Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

parcellated hemisphere into matlab
by Almarshad F. 01 Jun '17

01 Jun '17

Dear Freesurfer expert; I'm new to Freesurfer and confused about the workflow .. I am trying to create cortical surface mesh consisted of percolated areas, and have done manual percolation by creating my own labels and .annot file I don't know what is the next step to get the parcellated hemisphere into matlab Thanks in advance Yours sincerely, Fatima

3 4

convert .sphere to nii format
by Almarshad F. 01 Jun '17

01 Jun '17

Hi all, I just want to convert the resulting right and left spheres files to .nii.gz using mri_convert, do I can i do this? i could not find any demo to this

2 1

Average hemispheric R1 value
by Damien MARIE 01 Jun '17

01 Jun '17

Dear experts, I would like to extract the mean left / right R1 value for each of my subjects (R1 = 1/T1). I did that with mris_anatomical_stats (see below) and I’m assuming that “ average cortical thickness = 0.001 mm +- 0.000 mm “ is my average R1 value (in that case for the right hemi). Is that correct? Now I would like to get my average hemi R1 value with 5 decimal numbers if possible because R1 values are very low, for instance in the same subject considering the whole brain average R1 is equal to 0.000737 . Is it possible ? Thank you and best, Damien mris_anatomical_stats -t rh.R1.mgh ct_pp2_N4_bet_MP2RAGEcorr rh outputting results to R1file... using thickness file rh.R1.mgh. reading volume /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/mri/wm.mgz... reading input surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white... Using TH3 vertex volume calc Total face volume 293919 Total vertex volume 289553 (mask=0) reading input pial surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.pial... reading input white surface /home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white... structure is "/home/damien/bin/freesurfer6/subjects/ct_pp2_N4_bet_MP2RAGEcorr/surf/rh.white" number of vertices = 148874 total surface area = 103857 mm^2 total gray matter volume = 289553 mm^3 average cortical thickness = 0.001 mm +- 0.000 mm average integrated rectified mean curvature = 0.136 average integrated rectified Gaussian curvature = 0.030 folding index = 2174 intrinsic curvature index = 190.6

2 1

Contrast matrix format
by Taylor Hilton 01 Jun '17

01 Jun '17

Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> For my own analysis, I have 4 total groups, and I’m trying to do a contrast between two of those groups. My matrix file is formatted ‘0 1 -1 0’, since I’m trying to contrast the 2nd and 3rd groups. My fsgd file is formatted as the following: GroupDescriptorFile 1 Title PYSCan Class 1 Class 2 Class 3 Class 4 Input s70032 2 Input s70038 1 … Wanted to verify that this is correct since there doesn’t appear to be a group difference when comparing the clusters against the rest of the data. Any help is very appreciated! Sincerely, B. Taylor Hilton Lab Data Coordinator University of Pittsburgh

4 12

How to process ANCOVA with age as covariate
by Gwang-Won Kim 01 Jun '17

01 Jun '17

1 0

recon-all errors
by Maria Economou 01 Jun '17

01 Jun '17

Dear FreeSurfer developers, I am new to using the software, so forgive me if my mistake is something very basic! I've been trying to do recon-all for my first subject and I keep getting several errors like: ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 Too many open files ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt Loading pixel data ERROR: /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm is not a dicom file 70092 Requested element (18 82) not found in DCM_GetElementVM I have used the DICOM files from my 3D T1 MPRAGE SENSE images. This is the command i used: uos$ recon-all -subjid 147364 -i /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm -all FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c platform: OS X El Capitan Version 10.11.6 Please find attached the recon-all.log Many thanks, Maria.

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Freesurfer June 2017