Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

talairach and MNI305 Atlas
by Mark Plantz 15 Jul '13

15 Jul '13

Hello freesurfers, I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for infant MRI's. Currently, I have three of the four required arguments. I am lacking the talairach.lta file. In order to obtain this file, I must run recon-all. However, I do not wish to run recon-all until I have obtained the necessary .gca atlas described above. Is there possibly some sort of alternative iterative method to create the talairach transform? If so, does it require a different atlas than the MNI305 atlas? Thanks for the help! -Mark

3 2

Confused results from Qdec
by Wayne Su 15 Jul '13

15 Jul '13

Dear Freesurfers, I used Qdec to do two-group comparison on cortical thickness. Demeaned age was used as the covariate. The question I¹m looking at is that ³Does the thickness-age correlation differ between C1 and C3?² When FWHM=15mm was chosen, I got confused results: When I used threshold 1.3(0.05) in Monte Carol Null-Z Simulation, I didn¹t get any significant cluster. However when I used threshold 2(0.01), I did get one significant cluster. However I expected I at least got same significant area when I used lower threshold. If I chose FWHM=10mm, I got another significant cluster when the threshold 1.3 was used, and got nothing when the threshold 2 was used. However this cluster is not the same area I got when FWHM=15mm was used. At this point, I¹m totally confused, and don¹t know which one should be trusted. Should I used FWHM=10 or 15? Should I used threshold 1.3 or 2.0? My group one have 49 subjects and group two have 46 subject. All subjects are males. Hope someone can point the right direction for me. Thank you very much. Wayne

2 1

using mcextreg.bhdr in version 5.x?
by Caspar M. Schwiedrzik 15 Jul '13

15 Jul '13

Hi! I am doing motion correction outside Freesurfer and would like to use motion nuisance regressors in my GLM, which I run in FSFAST. I am externally creating mcextreg.bhdr, mcextreg_000.blfoat and mcextreg_000.hdr for analyses in Freesurfer v4.5, but I was wondering whether I can use the same files for analysis in Freesurfer v5.x. Or should I convert them to something else? The documentation is slightly ambiguous about this. Thanks! Caspar

3 5

Editing the endpoint ROIs, and re-running trac-all -path
by Susan Kuo 15 Jul '13

15 Jul '13

Hi Anastasia, For one of my subjects, I am noticing that the right uncinate fasciculus is very diffuse and more importantly, erroneously crosses from the frontal to the temporal lobe. I looked at the original endpoint ROI generated by trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the endpoints appeared to cross over into the frontal lobe. Attached is a snapshot for your perusal. On the left side is a display of the <subject>/dmri/dtifit_FA.nii with the <subject>/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. As you can see, the right unc tract crosses from the frontal to the temporal lobe. On the right side is a display of the <subject>/dmri/brain_anat_mni.nii.gz with the endpoints <subject>/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in green and <subject>/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the red dots are control points). As you can see, the blue endpoints bleed over from the temporal to the frontal lobe. I tried to eliminate these blue points with fslview and then writing over rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually editing rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I subsequently tried to re-run trac-all -path, and unfortunately, all my tracts looked much worse. Do you know if incorrectly placed endpoints impair the path reconstruction? Do you think you can help me? Any advice you can give would be much appreciated. -- Susie Kuo NIH Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

2 1

lh.curv VS lh.inflated.h
by 宋银南 15 Jul '13

15 Jul '13

Dear Sir， I have found two files in the surf folder.One is 'lh.curv',the other is 'lh.inflated.h'.I have found some one said that the 'lh.curv' can be used to quantify the curvature. but int the wiki, the command 'mris_curvature' can ouput the file 'lh.inflated.h' which is MeanCurvature. So I want to know which should I use. I also want to know what the 'lh.curv' is ? MeanCurvatur or GaussCurvatur,or some other? Thank you very much! Thank you for the freesurfer, it is really very good! Best Wish! YinNan Song

2 1

pathstats.byvoxel.txt
by Susan Kuo 15 Jul '13

15 Jul '13

Hi Anastasia, I noticed that my pathstats.byvoxel.txt files are missing the last four values (AD_Avg RD_Avg MD_Avg FA_Avg) even though I'm certain I ran trac-all -path -c <dmrircFile> correctly. Do you have any idea why this might be? e.g. a configuration file change? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

1 0

application of mri_cvs_register question
by Hoptman, Matthew 15 Jul '13

15 Jul '13

Hi all, I see how to apply mri_vol2vol to DTI data from dt_recon, but I'm not clear on how to do so to DTI data processed in Tracula. The command in the "Multimodal integration and inter-subject registration" tutorial is: mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg But in Tracula, there are no "register.dat" files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula transform should I choose? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

3 2

minor fsfast bug report
by Joseph Dien 15 Jul '13

15 Jul '13

In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g., cache.th20.pos.sig.ocn.annot), the names of the clusters take the form: cluster0 cluster-001 cluster-002 … but the last one is of the form cluster6 which is to say, no dash and no zero-padding. I assume they are meant to have a consistent format. Not a big deal, but consistency would be helpful for scripts. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

2 1

Loading thickness data in python
by Sebastian Urchs 15 Jul '13

15 Jul '13

Hi, I am trying to figure out how to load thickness data into python such that I would be able to identify the thickness at a given mesh node and also identify surrounding nodes. I searched the mailinglist and found this http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but this unfortunately did not solve my question as I was unable to find a downloadable version of pymgh. Is there some python package that you could point me to and that allows me to load thickness data and do analysis in python? Thanks in advance! Sebastian

2 1

Non-grey matter classified as grey matter
by ye tian 15 Jul '13

15 Jul '13

Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye

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Freesurfer July 2013