Re: [Freesurfer] VirtualBox Ubuntu Password Request

External Email - Use Caution Hello TSUJI, I will send the password to your email directly. - R. On Oct 6, 2020, at 01:49, tsuji...@mattohp.com wrote:External Email - Use CautionDear FreeSurfer Developers, My question is the same as that by Ms. XU Eileen Mon, 31 A

[Freesurfer] Freesurfer 5.3.0 recon-all error

External Email - Use Caution I am using freesurfer 5.3.0 (unfortunately this is the version I have to use) and I am encountering an error in the process. I have attached the recon-all.log file. Any pointers to identify the error would be very helpful, Thank you, Michele Tue Oct 6

[Freesurfer] Lobe segmentation

Hi, I have a question regarding lobe (temporal, frontal, parietal, and occipital) segmentation. I have already completed a recon-all for all subjects. I have seen that the surface stream has a -lobesStrict function which parcellates the lobes. I have also seen that you can convert the surface t

Re: [Freesurfer] Freesurfer 5.3.0 recon-all error

My guess is it is a problem with the install of the MNI tools. Does it run all the way through on other subjects? What happens when you run this command? mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz On 10/6/2020 9:16 AM, Michele Valot

Re: [Freesurfer] Lobe segmentation

In principle you can, but it might require a lot of work. You can use something like mri_binarize --i aparc+aseg.mgz --replaceonly X Y --replaceonly X2 Y ... where X is the seg no for a given cortical segmentation and Y is the seg no for the lobe it belongs to. You would do this for all segments/

Re: [Freesurfer] Parallel Run of Multiple Patients

No, you are not overwriting anything. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gunes Sent: Monday, October 5, 2020 12:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] Parallel Run of Multiple Patients External Email - Use

Re: [Freesurfer] surface/volume editing

External Email - Use Caution Hi Doug, just following up to see if you had any suggestions for resolving the problem of the ?h.wm surfaces not pulling back even after running it through the pipeline. If you are in need of more screenshots or details, let me know. Thanks, Jacob Je

Re: [Freesurfer] Resting state fMRI - volume analysis

External Email - Use Caution Thank you for your help. The smoothing issue occurs only on volume. It works okay with surface. When I smooth the volume by 5, the results look like below. The command I used was $preproc-sess -s sess01 -fsd rest -stc siemens -noreg -mni305 -vol-fw

Re: [Freesurfer] extracting beta coefficients and p-values

External Email - Use Caution Hi, I had a couple additional questions related to this topic. 1. The beta-coefficients I derived from using the mri_segstats command with the input beta.mgh, are these values unstandardized? 2. Just wondering, is there a possible way to also derive

Re: [Freesurfer] Turn off bias field correction for SAMSEG

There is no way to turn off fitting of the bias field. It is possible to reduce its influence, but not easy. If there is no bias field, then fitting it generally does not do any harm. On 10/5/2020 4:21 AM, Donatas Sederevicius wrote: > External Email - Use Caution > > Dear FreeSurfer te

[Freesurfer] create .nv or .pial file with atlas based values

External Email - Use Caution Dear freesurfer experts, We have some files containing the values for regions based on the Deskian/Killiany atlas like : ROI, value 'lh_bankssts', .9 'lh_caudalanteriorcingulate', .1 'lh_caudalmiddlefrontal', .5 'lh_cuneus', .2 'lh_entorhinal', .5 'lh_