Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

extracting pial surface area numbers...
by Karl Liu 22 Mar '16

22 Mar '16

Dear FS team, My question is how I should extract the measure of pial surface area from a significant cluster after group-analysis. I performed statistical analysis in QDEC, choosing pial surface area as the measure. I found a significant cluster. Now I would to extract the surface area of this cluster from each subject, so that I can plot the group means. But the numbers I got from the "cache.th20.neg.y.ocn.dat" file are quite small (mean centered at ~1). I am wondering how I should get the correct numbers from each subject. thank you in advance Karl

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Regarding: Freesurfer 6.0 dev version
by Dr Sampada Sinha 22 Mar '16

22 Mar '16

Dear freesurfer experts, I am trying to do hippocampal subfields segmentation on Mac. I will greatly appreciate if freesurfer 6.0 version link is forwarded to me. With thanks and regards, Sampada Pre-doctoral student KGMU, Lucknow India

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"Bump" - Fwd: lGI value is aberrantly high and misalignment fix
by Marco Bucci 22 Mar '16

22 Mar '16

Dear all, I forward again my original post. I also attach the recon-all.log of one of the several faulty cases. I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0) in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a and I have fixed the SearchProjectionOnPial.m. I also had to fix line 51 of make_outer_surface.m "v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation" with "v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) vol.vox2ras1(3,4)-v(:,2)];" in order to use the image coordinate to fix surface orientation and alignment. If I would use the original line 51, the surface produced by recon -lgi results misaligned with the reference pial and image. My problems remains the aberrantly high lgI value in most of my subject images. Can you help me? Yours, Marco Bucci ---------- Forwarded message ---------- From: Marco Bucci <bucci.marco(a)gmail.com> Date: 2015-12-22 23:49 GMT+02:00 Subject: Re: [Freesurfer] lGI value is aberrantly high To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution suggested by Marie Schaer to rereconstruct The images with "randomness" Recon-all -autorecon2-wm -randomness -autorecon3 I tried this fix on two of my subjects With errors. Not all subject resulted Errors in the computation of the gyrification. Can you help me? Marco Bucci Turku Pet Center Sent from my iPhone -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi ****************************************************

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Postdoctoral Position in Infant Brain MRI Analysis
by gangli 21 Mar '16

21 Mar '16

Postdoctoral research associate positions are available at the Infant Brain Mapping Lab in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill. Our current focuses are to better understand the dynamic and critical early brain development in health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate for Postdoctoral Research Associate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C/C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu)

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longitudinal data analysis
by John Anderson 21 Mar '16

21 Mar '16

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mri_cvs_register : output
by Elijah Mak 21 Mar '16

21 Mar '16

Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy. However, I can't seem to find the file combined_tocvs_avg35_elreg_afteraseg-norm.m3z, however, I have final_CVSmorph_tocvs_avg35.m3z. Is this essentially the same thing? Thanks for looking into this. Best Wishes, Elijah

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[freesurfer] XL defect correction?
by Jacky Lee 20 Mar '16

20 Mar '16

Dear freesurfer experts, I have encountered problems running recon-all on some subjects where the processes were stuck at "CORRECTING DEFECT 5 (vertices=14049, convex hull=3020) XL defect detected...". I have read from the mailing list that this is a large defect to be manually corrected or control points. So does that mean the recon-all cannot correct this? If that is the case, what are the steps for manual correction or control points and how should I re-run the recon-all afterwards with incorporation of this correction? Regards, Jacky Lee

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Replacing / turning off denoising filter
by Mojmír Vinkler 19 Mar '16

19 Mar '16

Hi, I was wondering if it's possible to replace or turn off your denoising algorithm `mri_nlfilter`. We'd like to try different denoising filters and compare how they influence segmentation performance. Right now we're applying filter before running recon-all, but I fear that applying your filter on already filtered image might degrade our analysis. I couldn't find any mention of mri_nlfilter besides this one on mailing list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020762.…. I hope I didn't miss something anything. Thanks! Mojmir

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mri_glmfit-sim ( cluster wise analysis)
by Alshikho, Mohamad J. 18 Mar '16

18 Mar '16

Dear FS experts, I ran cortical thickness analysis as previously explained in Wiki : Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 1. My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh 2. GLM analysis: mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir 3. Correction for multiple comparison mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces In order to do cluster-wise correction for multiple comparisons, I ran the command "mri_glmfit-sim" (step3). This command is calling, internally, the command "mri_surfcluster" as follow: mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh --vwsig lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Kindly, I have the following questions: 1. How the command mri_surfcluster choose the fwhm for the flag "csd" . In the previous command it shows fwhm=15. 2. What is purpose of using the flag Bonferroni in the previous command 3. If we are doing cluster wise correction, what is theexact usage of the flag "--vwsig" Thanks for your patience ! Looking forward to learn from you Mohamad

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preproc-sess in longitudinal stream
by Ji Won Bang 18 Mar '16

18 Mar '16

Dear. Freesurfer experts. Hi. How are you? I have dataset where a single subject was scanned twice on different days. I ran recon-all in logitudinal stream (cross, base, long). The recon-all -base gave me the within-subject template and the recon-all -long gave me the directory in the format of tp1id.long.templateID. By doing so, I get different time point's norm.mgz (under tp1id.long.templateID directory and tp2id.long.templateID etc) aligned in the same voxel space. As a next step, I'd like to register the functional scans to the anatomical scans via preproc-sess (or mc-sess, spmregister-sess etc). I guess, the anatomical can that I should use is norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc. (?) To register the functional scans to the newly created anatomical image obtained from recon-all -long process (norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc), I think I should specify this newly created norm.mgz in the command line... but couldn't figure it out yet. The preproc-sess command that I used in the cross-sectional process is as below: preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_decode -per-run -force -fwhm 0 What should I do to make registration process target a specific anatomical image? Please give me any advice! Thank you so much for your help! Best, Ji Won

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Freesurfer March 2016