[Freesurfer] Tracula prep help

*Dear Freesurfer experts, **I have encountered the following error while running the tracula **pre-processing command and was hoping you could help me understand how **to correct this.* *from the log file * *INFO: input image orientation is LPS INFO: input image determinant is 3.51562 fslswapdim

[Freesurfer] CNR in the hippocampus

Dear Freesurfer expert, I received a comment from the reviewer regarding CNR in the hippocampus. "CNR is known to decrease with age (see papers by Fischl’s group). How does the automated routine for hippocampal volumetry take this into considerations?" Any suggestions how to respond? Th

[Freesurfer] Fwd: CNR in the hippocampus

Dear Freesurfer expert, I'm reposting this mail. any suggestions? Thank you efrat -- Forwarded message -- From: Efrat Kliper Date: Tue, Jun 9, 2015 at 8:11 AM Subject: CNR in the hippocampus To: freesurfer@nmr.mgh.harvard.edu Dear Freesurfer expert, I received a co

[Freesurfer] Tracula problems (creating symbolic link)

Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am u

Re: [Freesurfer] Tracula problems (creating symbolic link)

dmri/dwi.nii.gz > /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz > > Can you please try it both ways and let me know if the former works on a > computer where the latter doesn't? > > And yes, if you fix error #1 it'll fix error #2 as well. > > Thanks, > a.y > &

[Freesurfer] Resting state analysis

Dear freeSurfer expert, I am trying to perform whole brain functional connectivity analysis Is there a wiki for resting state analysis? I have only found this wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc So far I have run the following commands: preproc-s

[Freesurfer] How to report aseg.state values

Dear FreeSurfer expert, If I want to report on hippocampal volume in an article, should I report the value as stated in the aseg.state table or should I normalize the value to the eTICV ( i.e aseg value/eTICV )? Thanks in advance Efrat ___ Freesurfer ma

[Freesurfer] Triangulated surfaces

Dear FreeSurfer Users, I have created a binary mask for the hippocampi and now i want to create the triangulated surfaces of the hippocampi? An one know how to do it? Thanks, Efrat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] ADC map negative values

Dear FreeSurfers Users, When i am using the dt_recon function to create adc map i get quite a lot negative values, dose anyone encounter this problem? Thanks, Efrat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

[Freesurfer] recon-all

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. After I ran the freesurfer recon-all -autorecon-all and checked the data I saw that the skull wasn't removed as a whole (yet it is not part of the pial or white matter margin). I was wondering if it just doesn't look good or that part

[Freesurfer] QA TOOL

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. I am dealing with some problems with recon_checker command. I cannot open the html file to see the figures. The command generates the images but they are not saved. It is written that: *converting snapshots to tiff and making html page..

[Freesurfer] QA Tool Help - Outliers

Dear FreeSurfer expert, I am using Freesurfer version 5.1.0. After I run the QA Tool and check my data, I am getting 39 outliers or more for each subject. When I look at the AsegMeans and DefaultAsegMeans files in the QATool library, i see that the mean values in these file for each anatomical lab

[Freesurfer] Surface to native space

Dear freesurfer expert, We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alter

[Freesurfer] QATools

Dear FreeSurfer expert, I am trying to run QA tools for verifying all steps of the FreeSurfer recon-all stream. I am working with FreeSurfer version 4.5.0. I don't see any optional flagged arguments in which i can specify the version i am working with (the default version is 5.1.). I will be grate

[Freesurfer] Question about version upgrade

Dear FreeSurfer expert, I am currently working on FreeSurfer Version 4.5.0 and already performed an analysis for approximately 200 subjects. Is there a way to change the version that I am working on (4.5.0) to 5.0.1 without the need to run recon-all again in the new version? Thanks in advanced,

[Freesurfer] Cortical Thickness of a Volume-defined ROI

Dear FreeSurfer expert I am trying to create a mask for the right hemisphere frontal lobe cortex in order to calculate the mean cortical thickness for this specific ROI. I am using the following commands: To create a mask for the specific region: mri_binarize --i /mri/aparc+aseg --match 2028 --m