[Freesurfer] White matter and white matter lesions

Hi FreeSurfer I am working on a project concerning Alzheimer's patients and I need to know the positions of white matter (WM) and white matter lesions (WML) from your segmentations. To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. To find the WM, I use labels 2 and 41 in the

Re: [Freesurfer] make movies of non eeg/meg temporal data ?

Hi Greg usually I do this with a tcl script. For example, here is a script that generates a movie of inflation (that is a snapshot for each frame, you can then use convert *.tif movie.gif to create an animated gif): cat make_movie.tcl set suffix inflated set surf_dir /homes/4/fischl/links/subje

Re: [Freesurfer] Two questions: 1. Regarding ASEG and reduced FOV; 2. Regarding ventral diencephalon contents

Hi Matthew 1. Sorry, we have little experience with this and I would be worried that even the fully collected hemisphere will have different results than if the whole brain/head had been acquired since there are global steps like linear alignment. 2. The label definitions come from various CMA

Re: [Freesurfer] Problems with manual grey matter editing

Hi Marta I don't see anything obviously wrong in your image, but it is hard to tell dura from gray matter in a single slice. If you upload the subject dir we will take a look. Usually you only need to add gray matter voxels back to the brainmask.mgz if there was a skull stripping problem. Is

[Freesurfer] tkmedit 'no license' error

Hello Freesurfer Team! I’ve been having an issue using the tkmedit function in freesurfer. I get the following error: ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.

Re: [Freesurfer] make movies of non eeg/meg temporal data ?

Hi Greg, I would use MNE either the C, MATLAB, or python code. All are able to create STC (surface time course) files. You can then generate movies using either the C code or the python package (feel free to post follow-up questions on the mne_analy...@nmr.mgh.harvard.edu list). D On Tue, Sep 30

[Freesurfer] create a label file in tkmedit

Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't work properly with e.g. all saved vertex IDs are set to -1. Example file: #!ascii label ….. , from subject ….. vox2ras=TkReg 19 -1 -40.000 52.000 21.000 110.00 -1 -39.000 52.000 21.00

Re: [Freesurfer] create a label file in tkmedit

Hi Ruthi you need to sample them onto the surface to get vertex indices. The easiest way is to just load it into tksurfer then write it out cheers Bruce On Wed, 1 Oct 2014, Adam, Ruth wrote: Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't

[Freesurfer] display thickness map in freeview

Hi, How does one go about loading a thickness map within freeview? The OutputData_freeview tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview) contains a long command line example, but I can't figure out how one would accomplish the same just within the GUI.  (S

Re: [Freesurfer] tkmedit 'no license' error

Hello Micheal, Can you please provide me the output when you 'cd' into the FREESURFER_HOME directory and type the command 'ls -a' -Zeke On 10/01/2014 08:56 AM, Smith, Michael wrote: > Hello Freesurfer Team! > > I’ve been having an issue using the tkmedit function in freesurfer. I > get the fo

Re: [Freesurfer] Two questions: 1. Regarding ASEG and reduced FOV; 2. Regarding ventral diencephalon contents

Thank you Bruce, this is helpful. Matthew On Wed, Oct 1, 2014 at 5:41 AM, Bruce Fischl wrote: > Hi Matthew > > 1. Sorry, we have little experience with this and I would be worried that > even the fully collected hemisphere will have different results than if > the whole brain/head had been acqu

Re: [Freesurfer] display thickness map in freeview

You can select a thickness file when loading as generic. Ruopeng On Oct 1, 2014, at 10:56 AM, Harms, Michael wrote: > > Hi, > How does one go about loading a thickness map within freeview? > The OutputData_freeview tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_fr

[Freesurfer] normalizing activation maps

Dear Freesurfers, I have a question regarding normalization of functional activation maps. Let us assume I have functional activation maps on a vertex space (e.g. mgh files reflecting degree centrality, which do not need previous normalization of functional data). After resampling activation maps

Re: [Freesurfer] tkmedit 'no license' error

Zeke, Attached is a screenshot. Thanks! On 10/1/14, 11:03 AM, "Z K" wrote: >Hello Micheal, > >Can you please provide me the output when you 'cd' into the >FREESURFER_HOME directory and type the command 'ls -a' > >-Zeke > > >On 10/01/2014 08:56 AM, Smith, Michael wrote: >> Hello Freesurfer Team!

Re: [Freesurfer] tkmedit 'no license' error

Hmmm... The error say: ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license not found. And according to your screen capture I also do not see that file. But I do see license.txt which should work. Can you try just renaming (or copying) the file "license.txt" to ".lice

Re: [Freesurfer] tkmedit 'no license' error

Zeke, That fixed it! Thank you. On 10/1/14, 1:05 PM, "Z K" wrote: >Hmmm... The error say: > >ERROR: FreeSurfer license file >/Users/smig9x/Applications/freesurfer//.license not found. > >And according to your screen capture I also do not see that file. But I >do see license.txt which should wor

Re: [Freesurfer] normalizing activation maps

If they are already in fsaverage space, then you just need to concatenate them together (mri_concat) and then use the concat file as input (--y) to mri_glmfit doug On 10/01/2014 12:09 PM, lorenzo pasquini wrote: > Dear Freesurfers, > I have a question regarding normalization of functional acti

Re: [Freesurfer] Boston FreeSurfer Course

Hi everyone, We have 31 people signed up for the course so far. A decision about whether this course will be held will be made by Friday. If you were thinking about registering, please do so before then so we know if we've met our minimum requirement of 40 registrants. Thank you, Allison On Mon

[Freesurfer] Fwd: OHBM 2015 Call for Council Nominations

FYI Original Message Subject:OHBM 2015 Call for Council Nominations Date: Wed, 01 Oct 2014 15:28:53 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM M

Re: [Freesurfer] White matter and white matter lesions

Why not just use the values in aseg.stats? On 10/01/2014 07:44 AM, Leise Borg wrote: > > Hi FreeSurfer > > I am working on a project concerning Alzheimer’s patients and I need > to know the positions of white matter (WM) and white matter lesions > (WML) from your segmentations. > > To find the

Re: [Freesurfer] A question about spherical registration

Hi Doug, Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was no obvious error for that on the screen. Not sure if this happened because of not having an annot file for mris_make_template. Here is what I saw on the screen: %% /usr/local/freesurfer/bin/make_average_surf

[Freesurfer] Input files format

Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be use