[Freesurfer] Cornell Weill is hiring new faculty in MR

FYI -- Forwarded message -- Date: Wed, 20 Sep 2017 16:53:34 + From: Mert Sabuncu To: Bruce Fischl Subject: Cornell Weill is hiring new faculty in MR Hi Bruce, Can you forward to folks? Thx!

[Freesurfer] Adjusted or unadjusted CT values and interpretation of volume values in ocn.dat from group analysis

Hello Freesurfer experts, I have performed a group level analysis of volume and cortical thickness using mri_glmfit and performed multiple comparisons correction with mri_glmfit-sim. I used the contrast matrix 0 1 0 to analyze 1 group with 2 covariates, along the 1st covariate (education) with

Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView

It looks like just wrong window/level setting in freeview. Have you tried adjust it? You can do it semi-automatically by drawing a ROI with Ctrl + middle mouse button on the slice. On 09/20/2017 12:12 PM, Linnea Marie Dramdal Borg wrote: Hi, My apologies, freeview_T207_dtifit_FA.nii.gz.png

Re: [Freesurfer] Test-retest reliability in longitudinal data

Hi Amanda, I would recommend you to quantify reliability using the same processing pipeline you will use to test for longitudinal effects in your sample. Relevant literature include those listed below. For reliability you would want to evaluate subjects over a time period in which you do not

Re: [Freesurfer] morphing ?h.cortex.patch.flat to sample subject

I don't think surf2surf knows how to deal with patches. We always flatten the individual subject surfaces. You could make a label from the patch and map that across subjects with label2label, then use label2patch to turn it into a patch, then flatten it cheers Bruce On Tue, 19 Sep 2017,

Re: [Freesurfer] Freeview Strange Behavior

Hi Angel, It appears you're running freeview from FS v5.3, which is over 4 years old. Anyway you can try v6.0 or the latest dev build? Best, Rubin On 09/20/2017 10:19 AM, Torrado Carvajal, Angel wrote: Good morning, We have been experiencing a weird behavior in Freeview when loading non

Re: [Freesurfer] lobes volume (WM and GM)

We did not have a strong reason, just that it seemed to give maps that looked reasonable On 09/20/2017 04:42 PM, Gonzalo Rojas Costa wrote: > Hi Douglas: > >Why you specified 5mm as the default value for the --wmparc-dmax > option in mri_aparc2aseg command? > >Sincerely, > > > Gonzalo

Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

Also I should add: I am running freesurfer from a Linux subsystem for Windows. Matlab was installed to Windows before obtaining freesurfer. Best, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: I am looking for papers that used the volume of each lobe computed using freesurfer, but I couldn't found it... Do you know any?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las

Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

It says that it's not on the path. I thought export MATLAB would fix that issue but apparently not. Best, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: Why you specified 5mm as the default value for the --wmparc-dmax option in mri_aparc2aseg command? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel:

[Freesurfer] Matlab(?) failure in selxavg3-sess

Hello freesurfer experts, When I run the selxavg3-sess command (for retinotopy) , the command exits with this "fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt') if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end" and then

Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

what happens if you run the getmatlab command? If you don't have a startup.m, then create one On 09/20/2017 04:34 PM, Yagmur Ozdemir 19 wrote: > Hello freesurfer experts, > > When I run the selxavg3-sess command (for retinotopy) , the command > exits with this >

Re: [Freesurfer] Test-retest reliability in longitudinal data

Hi Amanda it really depends what your goal is. If you want to estimate the noise for a power analysis and you are going to process the data longitudinally, then certainly you should use the longitudinal stream to measure the reliability cheers Bruce On Wed, 20 Sep 2017, Worker, Amanda

Re: [Freesurfer] Pial surface volume

it should be exact On Wed, 20 Sep 2017, Fereshte wrote: Does it give the exact volume ( the volume  which the surface was made from) or it gives an approximation of the volume? ( the toolboxes I've already worked with for such a purpose; give poor approximations).  Thank you!  On Tue, Sep

[Freesurfer] Test-retest reliability in longitudinal data

Hi all, I have a longitudinal dataset that I'd like to calculate test-retest reliability for. However, I am not sure whether to calculate this for the cross-sectionally processed data or longitudinal data? It would seem to make sense to use the cross-sectional data, as the time points are

Re: [Freesurfer] Mris_volume

Hi Fereshte, mris_volume does not create any output files, that number you see in the terminal is the total volume of a given closed surface. Try running mris_volume -v instead and you will see something like this in your terminal: reading ... surface file read in. Volume computation took