Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Including a hyperintensity in wm surface
by Rachel Hoel 16 Apr '19

16 Apr '19

External Email - Use Caution Dear Freesurfer Developers, Our study is using the longitudinal processing pipeline with version 6.0. We have one subject where there is a hyperintenisty in the right temporal lobe, and even after adding several control points and running recon-all, the white matter is still not fully being included in the surface. The coordinates are about [83, 163, 139]. For this particular subject, we are performing both white and grey matter edits starting at the cross-sectional. I've tried adding multiple rounds of control points; and also removed all the control points and tried filling in wm voxels, but I can never get that region to be fully included. I uploaded the subject about a week ago and was hoping that someone could take a look. Best, Rachel

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Resampling anatomical ROI to the functional images
by Juhyoung Ryu 16 Apr '19

16 Apr '19

External Email - Use Caution Hi all, I’d like to upsampling anatomical ROI data, what i created using ribbon file, to the functional resolution. As the anatomical and functional data were aligned, I need only re-slice processing except for coregistration. I tried upsampling using ‘mir_label2vol’, but i have no idea to create ‘register.dat’ file. ‘mri_convert’ with —voxsize flag provides upsampling, but that was all. Would you help me to re-slice ROI data to the functional coordinate? Thank you in advance, Juhyoung

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Re: [Freesurfer] Nucleus Accumbens Area or Volume
by Maksimovskiy, Arkadiy 16 Apr '19

16 Apr '19

Hi Bruce, Got it- thank you for clarifying. best, arkadiy

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Nucleus Accumbens Area or Volume
by Maksimovskiy, Arkadiy 16 Apr '19

16 Apr '19

Dear Experts, My apologies for the very basic question. I wanted to ask, because it keeps coming up in literature, and I wanted to make sure that I am not mistaken. Based on the documentation, my understanding is that Freesurfer ROI's do not generate Nucleus Accumbens volume, but just NAcc area of that structure (due to geometrical measurement accuracy). I was wondering if you could confirm if that is correct. Thank you for your time and information, Arkadiy

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Re: [Freesurfer] The mystery of the missing mcprextreg file
by Mcnorgan, Christopher 15 Apr '19

15 Apr '19

External Email - Use Caution Hi Doug, I attempted to send the mc-subjectname log files to the group, but they were bounced because of file size (one exceeds 1MB). I’ll try again with just the smaller of the two, and hopefully the same issue is at play in each case.

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Research Assistant Position, Prakash Lab, The Ohio State University
by Salerno, Joanna M. 15 Apr '19

15 Apr '19

External Email - Use Caution Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, starting May 2019 in the Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University. RA responsibilities will include assisting in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitating recruitment efforts between the laboratory and community partners; conducting neuropsychological assessment sessions with clinical populations; and assisting with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB. Desired qualifications include: Bachelor's degree in a psychology or neuroscience; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software package, such as FSL, AFNI, or SPM. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #448245 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: https://clinicalneurolab.org 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.

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the problem about XL defect detected...
by Abby tang 15 Apr '19

15 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) XL defect detected... Killed Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I don't know how to check and amend ?h.orig.nofix. please give me some commands in detail. Thank you for your help.

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recon-all error after maual control points definition
by Boris Rauchmann 14 Apr '19

14 Apr '19

External Email - Use Caution reading input surface xyz/fs_all_subjects/0031/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.3220 (-4.6610) -vertex loglikelihood: -6.6151 (-3.3076) -normal dot loglikelihood: -3.5637 (-3.5637) -quad curv loglikelihood: -6.1122 (-3.0561) Total Loglikelihood : -25.6131 CORRECTING DEFECT 0 (vertices=16503, convex hull=4824, v0=77) mrisAddEdge: too many edges (255) XL defect detected... Large defect found - not a problem, but a curiousity No such file or directory Linux linuxrechner 4.15.0-47-generic #50~16.04.1-Ubuntu SMP Fri Mar 15 16:06:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0031 exited with ERRORS at Sun Apr 14 16:45:47 CEST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what causes this problem? Thank you, Boris

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How to convert a functional FSL mask to an anatomical Freesurfer mask
by Jennifer Legault 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Freesurfer experts, We ran a functional language localizer analysis in FSL and we want to apply the mask from this analysis to our SMRI analyses using the mri_glmfit command with the --mask option. Basically, we want to examine whether GMV within these language localizer regions is correlated with performance on various tasks. I previously used mri_convert to convert the .nii file to .mgh, and tried to run the mri_glmfit --mask command but received an error (ERROR: dimension mismatch 1 between y and mask) which I believe is linked to the fact that the previously run mris_preproc files are 4D, while our functional mask is still only 3D. When I use tksurfer and overlay the 3D mask file, it looks fine. So the question is how can we convert our 3D functional mask into a format that we can use for the mri_glmfit command (Nverteces x 1 x 1 x Nsubjects)? Thanks for all your help! Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

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mri_segstats
by Nasiriavanaki, Zahra 12 Apr '19

12 Apr '19

Dear Freesurferers I was trying to do a connectivity analysis using subnuclei of Amygdala. I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked at the results, the values are too high (around 800). Could you please let me know what I'm doing wrong? P.S: the segmentation was basically done in MNI152-1mm and I moved it to MNI305-2mm by mri_vol2vol. mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt Thanks a lot MOna

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Freesurfer April 2019