Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

flirt: command not found
by michal heker 03 Jan '17

03 Jan '17

Hello freesurfer developers, I am trying to use TRACULA reconstruction with *Virtual Box* on my data (I have my own nii files). I have followed all the stages in the freesurfer tutorial. I get the following problem: INFO: SUBJECTS_DIR is /media/sf_share/diffusion_recons INFO: Diffusion root is media/sf_share/diffusion_ourbrains Actual FREESURFER_HOME /usr/local/freesurfer flirt: Command not found. dcmlist: Subscript out of range. What am i doing wrong? find attached is a copy of my dmrirc file Thanks for your help, Michal

2 1

Use CA and other subfields as seed for FS-FAST
by stdp82＠virgilio.it 03 Jan '17

03 Jan '17

Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Pizzi

2 1

Re: [Freesurfer] creating labels from aseg.mgz
by Ladan Shahshahani 02 Jan '17

02 Jan '17

Hi, Thanks for the reply.

1 0

Volume-based group analysis
by Hao wen 02 Jan '17

02 Jan '17

Hello: I want to do some volume-based group analysis with Freesurfer mri_glmfit, and I know in Qdec, this has not been implemented, the problem here is very simple: I want to do the regression between the sub-cortical structure voxels number and age, so try to find the correlation significance between age and subcortical structure in aseg.stats, from the tutorial of command-line of FS from here: it is important to realize that most of the concepts learned here apply to any group analysis in FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer>, surface or volume, thickness or fMRI. So I guess I can do it, but I can not find any tutorial about this for volume-based group analysis(fMRI pipeline, I got stats from recon-all), if I use third-party software to do the statistical analysis, the difficulties are how to mapping the p-value to the brain just like VBM in SPM. Actually, this is not really different for you, but I can not just find the relevant information, can you help me??? Thanks in advance Hao

1 0

creating labels from aseg.mgz
by Ladan Shahshahani 01 Jan '17

01 Jan '17

Dear experts, I'm trying to create labels for subcortical regions. I want to use these labels to extract time series from resting state fMRI data (I want all of the subcortical time series and I want them to be in mni305 space). I'm not sure if I'm doing the right thing. Here's an example of what I used: mri_cor2label --c $FREESURFER_HOME/subjects/fsaverage/mri.2mm/aseg.mgz --id 255 --l ~/Desktop/CC_Anterior.label After running this command, attached is the label file I get. The first column is all "-1"s. any ideas how I can go about doing such thing? Best, Ladan

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Freesurfer January 2017