an FS binary. I think this would happen for any binary. Desiree, can you run that command (mris_fwhm) outside of matlab to see if it runs? On 10/06/2015 10:21 AM, Z K wrote: >

Re: [Freesurfer] Error Messages for Accessing Bin

what operating system are you running? 64 bit or 32 bit? Why did you decide to install version 5.0 instead of the current stable 5.3? hth d On Mon, Oct 5, 2015 at 5:41 PM, Timothy Le wrote: > Hi, > From the following output, how should I proceed? > Thank you very much >

Re: [Freesurfer] Questions about the correction methods in Surfstat

>The output figure is attached. In the colorbar of the figure, left represents cluster corrected p value and right one represents the vertex >corrected p value, right? Right. >So, the warm color region in the figure can be survived by the RFT vertex correction, and the cool color region in the

Re: [Freesurfer] Questions about the correction methods in Surfstat

I see. Thanks a lot, Donald Best, Feng 发件人："MCLAREN, Donald" 发送时间：2015-10-07 11:01 主题：Re: [Freesurfer] Questions about the correction methods in Surfstat 收件人："Freesurfer support list" 抄送： >The output figure is attached. In the

Re: [Freesurfer] freeview and ?h.cortex.patch.flat

Hi Xiaomin, At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview. You can load it using tksurfer by loading your subject's inflated surface, then going to File -> Patch -> LoadPatch and choosing the correct patch.flat file. These instructions are detailed here:

[Freesurfer] Postdoctoral Positions - Headache & Orofacial Pain Effort Lab, University of Michigan: Migraine and TMD Neuroimaging and Neuromodulation Research

The Headache and Orofacial Pain Effort (H.O.P.E.) Lab at the University of Michigan requests applications for two postdoctoral positions to work on migraine and TMD research programs funded by the National Institute of Health. The programs use novel methodologies in neuroimaging and

[Freesurfer] Individual regions of CorticalParcellation_Yeo2011

Dear Prof. Yeo, I would like to extract the brain regions of the functional canonical network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have provided the split regions of 7&17 Network in previous discussion string. (https://www.mail-archive.com/freesurfer

Re: [Freesurfer] 7T thalamic segmentation inconsistencies.

Bruce, Thank you for such a quick response. I have attached a link to the T1 dicom files. The T1 was acquired using an MP rage sequence. ​ Thalamic T1 Files ​ Thanks, Ben (University of Minnesota, Noam

Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

Hi, Bruce Do you mean that if the tumor located in the subcortical area, there is not large impact to reconstruction; if the tumor located in the cortical regions, there will affect the cortex reconstruction? Another question is that I have MRI data from stroke patients. However, there are

Re: [Freesurfer] freeview and ?h.cortex.patch.flat

Thanks Xiaomin On Tue, Oct 6, 2015 at 11:35 AM -0700, "Lee Tirrell" wrote: Hi Xiaomin, At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview. You can load it using tksurfer by loading your subject's inflated surface, then going to File ->

Re: [Freesurfer] Query about the calculation of surface area

Thanks a lot, Bruce If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial? Or I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area

[Freesurfer] Query about the calculation of surface area

Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each

Re: [Freesurfer] mris_surf2vol

Hi Doug, sorry to be a bother, this doesn't work on my machine, running: file mri_surf2vol.mac64 gets me: mri_surf2vol.mac64: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.0, not stripped Cheers, *Dr Kevin Aquino* Research

Re: [Freesurfer] Lost toolbar in freeview

Dear Ruopeng, I am using Ubuntu 12.04. LTS 32bits. There is no directory ~/Library/Preferences in my home directory. There is only "GNUstep" directory containing subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults" contains .GNUstepDefaults file, which is very

Re: [Freesurfer] high area.pial values

Dear Bruce, Thank you for your response regarding high area values. I have indeed observed high values (I.e. >20) in both the white and pial surfaces of my subjects, albeit only at a few vertices. The vertices indices that contain the highest values in these surface appear around

Re: [Freesurfer] Query about the calculation of surface area

Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right? Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? Best, Feng

Re: [Freesurfer] Query about the calculation of surface area

yes, that is correct Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: Thanks, Bruce   So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right?   Is the area of each vertex obtained by the 

Re: [Freesurfer] Query about the calculation of surface area

Hi Feng we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: Dear Freesurfer experts,   I have a question about the calculation of surface

Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

Hi Feng it's impossible to give a comprehensive answer to this type of question other than try it and see if it works. Too much depends on the exact placement and contrast properties of the lesions Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: Hi, Bruce   Do you mean that if the tumor

Re: [Freesurfer] high area.pial values

Hi Derek if you run mris_info or mris_euler_number it will tell you how many vertices/faces are in the array. I'm not sure what would cause such a high value, but you should be able to visualize it and see (once you have the vertex numbers that are in the face you can use freeview to goto

Re: [Freesurfer] Lost toolbar in freeview

Dear Ruopeng, thank you, it worked! Only, just to let you know, this tiny popup menu item was completely blank in my case, without any inscription. When I left-clicked at it, the menu bar appeared, and on this popup menu item only checkmark newly appeared. Regards,

[Freesurfer] repeated measures ANOVA using the FSGD file

Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many

Re: [Freesurfer] Lost toolbar in freeview

In that case, simply click right-mouse button on the empty space on the menu bar. There should be a tiny menu item says “tool bar”. Check it and you should see tool bar again. Best, Ruopeng > On Oct 6, 2015, at 6:32 AM, Antonin Skoch wrote: > > Dear Ruopeng, > > I am using

Re: [Freesurfer] 7T thalamic segmentation inconsistencies.

Hi Ben if you upload the datasets we will take a look. I imagine this is due to dielectric resonance effects. What sequence did you use? Bruce On Tue, 6 Oct 2015, Benjamin Peterson wrote: > We have three 7T scans of the same person done on separate days. After > running all three T1 images

[Freesurfer] Tracula Tracts density

Hi Anastasia, How can I calculate the tract density from the output of tracula. For example in the final stats file for the cortico spinal tract I can see the number of sample paths in the WM tract. Is this number refer to the tract density ( number of DTI fibers comprising the tract - in other

[Freesurfer] 7T thalamic segmentation inconsistencies.

We have three 7T scans of the same person done on separate days. After running all three T1 images using the "recon-all" function, we obtain thalamic volumes. The volumes varied by up to 25% which seems quite drastic for the same person. Is there a way to decrease this variability? Are there some

Re: [Freesurfer] Error Messages for Accessing Bin

Hi, We have a 64 bit system. We chose to install 5.0 because we already have data processed in 5.0 and want to keep the data consistent. What would you advise us to do? Thank you Timothy > On Oct 6, 2015, at 7:47 AM, dgw wrote: > > what operating system are you running?

[Freesurfer] Postdoc position at Martinos Center for Biomedical Imaging

Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts General Hospital / Harvard Medical School The Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging has a job opening for a post-doctoral fellow to work on modeling cortical layers and

Re: [Freesurfer] problem fast_selxavg3b

Hello, I have seen errors that look like the error below (i.e. GLIBCXX_3.4.15) when their is an incompatibility between the OS, matlab, and the compiled binary. Looking at your path to matlab I see "/opt/matlab/R2010b". Thats pretty old. Doug, I recall you telling me these binaries are