Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Extract the ROI mapping
by 2016102110043＠whu.edu.cn 18 Apr '19

18 Apr '19

External Email - Use Caution Hello Freesurfer developers, After I recon-all my subjects, the label files are generated. Could you please kindly help me how can I extract the special brain region from these label files by matlab: But I don't know if it is the mean thickness for brain region BA1. Where can I get the detail information for these label files, such as 'lh.BA1.label'. Best Regards and thanks, Henry 2016102110043(a)whu.edu.cn

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MRI RA position available at Ohio State Buckeye Brain Aging Lab
by Hayes, Scott M. 18 Apr '19

18 Apr '19

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position in the Buckeye Brain Aging Lab (B-BAL; https://u.osu.edu/bbal/) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in unix, python, matlab, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, SPM, CONN, R. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com,under job listing #448534 (application portal opens this weekend) and submit a cover letter, writing sample (research paper from course, poster presented at a conference), current CV and arrange to have two reference letters emailed to bbal(a)osu.edu<mailto:bbal@osu.edu> . If you have questions about the position or the lab, please email bbal(a)osu.edu<mailto:bbal@osu.edu> . To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status. Best, Scott __________________ Scott M. Hayes, Ph.D. Assistant Professor Department of Psychology Chronic Brain Injury, Discovery Themes The Ohio State University <http://u.osu.edu/>http://u.osu.edu/bbal/

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fixing errors with pial boundary
by Morgan Botdorf 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Experts, I asked about this a few months ago, but didn't receive a reply so thought I would ask again! We have come across several subjects where the pial boundary line does not extend far enough outward and misses some gray matter. We know that control points can be used to fix a similar issue with white matter boundaries. Are there any tools that can be used to fix this type of gray matter error? Thank you, Morgan Botdorf -- Morgan Botdorf, M.S. Graduate Student Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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convert aseg to functional space
by Sam W. 18 Apr '19

18 Apr '19

External Email - Use Caution Hi, I just finished reconall and now I'd like to convert the aseg.mgz to native functional space. My first thought was to simply convert the aseg.mgz to native functional space with mri_vol2vol: mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader Is this a valid procedure to convert the aseg to functional space? I think the recommended way is to register the example_func to anatomical first: bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat and then use mri_vol2vol with the --inv flag mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader --inv But I'm not sure... Could someone confirm which of the above (or maybe none of them) is correct? Best regards, Sam

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mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Many thanks, Colleen

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Issue with longitudinal surfaces
by maxime GUILLAUME 18 Apr '19

18 Apr '19

External Email - Use Caution Dear freesurfer experts, I re-send this question because i didn't received (or missed) the answer from the first time i sent it. I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template using the command given in the fs tutorial, there are important differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the captures surfaces of the first visit are in red and blue and in lighter tones for the second visit)

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Thalamic segmentation
by 郑凤莲 18 Apr '19

18 Apr '19

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the latest version of Freeview. However, I can't find this version on Freesurferwiki. Could you share me the install steps and the latest version? Thanks very much for your help. Sincerely, Zheng

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same aparc ROI with mri_label2vol?
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label labels/lh.G_cingul-Post-dorsal.label --temp mri/rawavg.mgz --subject bert --hemi lh --o roi-in-rawavg.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg register.dat When I load the roi-in-rawavg.nii.gz and the aparc.a2009+aseg.mgz volume in freeview there are parts of the Cingulum in the aparc.a2009+aseg that are not included in the roi-in-rawavg. Probably this is related to the -fillthresh and -proj thresholds. Is there a way to get exactly the same ROI with mri_label2vol as shown in the aparc.a2008+aseg volume? Best regards, Sam

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same output with vol2vol and label2vol
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, In a Freesurfer help webpage it says that to convert an image (eg brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use mri_label2vol. I converted the aseg.mgz of bert using both vol2vol and label2vol and found no difference - The resulting output images look exactly the same. Is there really an advantage of using label2vol instead of vol2vol? Thanks! Sam

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correlation analysis
by TMS lab 17 Apr '19

17 Apr '19

External Email - Use Caution mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. < DGREVE(a)mgh.harvard.edu> ha scritto: > what is your command line? > > On 4/11/19 3:53 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Unfortunately I get such error message with the matrix 0 0 0 1 > > ERROR: dimension mismatch between X and contrast contrast.mtx X has > > 3 cols, C has 4 cols > > > > Instead if I use 0 0 1, it works > > > > Best, > > RAFAEL > > That should have failed because it only has 3 values (should have 4). I > > think it should be 0 0 0 1 > > > > > > On 4/11/19 3:20 AM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > You are right. I want simply to correlate myelin and nhpt regressing > > > out age. > > > I did it with the following matrix: > > > 0 0 1 > > > And it seems to work. Is it ok this matrix? > > > > > > Thanks a lot > > > Rafael > > > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > > <DGREVE(a)mgh.harvard.edu > > <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu > > <mailto:DGREVE@mgh.harvard.edu>>> ha scritto: > > > > > > That will compute the average of the Age slope and the NHPT slope. > > > Probably not what you want to do > > > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Dear Freesurfer team, > > > > > > > > I'm running a correlation analysis where I'd like to corelate > > > > myelination and a clinical parameter (NHPT) regressing out the > > > effect > > > > of age. > > > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > > > This is my FSGD FILE: > > > > GroupDescriptorFile 1 > > > > Title Myelin > > > > Class Main > > > > Variables Age NHPT > > > > Inputfs_CGaMain 19 18.2 > > > > ....... > > > > > > > > Is the matrix ok? > > > > > > > > Thanks > > > > Rafael > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > RispondiRispondi a tuttiInoltra > > > > > > > > > > > > > > Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna(a)gmail.com > > <mailto:tmslabna@gmail.com>> ha scritto: > > > > You are right. I want simply to correlate myelin and nhpt > > regressing out age. > > I did it with the following matrix: > > 0 0 1 > > And it seems to work. Is it ok this matrix? > > > > Thanks a lot > > Rafael > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto: > > > > That will compute the average of the Age slope and the NHPT > > slope. > > Probably not what you want to do > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer team, > > > > > > I'm running a correlation analysis where I'd like to corelate > > > myelination and a clinical parameter (NHPT) regressing out > > the effect > > > of age. > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > This is my FSGD FILE: > > > GroupDescriptorFile 1 > > > Title Myelin > > > Class Main > > > Variables Age NHPT > > > Inputfs_CGaMain 19 18.2 > > > ....... > > > > > > Is the matrix ok? > > > > > > Thanks > > > Rafael > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer April 2019