Re: [Freesurfer] analysing scans other than brain

Dear Matyas, this (not brain-specific) R package will be maybe more suitable for your purpose: http://onlinelibrary.wiley.com/doi/10./2041-210X.12035/full https://cran.r-project.org/web/packages/geomorph/index.html I generally would recommend to rather look for packages used in community of

Re: [Freesurfer] analysing scans other than brain

Thank you Antonin, however I am trying to move away from using landmarks and in general geometric morphometry. I wonder if it is possible to read OBJ, PLY, WRL, STL, AOP, ASCII, Disney PTEX, E57, XYZRGB files in Freesurfer? Thank you for your help! Mat From: freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

Yes, my understanding is the same.  The LME toolbox can in a way be regarded as a post-processing add-on to Freesurfer. The only interface with Freesurfer are the read/write functions, everything else is to the best of my knowledge independent of Freesurfer. So I cannot see any problems in using

[Freesurfer] Fwd: Question-optseq2

Hi, I’m interested in using optseq2 to optimize my experiment, but I wonder if the software was programmed for optimizing experiments such as the Attention network test, where some cues are presented before the stimuli (See below) [cid:D6F85C6A-6306-43C5-801E-54C09C00A93D] Ref. Fan et al Neuro

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

After downloading version 6.0. and running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1), I received the following errors. Error using parfor_progress (line 17) Do you have write permissions for /? Error in lme_mass_fit (line 155) fn = parfor_progress('init',nv); Error in lme_mass_fit_v

[Freesurfer] Demeaning covariates correctly?

Hi experts, I'm using QDEC to look at between group differences in LGI. According to a previous post I demeaned my covariates (age and surface area) inputted in my qdec.table.dat file by subtracting each value (i.e. each age) by the mean of all participant's ages and dividing it by the standard

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

The LME toolbox will create a text file ('parfor_progress1.txt') in Matlab's present working directory to indicate its progress in processing each vertex. To create this file it needs to have write permissions in Matlab's present working directory. I speculate that your present working directory

Re: [Freesurfer] freeview for FS-FAST results

Thanks. My question is only for visualization purpose, not for statistics. I would like to exclude from maps the clusters < 5 voxels. Stefano > > Il 5 marzo 2018 alle 21.42 Douglas N Greve ha > scritto: > > Set --cwp 1. This will keep all clusters regardless of size. Then look >

[Freesurfer] Clarification on interpreting results

Hi, I have a 2 questions regarding properly interpreting results from QDEC. Will you please clarify the following for me? 1. What is the difference between stats table generated after correcting for multiple comparisons (i.e. monte carlo), vs the stats table generated after clicking "find clus

Re: [Freesurfer] Demeaning covariates correctly?

Yes, you have done everything correctly. QDEC takes your table.dat file and creates an FSGD file. It is possible to specify in the FSGD file whether to do demeaning or not by including a keyword. It does not find that keyword and so does not do demeaning. But you've already done demeaning so it

Re: [Freesurfer] Clarification on interpreting results

On 03/06/2018 12:03 PM, Douglas N. Greve wrote: > > > On 03/06/2018 10:14 AM, Avideh Gharehgazlou wrote: >> Hi, >> >> I have a 2 questions regarding properly interpreting results from >> QDEC. Will you please clarify the following for me? >> >> 1. What is the difference between stats table gener

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

Changing the Matlab directory worked. Thanks for all your inputs, Kersten. Sorry to prolong the conversation but if possible, I would appreciate input on whether my thought process regarding the LME analysis is on the right track. I am looking to compare cortical thickness between 3 groups over

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

I have tabulated the columns for easier comprehension. Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 intercept time of each scan from base scan for a given subject age at first scan for a given subject group (1, 2, or 3) visit (1,2 3, or 4) Column 2 * Column 3 Thanks again. M

[Freesurfer] Clarification on Interpreting results cont'

Hi, Thank you so much for the clarification, so values listed under “CWP” column in "mc-z.abs.th13.sig.cluster.summary" file are my corrected p-values to be reported? (in this case having run monte carlo for multiple comparison correction) CONFIDENTIALITY NOTICE: This e-mail message, including

Re: [Freesurfer] Clarification on Interpreting results cont'

correct On 03/06/2018 01:41 PM, Avideh Gharehgazlou wrote: > Hi, > > Thank you so much for the clarification, so values listed under “CWP” > column in "mc-z.abs.th13.sig.cluster.summary" file are my corrected > p-values to be reported? (in this case having run monte carlo for > multiple compar

[Freesurfer] Reg Mapping automatic segmentations to functional space

Hello all, I have mapped a subject's fMRI Feat data onto the anatomical scan and then mapped the segmentations to the functional space using the following commands: reg-feat2anat --feat feat_folder.feat --subject sub_name aseg2feat --aparc+aseg --feat feat_folder.feat The file created does n

[Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

Dear Freesurfer export, When I chose colormap to lookup table with bert/mri/aseg.mgz freeview crash with the following message. [New Thread 0x7fffce7f4700 (LWP 78012)] /usr/local/freesurfer60/bin/freeview.bin: symbol lookup error: /usr/local/freesurfer60/bin/freeview.bin: undefined symbol

[Freesurfer] Compatibility of subcortical and cortical segmentations between Version 5.3 and 6.0

Hi Freesurfer Developers, i am currently collecting structural imaging data from several large cohorts that have been processed using different freesurfer versions (5.3 and 6.0). I would be interested on your experiences regarding compatibility between both versions for subcortical and cortical

[Freesurfer] getting h/o atlas into individual surface (and then volume) space

Hi, I’m trying to get an atlas (Harvard/Oxford sub&cortical) into individual space via surface registration. Motivation is to replicate a finding in volume space (functional data) in a normal population with that atlas in a lesion data set where transformation to template volume space is not fe

Re: [Freesurfer] mir_vol2surface registration file error

I am sorry but that is what I am unsure about it. I don't know how to obtain a registration matrix or which registration matrix to use for this. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W):

Re: [Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

Hi I found a walk around. I got freeview to work by adding by changing line 4 in freeview from source $FREESURFER_HOME/bin/qt_setup to #source $FREESURFER_HOME/bin/qt_setup. Then I am able to use lookup table as colormap. ldd /usr/local/freesurfer/bin/freeview.bin linux-vdso.so.1 (0x7f