[Freesurfer] tksurfer.tcl

Dear Freesurfer experts, tksurfer's "Configure Overlay Display" dialog gets clipped and I need *ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurfer.tcl* but the 'allplatforms' folde

[Freesurfer] Fwd: outer pial error

It could be that the error is due to a matlab path issue according to some previous posts, and it is true I cannot find matlab with getmatlab command. I have trouble setting up MATLABPATH. First, I can open matlab from terminal with commands matlab12 or matlab 13, I have 2 versions that I use for

Re: [Freesurfer] How does freesurfer smoothes the data?

Hello Doug and Bruce, Thank you! Another quick question, is there an option to select bandwidth using cross-validation? Sincerely, Ye On Mon, Nov 17, 2014 at 9:40 AM, Douglas Greve wrote: > > The way it is implemented is as a nearest neighbor smoothing which is an > approximation to convolvin

Re: [Freesurfer] White matter comparison

Hi Doug, I see, making wm masks and converting them to mni space sounds like a great idea for what I had in mind. Thanks for your help! Best, Panos > > We are not properly set up for doing VBM. I suppose you could make > binary WM masks and map them into mni305 space or CVS space, but we > don't

Re: [Freesurfer] White matter comparison

We are not properly set up for doing VBM. I suppose you could make binary WM masks and map them into mni305 space or CVS space, but we don't have a way to do jacobian modulation. If you want a VBM an analysis, why not use SPM or FSL? doug On 11/17/2014 01:27 PM, pfot...@nmr.mgh.harvard.edu wro

Re: [Freesurfer] White matter comparison

Hi Doug, Yes, doing a VBM analysis would be precisely what I had in mind. Thanks, Panos > > I'm not sure what you mean. Do you want to do something like a VBM > analysis on WM? > doug > > On 11/13/2014 04:31 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Experts, >> >> I am interested in doing

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

That is what I thought. For version 6, I have a work-around which you might be able to use with version 5. Copy these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_ldanaflac.m ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/flac_conmat.m to $FREESURFER_H

Re: [Freesurfer] White matter comparison

I'm not sure what you mean. Do you want to do something like a VBM analysis on WM? doug On 11/13/2014 04:31 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS Experts, > > I am interested in doing a group analysis between different cohorts using > the white matter volume as the variable of interest.

Re: [Freesurfer] Recon-all on 2 different DCM files

Hi Sravan if you only have 25 files or so then neither one is likely to give you good results. Typically you need at least 96 or 128 slices to get to whole-brain high enough resolution to get reasonable morphometry results cheers Bruce On Mon, 17 Nov 2014, Mattevada, Sravan wrote: I have

Re: [Freesurfer] Recon-all on 2 different DCM files

I have a CD with one session of MRI scans for one person. Under the DICOM folder I have 9 folders. Each folder typically has a series of 25 files and each series is different position (ex. Starts from the Top, starts from the front etc.) When I run dcmunpack I get the result as below 1 LOCAL

Re: [Freesurfer] How is the actual thickness data stored?

No, it is saved in result.vol. The 4th dimension should have 27 elements. doug On 11/17/14 1:23 AM, ye tian wrote: Hello freesurfers, Suppose I do the following mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.gende

Re: [Freesurfer] How does freesurfer smoothes the data?

The way it is implemented is as a nearest neighbor smoothing which is an approximation to convolving with a Gaussian. doug On 11/17/14 8:02 AM, Bruce Fischl wrote: > Hi Ye, > > yes, it is a Gaussian kernel along the surface > > cheers > Bruce > On Mon, 17 Nov 2014, ye tian > wrote: > >> Hello fr

Re: [Freesurfer] temporal lobe exclusion

Hi Andrew can you tell us more about the acquisition? Is it 3T? 1.5? Did you use any special options to recon-all (like the 3T one or the mprage one)? It's really tough to tell from just an image of a single slice. If you upload the dataset we can take a look cheers Bruce On Mon, 17 Nov 20

Re: [Freesurfer] Recon-all on 2 different DCM files

is this two different scans of the same person? Was it during the same session or on different days? It would also be easier for us if you just post the percent changes that you are asking about cheers Bruce On Mon, 17 Nov 2014, Mattevada, Sravan wrote: Hey Guys,   I did a recon-all on 2

[Freesurfer] Recon-all on 2 different DCM files

Hey Guys, I did a recon-all on 2 different dcm files the same subject. I posted the stats of the 2 recons below (blue and green). Can anyone please tell me if both the results are close enough to be considered as the same person? Thanks # Title Segmentation Statistics # Measure BrainSeg, Brain

[Freesurfer] outer pial error

Dear All, I tried to get an outer pial surface on a previously processed pt subjid, and I got the following error. (recon-all was running another subject in a separate window, for what's worth) Please advise, Octavian recon-all -localGI -s subjid WARNING: tcsh v6.17.06 has an exit code bug! Ple

Re: [Freesurfer] How does freesurfer smoothes the data?

Hi Ye, yes, it is a Gaussian kernel along the surface cheers Bruce On Mon, 17 Nov 2014, ye tian wrote: > Hello freesurfers, > I would like to understand intuitively how data is smoothed by Freesurfer. > Is it an analogue to kernel smoothing, with the different FWHM equivalent to > different ban

Re: [Freesurfer] prefrontal cortex label

I'm sure that there are a number of ways you could do it. I would suggest, however, making a coronal cut for your frontal labels at Talairach coordinate y = 26, so that only ‘prefrontal’ regions are included - this conforms to the conservative Talairach criteria described by Rajkowska and Goldma

Re: [Freesurfer] prefrontal cortex label

hi, anyone can help with this? On Tue, Nov 4, 2014 at 4:43 PM, Douglas N Greve wrote: > I don't know. Maybe someone else can weigh in. > doug > > On 11/04/2014 07:38 AM, Anna Jonsson wrote: > > thank you. which labels are normally included as prefrontal cortex for > > freesurfer purposes? > > >

[Freesurfer] Books

Hi, Are there any books you could recommend that give an overview of some of the techniques Freesurfer uses? My research involves structural MRI so other books related to that would be good if you know any. I've got a couple of books on functional MRI analysis which I think are somewhat useful, as