Freesurfer

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longitudinal data analysis
by John Anderson 21 Mar '16

21 Mar '16

2 2

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

2 1

[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

2 1

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

3 6

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

1 0

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

1 0

small numbers of extracted pial surface area‏
by Karl Liu 18 Mar '16

18 Mar '16

Dear Freesurfer experts, I am reposting my question from early this week since it is not answered. Any help much appreciated. My question is about the measure of pial surface area. Following a group comparison and correction in QDEC, I found a significant cluster (size: 760mm^2) when choosing area. pial as the measure. In order to plot group means in a bar graph, I extract numbers from the "cache.th20.neg.y.ocn.dat" file, but the average is less than 1. Why is the magnitude of supposed pial surface area so small? Is this actual or standardized measure ? Karl

1 0

Reg: Correcting Defect error
by Jesu Kiran Jk 18 Mar '16

18 Mar '16

Dear Freesurfer experts, I have been running freesurfer for a patient data, and have to find this retesselalation of defect. I have successful with some data but for some others it looks frozen even after 7 days. Would it be possible to please have a look and help me out? Also, how could I pass on the data? Looking forward for your kind reply, Kind regards, Jesu

2 1

Re: [Freesurfer] Extremely small numbers of extracted pial surface area
by Karl Liu 18 Mar '16

18 Mar '16

1 0

GM mask to native T1
by Patrick Beukema 18 Mar '16

18 Mar '16

I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native space. I see this thread that states this command is the correct way: mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz from: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33578.html However, when I do do, the alignment is off. All of my rawavg.mgz are rotated relative to the original T1 in native space, so the GM masks are also not properly aligned. Is there a transformation that I am missing somewhere between rawavg.mgz and native T1? Thank you, Patrick

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