Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Problem about the fMRI Analysis?
by Linda Xu 27 Mar '14

27 Mar '14

I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer) And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer. Next I using mri_vol2surf to aline the each one's functional result to the fsaverage offer by freesurfer. My question is :1 Should I need to do mri_vol2vol next for each subject? 2 I have two group of subjects. I want to know if there is some correlation different between them? What should I do next? Thanks very much! Linda

2 2

mri_glmfit-sim error
by yd li 27 Mar '14

27 Mar '14

Hello list, I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a mri_glmfit.log in folder /.../g2.lh, and copied this file to folder /.../g2.lh/C1/.But i still got an error 'fwhm: Undefined variable.' Can anybody help me settle this problem? Thank you! --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.5.0-23-generic x86_64

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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

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