[Freesurfer] Freeview 7.1.1 won't start on Mac: segmentation fault

External Email - Use Caution Hello again dear Freesurfer experts I recently updated to v7.1.1, in order to get the latest version of Freeview. I’m using Mac OS 10.15.6. Freeview seems to start once each time I boot up my machine, but if I quite it, I can’t re-start it again (

Re: [Freesurfer] left-right flip?

External Email - Use Caution Hi Douglas, I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire

Re: [Freesurfer] Freeview 7.1.1 won't start on Mac: segmentation fault

External Email - Use Caution Hello Alex, If you want to use the Finder to directly launch the freeview *application*, then I would double click on an application bundle (named *.app or in this case Freeview.app)  which is directly under /Applications/freesurfer/7.1.1.  You can d

[Freesurfer] error message using mri_robust_template

External Email - Use Caution Hello, I am using mri_robust_template with the ‘--affine’ option to create individual templates (using freesurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). For each timepoint I use that timepoint's T1.mgz as the input. For s

Re: [Freesurfer] Freeview 7.1.1 won't start on Mac: segmentation fault

Hi Alex, If you have a full crash report please do send it. It’d be helpful in any case. Thanks, Ruopeng On Sep 16, 2020, at 3:17 AM, Alex White mailto:alexander.l.wh...@gmail.com>> wrote: External Email - Use Caution Hello again dear Freesurfer experts I recently updated to v7.1.1,

[Freesurfer] Hippocampal and amygdala subregions using earlier freesurfer version segmentations

External Email - Use Caution Hello, I just wanted to verify that using segmentations from earlier freesurfer versions (5.3) are valid as input into the subsequent further segmentation into the hippocampal and amygdala subregions. I understand the input volumes will vary based on v

Re: [Freesurfer] left-right flip?

Hi Ellen Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing. Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ellen

Re: [Freesurfer] Hippocampal and amygdala subregions using earlier freesurfer version segmentations

Yes, you nailed it :-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Keith Harenski Reply-To: Freesurfer support list Date: Wednesday, September 16, 2020 at 10:32 To: "freesurfer@nmr.mgh.harvard.edu" Subject

Re: [Freesurfer] left-right flip?

External Email - Use Caution Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal) Something like: mri_convert --in_orientation LIA s

Re: [Freesurfer] left-right flip?

I think so, but I defer to Doug From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 11:05 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Thanks for your reply Bruce. Could

[Freesurfer] Resting state fMRI preproc-sess registration error

External Email - Use Caution Dear freesurfer developers, I am working on preprocessing resting state fMRI and used the following command. $ preproc-sess -s sess01 -fsd rest -stc siemens -surface fsaverage lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-session When I tried to

[Freesurfer] Converting Volume ROI to Surface .annot file

External Email - Use Caution Dear Freesurfer community, apologizes in advance for what may be a simple question. I have a volume region of interest file in .nii format. I would like to do a surface functional connectivity analysis in a MATLAB toolbox, and to do so, I would need t

[Freesurfer] Cohen's D calculation and interpretation

External Email - Use Caution Hi everyone, I reviewed some of the other answers on the mailing list to compute a Cohen's d value following the sequence of commands below for a Qdec Freesurfer analysis: 1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh 2) mri_

[Freesurfer] mri_surf2surf template rh.white to fsaverage5

External Email - Use Caution hello,Fs Because I want to build an N*N matrix based on the fixed-point number N of rh.white, but the original rh.white has too many fixed-point numbers, a memory error occurs. I saw a paper, which can be registered to the fsaverage5 space, and t

Re: [Freesurfer] Make BEM with corrected brainmask

Thank you, I got a brain surface using the mri_binarize function. Is there a function for expanding the surface radially by a few millimeters? I want to create the inner skull surface as an expansion of the brain surface. Thanks, Manorama From: freesurfer-boun...@

Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1

Hi Jim - There should not be any differences in TRACULA between recent stable releases. I've been committing the new features described on the wiki to the tracula beta branch on github, so they are available there only. Let us know if you run into any issues! Anastasia.

Re: [Freesurfer] Config File For Tracula Question

Hi Jason - This is still in rich text format unfortunately. The way to see this is to run the "cat" command on the file: % cat XXX7.24.14Configfile\ copy.txt {\rtf1\ansi\ansicpg1252\cocoartf1504\cocoasubrtf830 {\fonttbl\f0\fswiss\fcharset0 Helvetica;\f1\froman\fcharset0 TimesNewRomanPSMT;} {\colo

Re: [Freesurfer] outputs from step of trac- all prep

Hi Qi - Please see under "Output directories and files": https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Wednesday, September 9, 2020 1:23 AM To: Freesurfer support list Su

Re: [Freesurfer] display P-values for T-test on differences in mean FA/MD/… between groups

Hi Qi - Please see under "Anisotropy and diffusivity along the trajectory of a pathway": https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Wednesday, Sep