Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

R package for graph theory analysis of MRI data {Disarmed}
by Chris Watson 11 Apr '17

11 Apr '17

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the first major release of my R package "brainGraph" (v1.0.0), a collection of functions for performing graph theory analyses of brain MRI data. I chose R because it is free and is, in my opinion, the best choice for just about any statistical analysis. It is available on CRAN at https://cran.r-project.org/web/packages/brainGraph/index.html and development versions will be on my Github page (link below). You can use it for gray matter covariance networks (cortical thickness, volume, surface area, or LGI), DTI tractography data (FSL's "probtrackx2", PANDA, TrackVis, etc.), and for resting-state fMRI (the Matlab toolbox DPABI/DPARSF). It is very heavily dependent on the fantastic R package "igraph" (see igraph.org) which is based on C code and is quite a bit faster than many other R applications. My Github page for the package is https://github.com/cwatson/brainGraph <https://email.tch.harvard.edu/owa/redir.aspx?REF=AuYw-ae9TnjtRShTO7f-UJbUR6…>. At the bottom is the "README.md" file which provides some basic information. Most important is the link to the User Guide, which has extensive installation and usage information (warning: it is a direct PDF link). It is very long but should be helpful. You will find code for getting your data into R, and I have documented many analysis steps and include multiple figures. I hope this is intuitive for both veteran and novice R users. Additionally, there are links for help learning R, and links to other R packages relevant to neuroimaging applications. Some features that should be of interest include: * calculation of a large number of graph/vertex/edge measures (particularly those most common in neuroimaging) * between-group vertex-wise analysis using the GLM * implementation of the network-based statistic (NBS) * bootstrapping & permutation testing * random graph generation, small-worldness, and global/local/nodal efficiency * rich-club calculations * robustness ("targeted attack" or "random failure") & vulnerability * a basic GUI to explore your networks (up to 2 groups/subject at a time) Please see the NEWS.md file ( https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for the changelog. This remains a work-in-progress, so I am very happy to receive bug reports, feature requests, general questions asking for help with code, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-help Chris Watson

1 1

mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"
by Harris Hoke 11 Apr '17

11 Apr '17

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43697.html> . Does anyone know if a fix exists? I'm trying to move binary parcel files from the SPM default MNI152 space to Freesurfer cvs_avg35_MNI152 space. ~Harris

2 1

recon-all -parallel osx sierra
by jasi3k 11 Apr '17

11 Apr '17

Dear all, I am using Freesurfer 6.0 to run recon-all on 0.8 isotropic data. Whenever I use the parallel flag I get this error. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Same subject without the parallel flag runs smoothly but of course takes much longer. I have seen a similar problem on the list and the suggestion was to make a clean install of Freesurfer 6.0, which I did but unfortunately it didn’t help. Any suggestions will be appreciated. Best, Jan

2 1

Re: [Freesurfer] QDEC and ROI drawing
by Arnaud Boré 11 Apr '17

11 Apr '17

Is that normal ? Le 11 avr. 2017 12:34 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> a écrit : Yes, the label is shifted off the brain when I run that command On 04/11/2017 10:13 AM, Arnaud Boré wrote: > Hi Douglas, > > Yes I would like to draw ROIs, I understand I can use tksurfer. > I would like to know if your fs version has the same behaviour as mine. I > use: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 > Can you replicate this command line and tell me if the label is well > aligned to the surface ? > qdec --surface $SUBJECTS_DIR/bert/surf/rh.pial --label > $SUBJECTS_DIR/bert/label/rh.V1_exvivo.label > > Thank you in advance > Arnaud > > 2017-04-10 11:54 GMT-04:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > > Sorry, I don't know what is going on with qdec. Why do you need to > do this in qdec? If it is to draw labels, then you can also use > tksurfer. > > > On 04/10/2017 11:34 AM, Arnaud Boré wrote: > > Hi Douglas, > What more can I do to help you figure out what's wrong ? > Thank you in advance > Arnaud > > 2017-04-07 16:50 GMT-04:00 Arnaud Boré <arnaud.bore(a)gmail.com > <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com > > <mailto:arnaud.bore@gmail.com>>>: > > There is no shift in freeview. > > 2017-04-07 16:35 GMT-04:00 Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.edu>>>: > > Not yet. Did you try to load it into freeview? If so, > do you > still see the shift? > > > On 04/07/2017 04:14 PM, Arnaud Boré wrote: > > Do you want me to attach/upload a screenshot of > the shift ? > > 2017-04-07 13:10 GMT-04:00 Arnaud Boré > <arnaud.bore(a)gmail.com > <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com > <mailto:arnaud.bore@gmail.com>> > <mailto:arnaud.bore@gmail.com > <mailto:arnaud.bore@gmail.com> > <mailto:arnaud.bore@gmail.com > <mailto:arnaud.bore@gmail.com>>>>: > > I try to view it on O_Nap_04MB. > > I've tried these two command lines: > qdec --table qdec.all_subjs.table.dat --surface > O_Nap_04MB/surf/rh.pial --label > O_Nap_04MB/label/rh.M1_v4.label > qdec --table qdec.all_subjs.table.dat > --average O_Nap_04MB > --surface O_Nap_04MB/surf/rh.pial --label > O_Nap_04MB/label/rh.M1_v4.label > > I get the same results. > > > 2017-04-07 12:03 GMT-04:00 Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>: > > when you view it in qdec, are you viewing > it on > fsaverage or > on O_Nap_04MB ? > > > On 04/07/2017 11:47 AM, Arnaud Boré wrote: > > I used this command line: mri_label2label > --srclabel > rh.M1_v4.label --srcsubject fsaverage > --trgsubject > O_Nap_04MB --trglabel rh.M1_v4.label > --regmethod surface > --hemi rh > The output label overlaps the surface > using > freeview but > using qdec it is shifted. > Thank you for your help. > Arnaud > > 2017-04-07 10:23 GMT-04:00 basile pinsard > <basile.pinsard(a)gmail.com > <mailto:basile.pinsard@gmail.com> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com>> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com>>> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com>> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com> > <mailto:basile.pinsard@gmail.com > <mailto:basile.pinsard@gmail.com>>>>>: > > > ---------- Forwarded message > ---------- > From: *Douglas N Greve* > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > Date: Thu, Apr 6, 2017 at 4:53 PM > Subject: Re: [Freesurfer] QDEC and > ROI drawing > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > <mailto:freesurfer@nmr.mgh.ha > rvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>> > > > what is your label2label command line? > > > > On 04/06/2017 04:52 PM, Arnaud > Boré wrote: > > Dear Freesurfer's experts, > > I draw a specific region on > fsaverage > using QDEC, > then I mapped this > > label on each subject using > mri_label2label. I > looked at these > > registered labels using > freeview. Most > of them are > perfect but for > > some of them I would like to > correct the > segmentation. I would > like to > > modify it using QDEC but when I > overlay > this label > on the surface of > > my subject it has been shifted. > I think > this shift > is because > QDEC is > > using fsaverage as the standard > space. I > try opening > QDEC using the > > "average" option and use the > subject I > want but I > still get this > > shift. am I missing something ? > > Thank you in advance for your help. > > Arnaud Bore > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.ha > rvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 > <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 > > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > < > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > < > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > < > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh. > harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > < > https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh. > harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > < > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > < > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > < > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > < > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh. > harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > > The information in this e-mail is > intended > only for > the person to > whom it is > addressed. If you believe this > e-mail was > sent to you > in error and > the e-mail > contains patient information, please > contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > <http://www.partners.org/comp > lianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> > <http://www.partners.org/comp > lianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > <http://www.partners.org/comp > lianceline > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>>> . If the e-mail > was sent > to you in error > but does not contain patient > information, > please > contact the > sender and properly > dispose of the e-mail. > > > > > -- Basile Pinsard > /PhD candidate, > / > Laboratoire d'Imagerie > Biomédicale, UMR S > 1146 / UMR 7371, > Sorbonne Universités, UPMC, > INSERM, CNRS > /Brain-Cognition-Behaviour > Doctoral School > /*, *ED3C*, > *UPMC, > Sorbonne Universités > Biomedical Sciences Doctoral School, > Faculty of Medicine, > Université de Montréal > CRIUGM, Université de Montréal > > > > > -- Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 > <tel:514-647-8649> > <tel:514-647-8649 <tel:514-647-8649>> > <tel:514-647-8649 <tel:514-647-8649> <tel:514-647-8649 > <tel:514-647-8649>>> > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > < > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvar > d.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > <https://gate.nmr.mgh. > harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > < > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > > -- Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 > <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> > <tel:%28514%29%20647-8649> > > > > > -- Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 <tel:514-647-8649> > <tel:514-647-8649 <tel:514-647-8649>> > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.e > du/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh. > harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > > -- Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 <tel:514-647-8649> > <tel:%28514%29%20647-8649> > > > > > -- Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 <tel:514-647-8649> > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > -- > Arnaud BORE > Research assistant > Cellulaire : (001) 514-647-8649 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 4

freesurfer 5.1
by Suchandra Thapa 11 Apr '17

11 Apr '17

Hi, I'm trying to support some users that want to use Freesurfer 5.1 for their workflow. How do I get a license file for this version? A license for the current versions doesn't seem to work. Suchandra Suchandra Thapa sthapa(a)ci.uchicago.edu Computation Institute Searle Chemistry Laboratory #201A 5735 South Ellis Avenue Chicago, IL 60637

2 1

Re: [Freesurfer] QDEC and ROI drawing
by Arnaud Boré 11 Apr '17

11 Apr '17

I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard(a)gmail.com>: > > ---------- Forwarded message ---------- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Date: Thu, Apr 6, 2017 at 4:53 PM > Subject: Re: [Freesurfer] QDEC and ROI drawing > To: freesurfer(a)nmr.mgh.harvard.edu > > > what is your label2label command line? > > > > On 04/06/2017 04:52 PM, Arnaud Boré wrote: > > Dear Freesurfer's experts, > > I draw a specific region on fsaverage using QDEC, then I mapped this > > label on each subject using mri_label2label. I looked at these > > registered labels using freeview. Most of them are perfect but for > > some of them I would like to correct the segmentation. I would like to > > modify it using QDEC but when I overlay this label on the surface of > > my subject it has been shifted. I think this shift is because QDEC is > > using fsaverage as the standard space. I try opening QDEC using the > > "average" option and use the subject I want but I still get this > > shift. am I missing something ? > > Thank you in advance for your help. > > Arnaud Bore > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > > -- > Basile Pinsard > > *PhD candidate, * > Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne > Universités, UPMC, INSERM, CNRS > *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne > Universités > Biomedical Sciences Doctoral School, Faculty of Medicine, Université de > Montréal > CRIUGM, Université de Montréal > -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649

2 9

segmentation help
by Dilip Puri 11 Apr '17

11 Apr '17

Hi all, I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment HippoCampus. My input file xyz.img and output file will be like xyz_seg.img which contains only hippocampus image it like Grond Truth image for my original input image. Here is sample files including original and segmented mask link <https://drive.google.com/open?id=0B6rH1c6LupG_b3I4WUJ1RWZCbnM>. Even I am very new to FREESURFER so I don't know the procedure to reconstruct the images. Kindly help me.

3 8

Difference in Recon-All Output Between Freesurfer Versions?
by Taylor, Johnmark 10 Apr '17

10 Apr '17

Hello, Recently, I re-ran recon-all with Freesurfer version 5 on some subjects whose surfaces had previously been reconstructed with Freesurfer version 4. As a result, it appears that their surface reconstructions have subtly changed, such that the labels that were specified in the old reconstruction are all messed up in the new reconstruction (since the surfaces that they were once associated with have changed). Did recon-all change between Freesurfer versions, and if so, is there a way to go back to the old algorithm short of simply switching back to Freesurfer version 4? It is possible that I have accidentally changed something else and that's why the surface files are different, but I wanted to see if there were any changes in the reconstruction algorithm between versions that might have caused this. Thank you very much, JohnMark Taylor

2 3

Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation
by Antonin Skoch 10 Apr '17

10 Apr '17

Dear Doug, do you think that it is necessary/useful to rerun -normalization2 -maskbfs -segmentation steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell. In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm). Antonin I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote: > Dear experts, > > I noticed inconsistency between recon-all -help and actual code of > recon-all in -autorecon2-wm option. > According to the recon-all --help the -autorecon2-wm processes stages > 15-23 (fill through make white surfaces) and -autorecon2-cp processes > stages 12-23 (normalization2 throuhgh make white surfaces). But, in > the code both -autorecon2-wm and -autorecon2-cp are equivalently > processing stages 12-23. > > It seems to me that the stages 12-14 are not needed to process again > in -autorecon2-wm (which is used for re-processing after editing wm.mgz). > > Could you please comment on? > > Regards, > > Antonin Skoch

2 3

Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"
by Harris Hoke 10 Apr '17

10 Apr '17

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer