Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Re: [Freesurfer] Extremely small numbers of extracted pial surface area
by Karl Liu 15 Mar '16

15 Mar '16

Thank you for your comment, Bruce. Regardless of technical issues, I am still troubled by the small magnitude of extracted value of pial surface area. Following group comparison and correction in QDEC, there is a significant cluster (size: 760 mm^2). In order to make a bar group of group means, I use numbers from the "cache.th20.neg.y.ocn.dat" file, but the average is less than 1. Did I use the right file to plot group mean of pial surface area, but why the magnitude is so small ? Thank you for your help! Karl

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TRACULA messy tracts
by denizzgursel 15 Mar '16

15 Mar '16

Dear Anastasia and Tracula users, I succesfully ran the longitudinal Tracula procedure for one subject. However, when I visualized the tracts, they look a bit weird (not smooth). Even if I played with the threshold on freeview, I couldn't make them look nice as in the wiki page. I checked the registration and it looks accurate, so I am not sure what could be wrong. I am attaching the messy looking tracts for your reference. Could you tell me if I should run again with reinit=1 for these tracts? Thank you very much for your time. Best regards, -- D.

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Extremely small numbers of extracted pial surace area
by Karl Liu 15 Mar '16

15 Mar '16

Dear FS team: I want to ask for some advice on how to extract the values of pial surface area. I use QDEC to perform a surface-based F-test. The measurement is area.pial and the smoothing is 10 in QDEC. After correction, there is one significant cluster with size of ~760 mm^2. The problem comes when I want to extract the measure from each participant, so that I can plot the group means. Currently I used the values from the "cache.th20.neg.y.ocn.dat" file, but all the group means varies between 0.7-1.0 in magnitude. I believe the unit is mm^2, because this is pial surface area. But is 0.7-1.0 mm^2 too small? What is the correct way to extract surface area from this signficant cluster, so I can plot the pattern of group differences in a bar graph? Another question is the validity of surface-based analysis on pial or WM surface area. I found most FS publications focus on the thickness, but not the surface area. From your perspective, is the surface area as valid as the thickness measure? Many thanks in advance Karl

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Re: [Freesurfer] -autorecon2-cp
by Jaiashre Sridhar 14 Mar '16

14 Mar '16

Bruce, Thanks! Apart from the control points on the lesions, I have control points that were placed on consequent slices on the coronal view but they look stacked upon one another from a different view. But these control points are placed on voxels that are definitely white matter. Does placing controls points really close to each other change the intensity of the nearby region or whole brain in general? Thanks, Jaiashre.

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-autorecon2-cp
by Jaiashre Sridhar 14 Mar '16

14 Mar '16

Hi, I have a general question about control points. I have added control points to fix the white matter boundary errors throughout the brain. I think that some of these control points that were placed in brain lesions (lower intensity voxels or black spots that are supposedly white matter) have changed the overall intensity and boundaries of the structures. I would like to remove some of these control points but they have gone through several iterations of recon already. Would removing the control points at this point and running -autorecon2-cp set the intensities back to original (orig.mgz)? Or should I go back and fix them from scratch? Thanks, Jaiashre.

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Editing Lesions in FreeSurfer 5.1
by Allison Rainford 14 Mar '16

14 Mar '16

Hi Freesurfer Team, In FSTutorial, it states that control points should not be placed on lesions to try to normalize the intensity there and only white matter edits should be made. What should be done in the case that white matter edits alone do not resolve reconstruction issues at the site of a particularly bad lesion? Thank you! Allison

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group analysis all measures same results
by Kaiming Yin 14 Mar '16

14 Mar '16

Dear guys, I was doing group analysis (command-line) on two groups (patients and control, no age or other information). The data has been "qcached", and after following the three steps as "mris_preproc, mri_glmfit and mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained the difference on thickness in both left and right hemispheres, which seems great. However, when I repeated the above steps on other measures, e.g. area, area.pial, volume (also replaced the parts of "thickness" in the command lines), the results seemed to be exactly the same again as those in the thickness comparison, even the p-value numbers in the file "cache.th40.neg.sig.cluster.summary" were the same. I was using Freesurfer v6.0-beta, and I performed the individual data analysis on a linux cluster and I copied/downloaded the whole "qcached" subject directory to my linux laptop to perform the group comparison, both using the same version of Freesurfer, does it matter? Or do you know why it happened like this? Thanks, Kaiming

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mris_anatomical_stats -th3
by Kaiming Yin 14 Mar '16

14 Mar '16

Dear guys, I checked one of my subjects file /stats/lh.aparc.stats, in which it said the commandline as: mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject1 lh white what does the flag "-th3" mean? I'm using Freesurfer v6.0 beta. Thanks, Kaiming

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unknown option in new brainstem segmentation
by Claudia Testa 14 Mar '16

14 Mar '16

Dear Freesurfers, I've installed Freesurfer 6.0 beta in a virtual machine, and run the -brainstem-structures option to recon-all. The process stopped with an error: "ERROR: Option --DKTatlas40 unknown" In the following, all the information: _____________________________________________ FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64 ______________________________________________ 1) subject name is 11960 2) the command line is: recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz -s 11960 -brainstem-structures 3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 11960 exited with ERRORS at Wed Mar 9 23:53:10 CET 2016 4) in attach the recon-all.log file Thank you for your help Claudia

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Anterior to Posterior Length
by Heather Acuff 14 Mar '16

14 Mar '16

Good morning, I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather Acuff

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Freesurfer March 2016