Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

input segmentation masks in recon-all
by yao wu 18 Dec '18

18 Dec '18

External Email - Use Caution Dear Prof. Fischl, I hope to use Freesurfer to get some surface measures of brain structures. The 'recon-all' command will give the output of the surface measures when input the T1w MRI images. If my input files are the segmented binary masks (such as white matter or cortical grey matter masks) which do not need the segmentation-related steps in 'recon-all', which function/command I should use to get the surface measures of the left and right hemispheres (lh.curv, lh.inflated, lh.sphere, lh.sulc, etc.) and also the cortical thickness? Thank you so much! Regards, Yao

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Hippocampus cortical layers division
by Yixin Ma 18 Dec '18

18 Dec '18

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface files for pial and white/gray matter interface surface are required. But we don't have that surface data for hippocampus subfield division. Is that possible that I can generate those files? Thank you for your help in advance. Yixin

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VBM by freesurfer
by Maurizio Bergamino 18 Dec '18

18 Dec '18

External Email - Use Caution Hello, I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition? Thanks, Maurizio

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1) single subject surface activation in volume space and 2) small volume correction
by Loeffler, Martin 18 Dec '18

18 Dec '18

External Email - Use Caution Dear experts, I'm running a sensory mapping experiment, which I would like to analyse in single subject space. Everything seems to be working fine (see code excerpt below). Now I'd like to do two additional things: 1) show the surface results in single subject volume space (as overlay on T1). 2) Limit my surface analysis to BA3b, using correction for multiple comparisons in that region only. I've read that this should be possible with monte carlo simulation, but can't figure out how to do this for one subject only. Any help is much appreciated! Best, Martin mkanalysis-sess -fsd bold -surface self lh -fwhm ${fwhm_par} -event-related -paradigm Onsets.par -nconditions 5 -spmhrf 1 -TR 1.5 -refeventdur 12 -hpf 0.01 -nskip 3 -polyfit 2 -analysis MR.lh -force -per-run mkcontrast-sess -analysis MR.lh -contrast digit1_lh -a 1 -c 0 #... bbregister --s $subj --mov f.nii.gz --init-fsl --int whole.nii.gz --t2 --reg register.partial.dat preproc-sess -s $subj -fsd bold -surface self lhrh -fwhm ${fwhm_par} -projfrac 0.5 -per-run -update -regfile register.partial.dat selxavg3-sess -s $subj -analysis MR.lh -force freeview -f ${ANAT}/${subj}/surf/lh.inflated:curvature_method=binary:overlay=${FUNC}/${subj}/bold/MR.lh/digit1_lh/sig.nii.gz

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Link for Runtime still broken
by Aran 18 Dec '18

18 Dec '18

External Email - Use Caution Good morning, We also tried to downlowd the Matlab runtime for Linux to use the brainstem segmentation but we found that the link is still broken as Raúl Pérez said a week ago Not Found The requested URL /pub/dist/mcr/MCRv83_linux.tar.gz was not found on this server. ------------------------------ Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 443 Is there another way to obtain the runtime? Or do you have any ideas when this issue will be solved? Thanks in advance, -- Aran Garcia

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thalamus_proper or whole_thalamus volume measurement?
by Corinna Bauer 17 Dec '18

17 Dec '18

External Email - Use Caution Dear all, For the new thalamus nuclei segmentation there is a measurement for the whole left and right thalami. The values are different from the thalamus_proper values. Which output should be reported as the volume for the whole thalamus? Thank you Corinna

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Re: [Freesurfer] Program installation - fmriprep
by Alshelh, Zeynab 15 Dec '18

15 Dec '18

Hi, Please see below my issue with a freesurfer license when I try to run fmriprep. Kind regards, ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Neuroinflammation and Pain Imaging Laboratory A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu ________________________________ From: Help Desk -- Domenic Minicucci <help(a)nmr.mgh.harvard.edu> Sent: Friday, December 14, 2018 3:40 PM To: Alshelh, Zeynab Subject: Re: Program installation - fmriprep I recommend you ask freesurfer(a)nmr.mgh.harvard.edu about the license issue. My understanding is that you need to use the --fs-license-file flag and point it to a file that contains just these lines: dale(a)nmr.mgh.harvard.edu 001-4567-634 *Cler0.zkanMc FSAe6u/4WBa.E -- Domenic Minicucci (http://help.nmr.mgh.harvard.edu) On Fri, 14 Dec 2018 8:30pm, Alshelh, Zeynab wrote: > Is it returning an error : 'ERROR: a valid license file is required for FreeSurfer to run. ' > > > Also, the link you sent is broken. > > > Kind regards, > > > ---- > > Zeynab Alshelh, PhD | Postdoctoral Research Fellow > > Neuroinflammation and Pain Imaging Laboratory > > > A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 > > +1 (617) 794 6838 > > zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> > > ________________________________ > From: Help Desk -- Domenic Minicucci <help(a)nmr.mgh.harvard.edu> > Sent: Friday, December 14, 2018 2:48:31 PM > To: Alshelh, Zeynab > Subject: Re: Program installation - fmriprep > > What happens if you use the Singularity container we have built at > > /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg > > Here's their example snippet from > https://fmriprep.readthedocs.io/en/stable/installation.html: > > $ singularity run --cleanenv /my_images/fmriprep-1.1.2.simg \ > path/to/data/dir path/to/output/dir \ > participant \ > --participant-label label > > so you'd need to replace /my_images/fmriprep-1.1.2.simg with > /usr/pubsw/packages/fmriprep/1.1.8/fmriprep-1.1.8.simg > > -- > Domenic Minicucci (http://help.nmr.mgh.harvard.edu) > > On Fri, 14 Dec 2018 7:32pm, Alshelh, Zeynab wrote: > >> Hi Domenic, >> >> >> Thanks for your response. >> >> >> Can I update my singularity? The current version on my machine in 2.4.4 and any version <2.5 requires a docker installed. >> >> >> >> " >> >> Preparing a Singularity image (Singularity version < 2.5)<https://fmriprep.readthedocs.io/en/stable/installation.html#id2> >> >> In this case, start with a machine (e.g., your personal computer) with Docker installed. Use docker2singularity<https://github.com/singularityware/docker2singularity> to create a singularity image. You will need an active internet connection and some time. >> >> " >> >> Kind regards >> >> ---- >> >> Zeynab Alshelh, PhD | Postdoctoral Research Fellow >> >> Neuroinflammation and Pain Imaging Laboratory >> >> >> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 >> >> +1 (617) 794 6838 >> >> zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu>> >> >> ________________________________ >> From: Help Desk -- Domenic Minicucci <help(a)nmr.mgh.harvard.edu> >> Sent: Friday, December 14, 2018 2:13:15 PM >> To: Alshelh, Zeynab >> Subject: Re: Program installation - fmriprep >> >> Hi Zeynab, >> >> Docker is a container that requires elevated root privileges and so we do not >> support it. Please use the singularity container option instead. We have >> singularity installed on all CentOS computers at the center already. >> >> Best, >> -- >> Domenic Minicucci (http://help.nmr.mgh.harvard.edu) >> >> On Fri, 14 Dec 2018 6:23pm, Alshelh, Zeynab wrote: >> >>> Hi, >>> >>> >>> I'm having trouble installing fmriprep on my machine >>> >>> The link to the instructions: >>> >>> https://fmriprep.readthedocs.io/en/stable/installation.html#singularity-con… >>> >>> >>> When I follow the instructions to download the program as a docker container, it requires docker to be installed. However, when I attempt to install docker, I am denied access. >>> >>> >>> Is this something you can assist with? >>> >>> >>> Kind regards >>> >>> >>> ---- >>> >>> Zeynab Alshelh, PhD | Postdoctoral Research Fellow >>> >>> Neuroinflammation and Pain Imaging Laboratory >>> >>> >>> A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 >>> >>> +1 (617) 794 6838 >>> >>> zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu>>> >>> >> >

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Surface based analysis - circular analysis?
by john Anderson 15 Dec '18

15 Dec '18

External Email - Use Caution Dear experts, I have three groups: - pre treatment (baseline) - post treatment (follow-up after 6 month of the baseline visit) - healthy controls. The three groups have PET data. I ran surface based paired t test between pre and post treatment. The analysis failed to show significant change in the signal between baseline and follow-up visits. As an alternative approach I tried: - Surface-based analysis between pre treatment vs healthy controls. This analysis found cluster A of significant difference - Surface-based analysis between post treatment vs healthy controls. This analysis found cluster B of significant difference I subtracted the two clusters A and B then I used the resultant mask (the difference between the clusters A and B) to measure the required signal. Colleague of mine said that this might be criticized for being circular and it may not be acceptable? My understanding is that this analysis is not circular because the signal was measured in a completely new region represents the difference between two clusters. I appreciate any suggestion or highlights! John

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Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results
by Bruce Fischl 15 Dec '18

15 Dec '18

when you bring it up in freeview does it properly show left and right? If it ever went through analyze as a format you will have lost the information that lets us distinguish left from right cheers Bruce On Fri, 14 Dec 2018, Geha, Paul wrote: > It is NIFTI format. > —————————————————— > Paul Geha, MD > Assistant Professor of Psychiatry > Yale School of Medicine > Assistant Fellow, The John B. Pierce Laboratory > Email: paul.geha(a)yale.edu > Tel:(203)903-4334 > > > > On Dec 14, 2018, at 10:53 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > what is your input data format? > On Fri, 14 Dec 2018, Geha, Paul wrote: > > Dear Bruce, > > Thank you for your reply. > > However, we are obtaining an odd result with FreeSurfer when we examine the volume > of the left and right accumbens. In the UK BioBank data >20K subjects freesurfer > segmentations the left accumbens is clearly significantly larger than the right > accumbens (https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.cts… > bel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c > bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN > MMSLiAGyXq734%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.cts… > abel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8 > cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM > NMMSLiAGyXq734%3D&reserved=0>). Also, the attached paper used freesurfer and > found left accumbens > right. In our hands, and in 2 different data sets > collected in two different sites, we obtain the opposite with FreeSurfer (right > accumbens > left accumbens). > > Furthermore, when we segment these same data sets with FIRST from FSL we do obtain > Left accumbens > right Accumbens in both data sets in agreement with the > literature. > > Any help in solving this discrepancy is much appreciated. > > Regards, > Paul > —————————————————— > Paul Geha, MD > Assistant Professor of Psychiatry > Yale School of Medicine > Assistant Fellow, The John B. Pierce Laboratory > Email: paul.geha(a)yale.edu > Tel:(203)903-4334 > > > > On Dec 13, 2018, at 3:49 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > Hi Meena > > it shouldn't. We reorient everything to radiological > > cheers > Bruce > On Thu, 13 Dec 2018, Meena M. Makary wrote: > > External Email - Use Caution > Hi; > I am wondering if the orientation of the input data to > recon-all (i.e. Neurological Vs. Radiological) > produces different results in terms of laterality (right > vs. left)? > Thanks; > --Meena > — > Meena M. Makary, Ph.D. > Assistant Professor | Cairo University > Postdoctoral Fellow | Yale University School of Medicine > Postdoctoral Associate | The John B. Pierce Laboratory > Postdoc Committee Chair | The John B. Pierce Laboratory > Career Development and Mentoring Manager Elect | OHBM > Student and Postdoc SIG > 290 Congress Avenue, New Haven, CT 06519 > +1 (475) 731-5592 > > > > >

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mri_surf2vol: has many more faces than vertices
by Winkelbeiner, Stephanie A 14 Dec '18

14 Dec '18

External Email - Use Caution Hi Freesurfers, I'm trying to project the surface, a fine-grained parcellation (?h.250.aparc.annot), into volume space (dti_FA) with for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ mri_surf2vol \ --o FA/annot2FA.nii.gz \ --subject $subj \ --so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot $dtipath/$subj/dti_FA.nii.gz cd ../ fi done However, I get ERROR: MRISread: file '$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot' has more faces than vertices! How can I solve this? Thanks, Stephanie Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Freesurfer