[Freesurfer] Quetion about thalamic nuclei segmentation in freesurfer v7

External Email - Use Caution Hi. I have a quetion about thalamic nuclei segmentation process in freesurfer v7. Now, I’ve got a large amounts of patients samples which were already pre-processed using “recon -all” pipeline in freesurfer version 6, but I want to know their spec

Re: [Freesurfer] recon-all error

Hi Nina, The recon all pipeline uses an adult atlas. We have had collaborators successfully using it with subjects all the way down to age 4.5yrs, but under that it would not be recommended. Have you looked at the infant pipeline? Best, Lilla From: freesurfer-boun

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Freesurfer experts, Just wanted to follow up my last email - does anyone know what might be wrong with my code? Thank you and stay safe, Alex On Sat, Aug 1, 2020 at 5:40 PM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developm

[Freesurfer] Converting surface files to ASCII - order of vertices

Hi FreeSurfer community, I have a set of .mgh patch files that are mapped to the FsAverage4 atlas. I'd like to do some calculations on the xyz coordinates of the vertices that make up a patch. I've been able to get ahold of these xyz coordinates by using mris_convert to convert FsAverage4 surfa

[Freesurfer] Change in volume driven by SA or CT?

External Email - Use Caution Dear Freesurfer Experts I am trying to get more information about a cluster indicating a change in cortical volume as a function of a continuous variable. I am currently considering different approaches to find out if this change in volume is primar

[Freesurfer] Fwd: using own skull stripped t1

External Email - Use Caution Hi Freesurfer team I was wondering if you’d have some time to take a look at question below. Thanks! -- Forwarded message - From: Julie Ottoy Date: Thu, 30 Jul 2020 at 13:22 Subject: using own skull stripped t1 To: Freesurfer support

Re: [Freesurfer] How to do permutation for multiple comparison correction?

8:27:47 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200804> There are actually only N-1 permutations that you can make: Real matrix: 1 0 0 1 0 1 0 1 0 1 Permutation 1: 0 1 1 0 0 1 0 1 0 1 Permutation 2: 0 1 0 1 1 0 0 1 0 1 On 8/4/2020

Re: [Freesurfer] How to do permutation for multiple comparison correction?

There are actually only N-1 permutations that you can make: Real matrix: 1 0 0 1 0 1 0 1 0 1 Permutation 1: 0 1 1 0 0 1 0 1 0 1 Permutation 2: 0 1 0 1 1 0 0 1 0 1 On 8/4/2020 10:41 AM, Xiaojiang Yang wrote: External Email - Use Caution Hi Doug, I am still uncertain how to pe

Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

External Email - Use Caution Thanks a lot! I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ coordinates are those of the vertex with maximum intensity within the cluster? (it could be those of the cluster's center of gravity) Finally, I would be very gratefu

Re: [Freesurfer] How to do permutation for multiple comparison correction?

External Email - Use Caution Hi Doug, I am still uncertain how to permutate the data for multiple comparisons. Please help me with a little more details on this. For example, could you give me 2-3 examples of the permutations for the matrix you gave to me? In addition, if you can

Re: [Freesurfer] Change in volume driven by SA or CT?

I would probably just extract the values. Anderson Winkler wrote a paper on this a few years ago, so you might want to look that up. On 8/4/2020 10:03 AM, Meike Hettwer wrote: > External Email - Use Caution > > Dear Freesurfer Experts > > I am trying to get more information about a clus

Re: [Freesurfer] Recon-all Soft Errors

Can you send a picture of the type of errors you are seeing? On 7/31/2020 9:03 AM, Elana Sarabin wrote: External Email - Use Caution Here is the recon-all.log file. Thanks, Elana -Original Message- From: Elana Sarabin Sent: July 30, 2020 10:21 AM To: freesurfer@nmr.mgh.harvar

Re: [Freesurfer] Recon-all error when refining pial surfaces with T2 FLAIR

Can you send the subject to us? See below for instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous"