Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

White Matter Edits
by Kirkish, Gina 01 Nov '16

01 Nov '16

Hello, I am a staff research associate for a group that specializes in MRI of Multiple Sclerosis. We use freesurfer's reconstruction approach, however the white matter masks are not very good for the MS disease population. We have combined the FreeSurfer algorithm with ANTS in order to get more precise white matter masks – which in theory should improve the surface volumes and aparc+aseg masks. When we have tried putting the ANTS white matter mask into freesurfer and re-running recon-all (recon-all -autorecon2–wm –autorecon3 –w <subID>), the wm_surface and aparc+aseg mask do not seem to follow the white matter surface volume (see attached pictures for an example). How do we insure that the white matter mask is taken into consideration? I know that edits to the white matter mask are done with a value of 255 but the actual white matter volume is 110 – could this be the problem? Let me know if I need to explain anything further. [cid:F06B2C58-32ED-45A4-9FB4-27D90ECFA496][cid:CC736D56-1123-458E-8ADF-D6372F0ACCD9] Thank you, Gina

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Re: [Freesurfer] BBR not recommended for PETSurfer?
by Elijah Mak 01 Nov '16

01 Nov '16

Hi Christopher, We have very positive experiences with mri_coreg too. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html Quite a bit of manual tweaking had to be done along with BBR for our AV and PK BPnd data. It works just fine on the PIB SUVRs though. Then, we switched to mri_coreg and manual tweaking was hardly necessary after that. It truly works wonders :) Best Wishes, Elijah

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tkregister2 + mri_vol2vol do not transform
by Chiara Giacosa 01 Nov '16

01 Nov '16

Dear experts, I am new to freesurfer and I am struggling making transformation of images from one subject to another as well as to a template. I have tried different ways, but I always end up with the original image as if the transformation was never applied. I used tkregister2 from command line and mri_vol2vol. I noticed that the transformation matrices are always the identity matrix in the first 3 columns/rows, no matter what transformation I tell the program to do. I don't think that this makes sense so I wonder if I am doing something wrong or if there might be an issue with the version of tkregister I have. My *commands *are: tkregister2 --mov $subj/mri/orig.mgz --targ my_template/mri/orig.mgz --regheader --reg $subj/reg/orig2templ_tkreg.dat --noedit mri_vol2vol --mov $subj/mri/rh.hand_manual.nii.gz --targ my_template/mri/orig.mgz --o $subj/mri/rh.hand_subj_in_mytempl.mgz --reg $subj/reg/orig2templ_tkreg.dat *Output Matrix *$subj/reg/orig2templ_tkreg.da: subject-unknown 1.000000 1.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.370635986328125e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 -4.750839233398438e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -1.000000000000000e+00 0 0 0 1 round Contents of my $FREESURFER_HOME/build-stamp.txt file: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Any suggestion will be much appreciated! -- Chiara Giacosa Ph.D. candidate Concordia University

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Re: [Freesurfer] Questions about outputs in Longitudinal Stream
by Tamara Tavares 01 Nov '16

01 Nov '16

Thank you for the clarification Martin I have a follow-up question. When I load the base to make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Similarly, when I open the base and the longitudinal runs to see whether they align, again should I load the brainmask.mgz for these as well? Thank you in advance for your help, Tamara

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Re: [Freesurfer] BBR not recommended for PETSurfer?
by Douglas Greve 01 Nov '16

01 Nov '16

Hi Christopher, yes, my position on BBR for PET has changed. I ran an analysis on FDG from an HR+ using BBR and coreg, and the results were not different enough to warrant choosing one over the other. However, coreg performed better on simulated FDG HR+ data, so I'm recommending coreg over BBR, at least for typical resolution scanners like the HR+. For high res (eg, HRRT), BBR may still be better. But for data with a PSF of around 6mm or higher, I would go with coreg. BBR remains the method of choice for all MRI volumes. doug On 11/1/16 10:21 AM, Schwarz, Christopher G., Ph.D. wrote: > > Dr. Greve, > > I noticed on https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer > <https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer> that you’re > recommending mri_coreg instead of bbregister for PET-MRI alignment in > PETSurfer. This seems inconsistent with your 2014 NeuroImage paper > http://www.sciencedirect.com/science/article/pii/S1053811913012251 > “BBR is very robust with respect to image artifacts and so an ideal > candidate for PET-MR registration” > > Has your position on BBR for PET-MRI changed? Was mri_coreg later > found to be more robust? > > Thank you for your time, > > Christopher Schwarz > > *--* > > *Christopher G. Schwarz, Ph.D.*| Research Associate, Diagnostic > Radiology | Opus Center for Advanced Imaging Research | 507-538-4867 | > schwarz.christopher(a)mayo.edu <mailto:schwarz.christopher@mayo.edu> > > *Mayo Clinic*| 200 First Street SW | Rochester, MN 55905 | > http://mayoclinic.org <http://mayoclinic.org/> >

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Freesurfer recon-all error after installing
by Lehr, Albert 01 Nov '16

01 Nov '16

Dear FreeSurfers, I just recently installed FreeSurfer and as Saeed ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49263.html) had troubles running recon-all. My info: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Linux version: Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux I attach my recon-all.log but I guess it is very similar to Saeed's. Also running mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz gives the exact output and error code as he had. I already read that downloading the Development Version should get the job done, but noticed some stuff and wanted to ask about it: Running "recon-all -s bert -all" , the following lines are shown and the build stamps do not match. INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/bin/freesurfer/subjects Actual FREESURFER_HOME /usr/local/bin/freesurfer -rw-r--r-- 1 albert albert 513977 Oct 31 16:30 /usr/local/bin/freesurfer/subjects/bert/scripts/recon-all.log Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/bin/freesurfer Previous: /space/freesurfer/centos4.0/stable Equally in the attached recon-all.log file "FREESURFER_HOME /space/freesurfer/centos4.0/stable Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0/stable5" is written and although I downloaded the centos6-version and not the centos4.0 version. Might this be a problem or is the error solely due to the new perl versions? Just wanted to bring it to your attention and hear your feedback. I am currently downloading the 6.0.0-beta version, which hopefully makes recon-all work again. Have a great day, Albert

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freesurfer preproc output
by Bernardoni, Fabio 01 Nov '16

01 Nov '16

Dear all, after running a freesurfer preprocessing, in each subject subdirectory, the following files are produced: lh.avg_curv lh.curv lh.curv.pial (and the analogue for the right hemisphere) what is the content of these files? sure, I can guess they represent the local curvature. but which one? the intrinsic? the extrinsic? what is the relation with the measures: gauscurv, meancurv, foldind, curvind obtained through the aparcstats2table? It was quite surprising to me that on the wiki no precise definition is present, although one can guess that gauscurv is the intrinsic and meancurv the extrinsic curvature. what are foldind and curvind by the way? how can one get the intrinsic and extrinsic curvatures from the lh.curv files? since these are all very useful measures, it would be of much help for me and other users (I believe) if some more intormation could be written on the wiki. thanks for any help, fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Psychosoziale Medizin und Entwicklungsneurowissenschaften Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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tksurfer viewing issues
by Paige Scalf 01 Nov '16

01 Nov '16

Hi Bruce, I'm analyzing phase encoded retinotopy, and it is not clear to me how to load complex overlays in freeview. Perhaps I am missing something? Best, Paige Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionality that you need that is unique to tksurfer? cheers Bruce On Thu, 29 Sep 2016, Paige Scalf wrote: >* Hello, *> >* I too am having trouble with tksurfer displaying the surfaces upside down *>* and back to front, but believing that they are correctly oriented (i.e. *>* Talairach coordinates change in the wrong direction wrt to the surface but *>* in the correct direction wrt the display window). I"m also running a CentOs *>* flavor. Did anyone manage to solve this issue? *> >* All the best, *>* Paige* -- Paige E. Scalf, Ph.D. Lecturer Department of Psychology Durham University Psychology Department Durham University Science Laboratories South Road DURHAM DH1 3LE

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Re: [Freesurfer] Amygdala subfields
by Dorit Kliemann 31 Oct '16

31 Oct '16

Hi Sascha, yes, we have developed an amygdala nuclei atlas similar to the hippocampal subfields . Its currently being tested and to be implemented (hopefully) soon. Stay tuned. Dorit > From: "sf" <fruehholz(a)gmail.com> > Subject: [Freesurfer] Amygdala subfields > Date: 31 October 2016 at 15:13:21 GMT > To: "'Freesurfer support list'" <freesurfer(a)nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Hi all, is there any possibility to segment amygdala subfields with freesurfer? Similar to the hippocampal subfields segmentation? > Cheers - Sascha > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Recon-all Exiting without Error
by Harms, Michael 31 Oct '16

31 Oct '16

Hi, Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Natalie Busby <natalie.busby(a)manchester.ac.uk<mailto:natalie.busby@manchester.ac.uk>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, October 31, 2016 at 9:30 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Recon-all Exiting without Error Hi, I have just started using FreeSurfer and I am trying to do the subcortical segmentation on some Human Connectome Data. In the command line I typed, ‘recon-all –i T1w_acpc_dc_restore_1.25.nii –subjid 100307’ The following output was produced: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /usr/local/freesurfer/subjects/100306 mri_convert /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz mri_convert /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz... #------------------------------------------ Started at Mon Oct 31 10:12:26 EDT 2016 Ended at Mon Oct 31 10:12:31 EDT 2016 #@#%# recon-all-run-time-hours 0.001 recon-all -s 100306 finished without error at Mon Oct 31 10:12:31 EDT 2016 done I was wondering if you knew what the problem was? Thank you! Best wishes, Natalie ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer