[Freesurfer] Mapping labels created in fsaverage_sym into subjects.

External Email - Use Caution Hello, I have a question regarding label mapping. I did a whole-brain analysis in the fsaverage_sym space and extracted some of the clusters that I obtained as labels. I would like to use those labels to obtain the mean cortical thickness values for

Re: [Freesurfer] Log transformation vertex-wise

External Email - Use Caution Yes, that worked. Thank you. Douglas N. Greve schrieb am Di., 8. Sep. 2020, 17:04: > you just want to compute the log of the voxel values in a volume? You can > use fscalc > > On 9/8/2020 6:30 AM, Jose Graterol wrote: > >

Re: [Freesurfer] Log transformation vertex-wise

asier way to do this with some FreeSurfer command > that others can suggest (and I am not aware of), but I would do it in R > with this script: > https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397 > > Best, > > Tim > > > On September 8, 2020 at 10:25 AM Jose

[Freesurfer] Log transformation vertex-wise

External Email - Use Caution Hello FreeSurfer Developers, I have a technical question for which I have not yet found the answer. First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7. Now to the question: is there a way to apply, say, a logarithmic transformation

Re: [Freesurfer] FSGD file formatting for Xhemi

uot;flip" them? > > On 11/5/2019 6:10 AM, Jose Graterol wrote: > > External Email - Use Caution > I believe I found my problem. I was trying to run the analysis with xhemi. > Therefore it asked for 34 inputs (17subjects * 2 hemispheres). I was doing > it that way becaus

Re: [Freesurfer] FSGD file formatting for Xhemi

input (paired diff) and x1, x2, etc, are your factors. > You are the one who knows your data and what models would be appropriate > > On 10/31/19 12:41 PM, Jose Graterol wrote: > > > > External Email - Use Caution > > > > My doubt is, if it is possible to use

Re: [Freesurfer] FSGD file formatting for Xhemi

dgr...@mgh.harvard.edu> wrote: > I don't understand. What per hemisphere variable? > > On 10/25/2019 3:15 AM, Jose Graterol wrote: > > External Email - Use Caution > Thanks for your answer. A follow up question: > How should I then specify the variable's values per hemisphere &

Re: [Freesurfer] FSGD file formatting for Xhemi

m in a single file > > On 10/21/19 4:58 AM, Jose Graterol wrote: > > > > External Email - Use Caution > > > > Thanks for your answer. > > > > I want to correlate TMS values in 17 stroke patients. Following the > > instructions provided to Anders i

Re: [Freesurfer] FSGD file formatting for Xhemi

at 3:57 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > What are you trying to test? Usually you don't have lh and rh in the same > glm > > On 10/17/19 7:09 AM, Jose Graterol wrote: > > External Email - Use Caution > Dear Freesurfer Community, >

[Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y file was created as previously explained in another discussion (

Re: [Freesurfer] Label created in the symmetric space

ject and hemisphere (the order will be subject.lh, subject.rh, > nextsubject.lh, nextsubject.rh) and a column for each cluster. The > values will be the thickness. > > > > On 10/8/19 12:22 PM, Jose Graterol wrote: > > > > External Email - Use Caution > >

Re: [Freesurfer] Label created in the symmetric space

> > > > > > > > > On Tue, Oct 8, 2019 at 4:45 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > The input has both positives and negatives, so is is not > > surprising that the y.ocn.dat also has positive and

Re: [Freesurfer] Label created in the symmetric space

urprising that > the y.ocn.dat also has positive and negative. Not sure what is going wrong > here ... > > On 10/7/2019 5:48 PM, Jose Graterol wrote: > > External Email - Use Caution > Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar.gz". I had to > log in as

Re: [Freesurfer] Label created in the symmetric space

> It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > put subject.tar.gz > > Send an email that the file has been and the name of the file. > > On 10/7/2019 11:53 AM, Jose Graterol wrote: > > External Email - Use

Re: [Freesurfer] Label created in the symmetric space

matic values? > > On 10/4/2019 4:58 AM, Jose Graterol wrote: > > External Email - Use Caution > Dear Freesurfer Experts, > > I would appreciate your help. I will explain first what I have done and > where my problem is. > > I want to measure the cortical

[Freesurfer] Label created in the symmetric space

External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to measure the cortical thickness in stroke patients. Therefore I followed Douglas' instructions provided in this link