New subject: mritotal failed - help with manual registration (Bruce Fischl)

28 Jan 2016

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  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@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@virgilio.it)
    17. R: Re:  FDR map: hide very little cluster
  (stdp82@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@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@virgilio.it)

  ----------------------------------------------------------------------

  Message: 1
  Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST)
  From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  Subject: Re: [Freesurfer] mritotal failed - help with manual
          registration
  To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
  Message-ID:

  <alpine.LRH.2.20.1601241858240.29174@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@usc.edu>
  Subject: [Freesurfer] recon -all errors
  To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
  Message-ID:

  <CACuamQ5whG9jjQLPvD5Hq4BAF+=C4ZvrACb3PrF2+KAx=aLN=Q@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@usc.edu

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)