Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Cerebellum for PetSurfer, edit aseg or brainmask?
by Shane S 12 Apr '17

12 Apr '17

Hello Experts, I want to use the cerebellum as the reference region for PET analysis using the PetSurfer. Unfortunately in very few cases, the segmentation is not good. I have attached some pictures. In this case, should I be editing the aseg or the brainmask.mgz? Thank you for your help. -- Shane Schofield

1 0

mri_concat pet images into 1 template image
by Shane S 12 Apr '17

12 Apr '17

Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct? Thank you for helping. Best Wishes, S -- Shane Schofield

3 7

Manual edits
by John Anderson 12 Apr '17

12 Apr '17

Dear Freesurfer experts, I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached. Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz" 1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz” 2. I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz” 3. I fixed some issues related to dura and bad skullstipping Then I ran the command: “recon-all -autorecon2-wm -autorecon3 -subjid <subject>” which output the file “brain.finalsurfs.mgz” and the command “recon-all -autorecon-pial -subjid <subject>” Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help. John

1 0

glmfit mismatch between X and C with same no of columns
by Clara Kühn 12 Apr '17

12 Apr '17

Dear Freesurfer experts, I'm trying to run a repeated measures anova as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova I have 40 subjects with 2 time points each, so it's quite a large matrix. When running the mri_glmfit command I get the following error: ERROR: dimension mismatch between X and contrast /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx X has 41 cols, C has 81 cols I'm not sure what to do as the matrix and the contrast (see attachments) actually have the same amount of columns... Any help would be much appreciated, thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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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/

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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

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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

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Freesurfer April 2017