[Freesurfer] Hippocampal subfield: average standard T1 ore use higher resolution

Dear FreeSurfer-User, some of my questions are mentioned in some older postings, but I still struggle with some basic questions. We are planning to use the new hippocampal subfield segmentation of FS 5.1 with 3 T Siemens TRIO with 32 channel head coil. Still, I do not fully understand

Re: [Freesurfer] TRACULA bvecs question

Hi Tanja, It is supposed to be created automatically. Can you send your configuration file and log file for us to see what's going on? Thanks, Priti Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder

[Freesurfer] FA values

Dear All, How I can get the FA values in a table after running the GLM group analysis for my FA data. I have GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.mgz and the gmldir. Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Can I do multiple comparison correction in one area (not whole brain)

Dear Freesurfer experts, Can freesurfer do multiple comparison correction in part of the brain (not the whole brain)? How can it do? Thank you very much in advance. Mingxia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Can I do multiple comparison correction in one area (not whole brain)

Hi Mingxia, when you run mri_glmfit specify a label of the area that you want to constrain you analysis to. Then run mri_glmfit-sim and perform the simulation (use the --sim flag, not the --cache flag). doug zhang mingxia wrote: Dear Freesurfer experts, Can freesurfer do multiple comparison

[Freesurfer] Algorithm for cluster-wise simulation

Hello folks, We are in the processing of writing a paper on cortical thickness. The cluster-wise simulation that we use is it similar to alphasim monte-carlo simulation by afni? Do you have any paper on it? Best Regards, Manish Dalwani Instructor Dept. of Psychiatry Univ. of CO

Re: [Freesurfer] Algorithm for cluster-wise simulation

You can site this Hagler paper ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hagler.2006.ni.surfcluster.pdf Dalwani, Manish wrote: Hello folks, We are in the processing of writing a paper on cortical thickness. The cluster-wise simulation that we use is it similar to alphasim

[Freesurfer] mri_compile_edits

Hi Nick, Why does mri_compile_edits (-showedits flag) report edits to brainmask.mgz (both in the edits.mgz volume and its text output) if no manual edits were actually performed -- i.e, if brainmask.mgz and brainmask.auto.mgz are identical? thanks, -MH -- Michael Harms, Ph.D.

[Freesurfer] FA question

Dear all, I use dt_recon to process my DTI data and get my fa.nii for the individual subjects. I wonder if the FA values can be greater that one since for all my subjects I got the FA max  value graeter than one. Is something wrong with my data or this is acceptable? I saw in  most of the

[Freesurfer] QDEC question

Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] QDEC question

Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks, Manish On 2/2/12 2:47 PM, Manish Dalwani manish.dalw...@ucdenver.edu wrote: Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on

Re: [Freesurfer] QDEC question

Nevermind, I figured out both my questions! I just have to read the instructions carefully :) Manish On 2/2/12 3:02 PM, Manish Dalwani manish.dalw...@ucdenver.edu wrote: Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks,

Re: [Freesurfer] Two questions when using the new trac-all

Hi there - First of all, let me clarify that the new and old trac-all have no differences in terms of usage, so all of this applies to both. 1. Yes, we did come across the issue of jot not being part of some platforms. It'll be fixed in the next release. If you're getting this error,

Re: [Freesurfer] TRACULA bvecs question

Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y