Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

if: Expression Syntax.
by Lars M. Rimol 28 Jan '16

28 Jan '16

Hi, I have a large amount of data (FS scanworkups) where all the files within every subject's directory are zipped. Is there a way to run mris_preproc on zipped data? For instance, mris_preproc crashes because it can't find lh.thickness unless I unzip it Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 28 Jan '16

28 Jan '16

Hi Bruce, I've attached a shot of the misalignment as seen in freeview. Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. Thanks, Will On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mritotal failed - help with manual registration (Bruce Fischl) > 2. recon -all errors (Jasmin Alves) > 3. Re: Processing .mnc files (Ankita Chatterjee) > 4. Re: Processing .mnc files (Bruce Fischl) > 5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) > 6. hippocampal subfields - multispectral segmentation with FLAIR > (Luigi Antelmi) > 7. Re: hippocampal subfields - multispectral segmentation with > FLAIR (Eugenio Iglesias) > 8. Re: recon -all errors (Bruce Fischl) > 9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) > 10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) > 11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) > 12. FDR map: hide very little cluster (stdp82(a)virgilio.it) > 13. [All] position available immediately (Bruce Fischl) > 14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Douglas Greve) > 15. Re: FDR map: hide very little cluster (Douglas Greve) > 16. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 17. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 19. R: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 21. R: Re: R: Re: FDR map: hide very little cluster > (stdp82(a)virgilio.it) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look > out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given > this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will > > > > > > > ------------------------------ > > Message: 2 > Date: Sun, 24 Jan 2016 18:36:11 -0800 > From: Jasmin Alves <jalves(a)usc.edu> > Subject: [Freesurfer] recon -all errors > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CACuamQ5whG9jjQLPvD5Hq4BAF+=C4ZvrACb3PrF2+KAx=aLN= > Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello Freesurfer, > > I am trying to learn freesurfer and ran into the following issues below > running the recon -all command. > > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Kernel info: Darwin 14.5.0 x86_64 > > 1) > > joya > > 2) > > Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i > T1_original_joya.nii -subject joya -all & > > > 3) > > [1] 12300 > > Jasmins-MacBook-Pro:subjects jasminalves$ mkdir: > /Applications/freesurfer/subjects/joya: Permission denied > > mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied > > mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied > > cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such > file or directory > > cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No > such file or directory > > INFO: FreeSurfer build stamps do not match > > Subject Stamp: > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > > Actual FREESURFER_HOME /Applications/freesurfer > > /Applications/freesurfer/subjects/joya: No such file or directory. > > > [1]+ Exit 1 recon-all -i T1_original_joya.nii -subject > joya -a > Thank you, > Jasmin > > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jalves(a)usc.edu >

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wm correction
by maryam koochaki 28 Jan '16

28 Jan '16

Hi Bruce, I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral Ventricle. As you can see in the image attached, the big part is excluded in both hemisphere. I tried to fill it by editing wm volume but the problem still exists.Do you have any suggestion?Thanks,Maryam test_vumc_158_rh.png test_vumc_158_lh.png

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mail option to email custom status of job completion
by Sneha Pandya 27 Jan '16

27 Jan '16

Dear experts, I usually setup batch jobs for my studies and use '-mail' option that emails me completion of recon-all with or without errors. Is there a way or any other option that I can use alongside '-mail' to give me custom status message than the usual one which says "recon-all -s XYZ finished without error at ...". For example if I have set up to run subjects XYZ for only autorecon2 stage, I would like it to send me an email message saying "recon-all autorecon-2 finished without error" or something? Thanks, Sneha

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[FreeSurfer] WM Parcellation
by VA Research 27 Jan '16

27 Jan '16

Hello FS experts, Does anyone have some form of step-by-step instructions on how to do this ? Thanks so much Joseph Brainiac . wrote: >* Hi All, *>>* I need to classify WM into different lobes (temporal, parietal, *>* frontal, occipital). I tried to do the lobe mapping using *>* parcellations from wmparc.mgz. *>* http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation <http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation> *> >* My problem is the "unsegmented white matter" in wmparc.mgz. My *>* understanding is that these unsegmented areas are classified so *>* because they are beyond 5mm from any pre-classified cortex area. *>>* My questions: *>* (1) So in order to classify "unsegmented WM" into lobes, do I need to *>* take each voxel in the unsegmented WM region and then assign it to the *>* closest cortex area to classify it into respective parcellations. Then *>* re-group into lobes. Is this correct? * >>* (2) Are there any tailor made function or any other easier way to do *>* this? Is there any easier way to segment WM into lobes directly that I *>* have missed? *>>* Thanks, *>* Brain* You can do this in a couple of steps. First, you'll need to create a lobe annotation. You can do this in 3 ways: 1. mri_annotation2label --lobesStrict 2. mri_annotation2label --lobes 3. Custom: break up annotation and recombine: a. mri_annotation to create separate label files b. mri_mergelabels to create single label files for each lobe label c. mris_label2annot to create the lobe annotation Next, create the WM segmentation with mri_aparc2aseg, specifying your new lobe annot and adding --labelwm. You can control the distance with --wmparc-dmax doug

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Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration
by John Plass 27 Jan '16

27 Jan '16

Hello, I've been following the Ex-Vivo Recon instructions https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan of a formalin-fixated brain. With considerable manual editing, I've been able to produce convincing white and pial surfaces, but I am having trouble getting a good parcellation. The labels are reversed from anterior to posterior (e.g., superior parietal lobule area is labelled as middle frontal gyrus). I am assuming this has to do with problems with the surface registration. Also, when viewing the surfaces in Freeview, they appear pretty dark (perhaps similar to https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.html) although the correspondence between red/green and gyri and sulci appears to be correct. Might this be part of the problem? Any advice would be much appreciated! If you'd like to take a look at the files, please let me know what and where to upload. Thanks very much for your help. Best regards, John Plass

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R: Ref FAST and results visualization issue
by stdp82＠virgilio.it 27 Jan '16

27 Jan '16

Briefly, is possible to map the fictional connectivity between a right seed and left cortex? Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 27-gen-2016 18.57 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] Ref FAST and results visualization issue Hi list, I have two requests please. A- I need to have a reference for FS-FAST (seed based analysis on rs data) B- I have difficulties for results visualization. How can I do to visualize the the cortical areas which are functionally connected with the controlateral seed? For example, my seed are right and left amygdala.To visualize RIGHT amygdala - RIGHT cortex connectivity I'm doing: cd my-group/fc.ramgseed.surf.lh/R_Amygdala tksurfer fsaverage rh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz and all is fine. To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing: tksurfer fsaverage lh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz but the image is so confused. It seem to be the translated image which I have projected in the right semi. Thanks Stefano

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watershed bem surface problems
by Keith Doelling 27 Jan '16

27 Jan '16

Hi All, I'm trying to source localize MEG data in MNE-Python but have run across an issue with a subject's MRI in the freesurfer watershed algorithm. Namely, the outer skull surface ever so slightly overlaps with the inner skull (I've plotted this in freeview for your viewing pleasure). This is a problem as MNE stops with an error in the make_bem_model function when such overlap occurs (understandably). I have tried deleting the bottom slices of the T1.mgz and rerunning the watershed algorithm but that actually made the overlap worse. I have also tried using the -atlas parameter which made it a bit better but not quite (that's actually what is plotted). What I would really like to do at this point is manually edit the surfaces to avoid the overlap which I think given the location and minuscule nature of the overlap. Any tips on how to get this done? Or on how to edit the MRI to avoid this overlap to begin with? Thanks for your help! Keith https://dl.dropboxusercontent.com/u/5190414/skulloverlap.png [image: Inline image 1] Keith Doelling Dept of Psychology Center for Neural Science NYU science.keithdoelling.com

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recon -all errors
by Jasmin Alves 27 Jan '16

27 Jan '16

Hello Freesurfer, I am trying to learn freesurfer and ran into the following issues below running the recon -all command. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 1) joya 2) Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii -subject joya -all & 3) [1] 12300 Jasmins-MacBook-Pro:subjects jasminalves$ mkdir: /Applications/freesurfer/subjects/joya: Permission denied mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/joya: No such file or directory. [1]+ Exit 1 recon-all -i T1_original_joya.nii -subject joya -a Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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How YOU can help FreeSurfer
by Douglas N Greve 27 Jan '16

27 Jan '16

We are in the process of preparing a grant to support FreeSurfer development and maintenance: Title: FreeSurfer Development, Maintenance, and Hardening. PIs: Greve and Fischl. Grant reviewers need to know that FreeSurfer is useful to a lot of people, so we encourage you to do one of two things: (1) fill out the form below (probably takes less than 1min) or (2) write a letter of support on your institution's letterhead including the information requested on the form and send to greve(a)nmr.mgh.harvard.edu Feel free to forward this survey to others who might not be on the FreeSurfer mailing list (but use FS) Please respond by Friday Jan 29. Thanks! doug https://docs.google.com/forms/d/1FreWjajItomNlmq190TYl7IS3kPXrHViPJQfjAlg2A… -- 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 January 2016