Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

adding time points to longitudinal base template
by Govindarajan, Koushik Athreya 27 Mar '14

27 Mar '14

Dear FS experts, I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template? Thanks Koushik

2 7

local gyrification index in matlab
by Crofts, Jonathan 27 Mar '14

27 Mar '14

Hi I would like to analyse local gyrification data for a number of brains in Matlab. I have ran the command mris_compute_lgi -i lh.pial which results in a file called lh.pial_lgi. However, I was expecting an output of the form lh.pial_lgi.mat which could be immediately read into Matlab. Do you know how I can convert the file I have into a .mat file? Thanks in advance, Jonathan Dr Jonathan J Crofts School of Science and Technology Nottingham Trent University Clifton Campus Nottingham NG11 8NS Office: ERD 181 Tel: +44 (0)115 84 88419 Office hour: 10am-11am Monday DISCLAIMER: This email is intended solely for the addressee. It may contain private and confidential information. If you are not the intended addressee, please take no action based on it nor show a copy to anyone. In this case, please reply to this email to highlight the error. Opinions and information in this email that do not relate to the official business of Nottingham Trent University shall be understood as neither given nor endorsed by the University. Nottingham Trent University has taken steps to ensure that this email and any attachments are virus-free, but we do advise that the recipient should check that the email and its attachments are actually virus free. This is in keeping with good computing practice.

5 17

mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 27 Mar '14

27 Mar '14

Hello list, I'm trying to get aparc surface area from the pial surface in a table using aparcstats2table but I'm not being able to... I've already created the file aparc_pial.stats inside the stats dir running the following command line from the subjects's label dir: mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial And if I open the aparc_pial.stats file the surfaces are bigger then in aparc (white matter). But when I try to get the table using: aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial --meas area -t rh_aparc_surface_pial.txt I get the message: Number of subjects : 1 Building the table.. ERROR: cannot find /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats Use --skip flag if you want to continue in such cases What's wrong? Thank you, Andreia

2 2

Re: [Freesurfer] Tksurfer + Histogram
by Bruce Fischl 27 Mar '14

27 Mar '14

try configure->functional overlay or something like that after loading the thickness into a functional overlay On Tue, 11 Mar 2014, Saurabh Thakur wrote: > I am referring one paper. > It mentioned about the freesurfer and cortical thickness they hv got in > tksurfer. > > I m just want to know how to get that done in tksurfer. > > I hv attached that paper for the reference. > > cheers > Saurabh Thakur, > > > > > > > On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > what is it that you want to histogram? If the thickness, > tksurfer will do > this for you if you load it as an overlay. Or you can read it > into matlab > and show it there > > On Tue, 11 Mar 2014, Saurabh Thakur > wrote: > > > Hello Freesurfer Expert, > > > > Can anyone help me with histogram plotting of different > surfaces in > > tksurfer. > > > > I looking to calculate the thickness of cortex. > > > > Thanks in advance, > > > > > > Saurabh Thakur, > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > >

2 4

White matter edits
by Eleanor Stahura 26 Mar '14

26 Mar '14

Hello, I am visually checking wm.mgz after running recon-all. There seems to be a pattern where I'm seeing white matter "bleed" past the (correct) white matter surface and into gray matter or appear in the sagittal sinus/dura. However, when I look at wmparc.mgz, the problem is no longer there and the white/gray matter is correctly segmented. Even if the wmparc volume is correct, do I need to do white matter edits? Thanks, Elle

2 1

removal oblique sforms
by Righart, Ruthger 26 Mar '14

26 Mar '14

Dear Freesurfers, To obtain an accurate volume-surface alignment of Freesurfer surfaces in Caret, it is advised that oblique sforms should be removed from the header of the t1w images. I tried to remove the sform (using sform_code='0' and qform='1') and changed the nii header using fslcreatehd. However, something seems to go wrong, as my thickness data of the same subject are different than the thickness data from the original t1w images. In addition, alignment in Caret is still poor. I am puzzled and I would be happy to have your suggestions about removing sforms. Thank you very much in advance! FS 5.3. was run on a Linux machine x86_64. Ruthger

1 0

norm2b, norm2n
by Jason Tourville 26 Mar '14

26 Mar '14

Greetings, I am working with pediatric data and have some early evidence that running recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior temporal lobe segmention as suggested in the v5.2 release notes (I am running this with v5.3). I'd like to experiment more with this parameters to see if I can further improve the segmentation but have been unable to find a a description of how these parameters influence the 2nd norm. Can someone point me to such a description? Thanks, Jason Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

2 1

Thickness analysis on fetal brain
by stdp82＠virgilio.it 26 Mar '14

26 Mar '14

Hi list, we would like to perform cortical thickness analysis on fetal brain. We have a single shot T2 image (good quality) and T1 image (poor quality). All images are in 2D with overlapping and they are acquired by using 1.5 tesla. We have some questions: 1. Do you know a post-processing way to trasform 2D in 3D images and to reduce motion artifacts? 2. Is adapt single shot T2 image to measure the thickness? 3. Given that we are still acquiring data, do you advise a specific protocol to improve T1 or other sequences? Thank you very much, Stefano

1 0

fsaverage -> fsaverage3
by Itamar Kahn 26 Mar '14

26 Mar '14

Greetings, We would like to downsample surfaces (e.g. using mris_decimate) but we want to duplicate the way it was done with fsaverage (namely, find out how fsaverage3/4/5 were created from the original fsaverage). Also, we wish to be able to project using mri_surf2surf but we don’t have sphere registration available (these are fetal imaging surfaces). Thanks, Itamar _________________________________________________ Itamar Kahn, Ph. D., Assistant Professor Department of Physiology and Biophysics The Ruth and Bruce Rappaport Faculty of Medicine Technion – Israel Institute of Technology POB 9649 Bat Galim Haifa 31096 Israel (o) 972-4-829-5461 http://kahnlab.technion.ac.il/ _________________________________________________

2 1

missing codecs for mne_make_movie
by Joseph Dien 26 Mar '14

26 Mar '14

Hi, I tried to use mne_make_movie but got the following error: Movie production selected (from data)... Scanning /Applications/MNE-2.7.3-3268-MacOSX-i386/lib for plugins Found lqt_mjpeg.so...Getting codec info from module Trying to load /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so... dlopen failed for /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so: dlopen(/Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so, 2): Library not loaded: /opt/local/lib/libjpeg.62.dylib Referenced from: /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so Reason: image not found ERROR: lqt_find_video_codec failed to find codecs! The command was: mne_make_movie --inv RPforMNE-eeg-inv.fif --meas RPforMNE.fif --tmin 0 --tmax 250 --tstep 10 --stc RPforMNE --view lat --mov RPforMNE I’m using MNE 2.7.3 under OS X 10.9.2. Any help would be appreciated. Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com

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