Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Reviewer questions...
by Jerome Maller 10 Jan '17

10 Jan '17

Dear FreeSurfer development team, I have received Reviewer comments from a manuscript I recently submitted based on results from FreeSurfer (beta version) output. The focus of the study is the hippocampal tail. Whilst one Reviewer likes it, the other has asked a number of questions regarding the segmentation validity. Specifically, the Reviewer refers to Schoemaker D, et al (2016) Hippocampus and amygdala volumes from magnetic resonance images in children: Assessing accuracy of FreeSurfer and FSL against manual segmentation. Neuroimage. 2016 Apr 1;129:1-14. The Reviewer has also stated that the authors of the FreeSurfer software “have never provided detailed volumetric protocol for hippocampal volume segmentation or its subregions/subfields. For instance, I am not sure how they separate the hippocampal tail from the hippocampal body or amygdala from hippocampus. Therefore, it is not clear how the segmentation of those brain structures is done.” The Reviewer then goes on to state that “Fimbria is so small compared to the resolution used in this study in order to be measured separately on conventional T1 images (See see Frisoni et al., 2015 or Boccheta M et al., 2015 EADC-ADNI protocol). Molecular layer is not even visible on T1 images (please provide the MRI images when it can be seen and quantified on T1 MRI images). The entire stratum lacunosum-moleculare is less then 0.6 mm thick so I do not know how the FreeSurfer can split it in half with the resolution of 1mm and measure it separately from CA…”. Can you please suggest how I should respond to these Reviewer questions? Regards, Jerome Maller -- *Dr Jerome J Maller BSc,GradDipPsych,MSc,PhD* Neuroscientist Adjunct Senior Research Fellow *Monash Alfred Psychiatry Research Centre (MAPrc)* *Central Clinical School, Monash University and Alfred Hospital* *4th Floor, 607 St Kilda Rd, Melbourne VIC* Adjunct Associate Professor *Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University.* *T: +61 3 9076 2404* *F: +61 3 9076 6588* *M: +61 419 221 454* *E: jerome.maller(a)monash.edu <jerome.maller(a)monash.edu> *

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Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use
by miracooloz＠gmail.com 09 Jan '17

09 Jan '17

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Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use
by Antonin Skoch 09 Jan '17

09 Jan '17

Dear Paul, you can also try to play with "reposition surface" tool in freeview, where you (apart from other options) can directly edit coordinates of the surface vertices. However, this tool is not well documented and I myself would like to know the significance of some of the parameters - see my unanswered post from 4th january 2017: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50759.html And, I am not sure how this works in 5.3 version of freeview, I have used it only in V6beta (dev) version. Regards, Antonin I think this problem is fixed in 6.0 (if and when we get it out) On Mon, 9 Jan 2017, miracle ozzoude wrote: Thanks bruce for your response. I accidentally listed number 3 twice instead of 4. Here's my 4th question: Which of the mris_make_surfaces can I use to correct the pial surface when it does cross the white matter and also, which is helpful with white matter surface extension? Please see attached screenshot. I came across a post with similar error in the forum and you diagnosed but it wasn'tfix https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-April/045097 .html Best, Paul

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PETSURFER Tutorial Problems
by Anderson Napolitano 09 Jan '17

09 Jan '17

Good Afternoon Support Team, Per step one of your PETSURFER tutorial, the command: gtmseg --s <subject>?, where the <subject> is the name of the subject that we had ran recon-all, outputs the error as described in out.txt attached in this email. If you have the time, it would be much appreciated if you can help us resolve this issue. Thank you for your time. Warmest Regards, Anderson Napolitano

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mris_make_surfaces scripts and how and when to use
by miracle ozzoude 09 Jan '17

09 Jan '17

Hello Freesurfer, I was going to the ReconAllDevTable ( https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) and i came across 3 different mris_make_surfaces scripts. 1) When do I use any of the 3 mris_make_surfaces scripts after running recon-all -all? 2) Is there a default/standard nsigma above/below the mean to use when running the third mris_make_surfaces? 3) Which of the mris_make_surfaces can I use to correct the pial surface when it does cross the white matter and also, which is helpful with white matter surface extension? 3) Is this the correct recon-all script to use after wm edits with T2pial option? "recon-all -autorecon-wm -autorecon3 -T2 /T2_volume T2pial -s" Thanks Paul

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Re: [Freesurfer] aseg error - ventricle mislabeled, negative values in aparc.a2009s+aseg
by Antonin Skoch 09 Jan '17

09 Jan '17

Dear Bruce, I downloaded the recent build from 3rd January 2017 and tried to re-process the problematic subject. Unfortunately, the posterior part of lateral ventricle is still not in large extent not correctly labeled. Moreover, I noticed that the T2 normalization in ventricle part contains artificially low values. See the screenshot of aparc.a2009s+aseg, raw T2 and errors in normalized T2. I have uploaded the updated reconstruction at your server with name aseg_error_fs_20170103.tar.gz so you can take a closer look. Regards, Antonin Hi Antonin, yes, we came across that bug and have fixed it (it's one of the reasons that we didn't release before Christmas)Thanks for catching it thouggh Bruce On Wed, 4 Jan 2017, Antonin Skoch wrote: > Dear experts, > > while testing V6beta version I encountered problem with aseg. In one subject > (with quite large ventricles) posterior part of right lateral ventricle is > not labeled as brain at all and part is labeled as WM-hypointensities and > nonWM-hypointensities. Moreover, in aparc.a2009s+aseg there are > periventricular regions with value -1 (not present in aseg.presurf). > > These negative values I observed in one more subject. > > I am uploading the problematic subject named aseg_error.tar.gz to your > server. > > Linear Talairach registration seems OK in this subject. > > Could you please comment on, how to correct this error? > > My second question, is it possible to check non-linear Talairach > registration, i.e. talairach.m3z? > > Regards, > > Antonin Skoch > > >

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mris_make_surfaces -first_wm_peak - change of behavior in V6beta version
by Antonin Skoch 07 Jan '17

07 Jan '17

Dear experts, I have noticed changes in behavior of mris_make_surfaces with -first_wm_peak option in V6beta version after 20th December 2016. (This option is used in HCP pipelines in FreeSurferHiResWhite.sh script). This new version or mris_make_surfaces produces white surfaces much internally (i.e. away from pial surface) than version before 20th December which appeared to me more anatomically correct. See the screenshot (yellow surface is white surface before 20th December, red surface is white surface after 20th December, it seems to be placed too internally wrt white/gray interface. The commit from 20th December relating to this modification states that there is change of -first_wm_peak behaviour to look for peaks in 2nd derivative. Could you please comment on? Regards, Antonin Skoch

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Getting aparc+aseg without running the whole recon-all process
by Halász László 07 Jan '17

07 Jan '17

Dear fellow Freesurfer users, I just wanted to ask whether there is simpler and shorter way for getting aparc+aseg without running the whole recon-all process? I'm not familiar with all the steps that run during recon-all. If there is a shorter way that is not so time consuming, please guide me through the required steps. Thank you for your help, László Halász

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change the background color of screenshot of Freeview
by Hao wen 07 Jan '17

07 Jan '17

Hi, everyone: I have a simple question, i want to save the screenshot in Freeview, but the default background is black, I can not find the option to change the black background to be white, do you have any idea??? Here is the default output screenshot in Freeview: [cid:0d359a84-c5fa-41b6-aac0-1715cf7bcfc7] Can you give me any clue?? Change the background from preference does not work.. Thanks in advance Hao

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freeview error (libpng12.so.0) on Ubuntu
by Jeffrey Crawford 06 Jan '17

06 Jan '17

Hello all! I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing them. I am currently getting this error when typing "freeview" into the command prompt: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" My current version of Freesurfer is: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a.tar.gz >From the research I did online, first, I used these commands from this mail archive https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43219.html then installed what was supposed to fix something similar from the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/Download by doing "sudo apt-get install libjpeg62" Now I have been trying to install "libpng12.so.0" or some variation on that, but linux does not seem to be able to find it. Any help? -Jeff

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