Re: [Freesurfer] T1 error

Hello Bruce: My apologies for the incomplete way to raise the question. Anyway, we have solved it. Thank you very much. On Fri, Mar 17, 2017 at 3:30 PM, Bruce Fischl wrote: > Hi Manuel > > how do you know it is binary? Have you tried changing the window levels in > freeview when you view it? An

[Freesurfer] Multiple comparisons

Dear FS team, I would like to correct for multiple comparisons after I run command-line GLM analysis on stats tables. I would like to make a second level analysis between a control group and an autism group. I would like to know if there is a command-line in FreeSurfer or if there i

Re: [Freesurfer] Error in Reconstruction of bert samples.

Hi, It looks like Freesurfer can't read bert's brainmask.mgz volume. Can you ls -l bert's mri directory and see if that file is there and you have proper permission to read it? mri_watershed is looking for that file because the command says to keep the edits from brainmask.mgz, but that file

[Freesurfer] freesurfer license tx

i received the license through the email and tried to make a new text file contains the emailed licensed details .. i am confused where exactly to save it i tried to save it in the user/local/freesurfer but it show a permission error "ou do not have the permissions necessary to save the file. P

[Freesurfer] preproc-sess -per-run vs. -per-session

Hi FreeSurfer Experts, I was reading the document of preproc-sess, and it seems -per-run is recommended instead of -per-session. Here is the part: > -per-run > Motion correct and register using the middle time point of each run. > This is the option that you should use. > -per-session > Motion c

[Freesurfer] Postdoctoral Position - Multimodal neuroimaging in dementia

Postdoctoral research fellow positions are available in the Department of Neurology Research at the National Neuroscience Institute, Singapore. Our focus is to use neuroimaging techniques as a surrogate pathological marker to understand the underlying neurobiological basis of dementia especially in

Re: [Freesurfer] freesurfer license tx

Usually it would be /usr/local/freesurfer If thats what you did than you may need root access to the machine to be able to do that. So basically create the license.txt file in your home directory than copy it to the frresurfer folder: sudo cp license.txt /usr/local/freesurfer/ Bottom line is

Re: [Freesurfer] Error in Reconstruction of bert samples.

Thats odd. Does that file exist? What are the permissions of it? ls -l /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz > IPL Neurosurgery has shared a OneDrive file with you. To view it, > click the link below. > > >

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Andrew, thanks for your response. I am still not seeing the white matter edit performance that I am expecting, or that I have seen from using the cross stream on 5.3 in the past with a different dataset. I started with a new subject with two timepoints. I ran recon-all on both for the cross str

[Freesurfer] Postdoc position at the Ohio State University

POSTDOCTORAL FELLOW, The Ohio State University, Dept. of Psychology – Saygin Lab. We seek an outstanding scientist with a recent Ph.D. in cognitive neuroscience, developmental psychology, or related area, who has experience with neuroimaging methods (MRI, fMRI, DWI, and/or functional connectivity)

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Dear David, did you use -uselongbasewmedits in your recon-all -long run? If this flag is not used, the wm edits are transfered to long from cross, not from the base. Regards, Antonin Skoch Andrew, thanks for your response. I am still not seeing the white matter edit performance that I am