Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

reposition surface for pial surface
by miracle ozzoude 10 Jan '17

10 Jan '17

Hello Freesurfer, I would like to learn how to use the reposition surface tool in freeview. Specifically, what parameters to enter in the gui (see screenshots). Is there any documentation on how to use it if not, can someone with experience work me through it. Thank you. best, Paul

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ERROR: fast_selxavg3() failed\n
by Michael Schirner 10 Jan '17

10 Jan '17

Dear experts, I'm attempting to perform step 6 in the FsFastTutorialV5.1 (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLev…; "First-level Analysis using selxavg3-sess"), but get the following error when I run the selxavg3-sess command: ------- octave output -------------------- LD_LIBRARY_PATH /homec/hbu23/hbu231/Software/Octave/3.8.2/lib:/homec/hbu23/hbu231/Software/Libraries/octave /homec/hbu23/hbu231/Software/Octave/3.8.2/bin: Permission denied. ------------------------------------------ ERROR: fast_selxavg3() failed\n I've searched the list and a similar error has been reported but the proposed solution did not work. (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-April/044814.ht…) Specifically, it does not work despite the named directory and several enclosing directories received full read, execute and for tests even write permissions (also, as a test, the freesurfer folders received full permissions): drwxrwxrwx 2 hbu231 hbu23 512 Jan 9 16:52 bin As I’m attempting to run it on a supercomputer I cannot execute it as a superuser. Does anyone have any thoughts on how to solve this? Thanks! Michael ----------- 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: CentOS Linux release 7.2.1511 3) uname -a: Linux jrl11 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

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automatic segmentation of hippocampal subregions in young children
by Tracy Riggins 10 Jan '17

10 Jan '17

Dr. Inglesias I am a developmental psychologist studying memory and brain development in early childhood at the University of Maryland. My lab has acquired whole-brain standard resolution T1-weighted scans and ultra-high resolution T2-weighted scans from 125 child participants aged 4-8 years. We are using your automatic segmentation for hippocampal subregions to obtain volumes for assessment in our study. As we write up the results for publication, I began to wonder if reviewers will ask for verification that the automatic segmentation is valid for our young age group. I know you tested Alzheimer's and an elderly sample in your paper, so I suspect it is valid for a variety of populations. But I am writing to inquire your thoughts on this issue. Do you think verification is needed? If so, would you suggest we hand trace a subset of our data to verify the automatic methods? I would appreciate any advise as to how to best approach this. Thank you, in advance, for your consideration of my inquiry. Sincerely, Tracy Tracy Riggins, Ph.D. Associate Professor University of Maryland

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dice coefficient computing
by N Saf 10 Jan '17

10 Jan '17

Dear freesurfers, I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have manual segmentation for hippocampus in my subject space(208x176x176)as well. I want to compute the dice coefficient with one simple Matlab code. how can I do it correctly ?if I want to bring the aseg to subject space , which command with which options is the best way to do it correctly ?any help can be appreciated.(I did it for the FSL segmentation result but it was simple because the result is in my subject space). Best Regards, Nazanin

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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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Freesurfer January 2017