28 Jan
2016
28 Jan
'16
8:52 a.m.
Hi Will
it looks like there is incomplete myelination, which is probably part of your problem. You could try manually adjusting the transform in tkregister2
cheers Bruce On Thu, 28 Jan 2016, will brown wrote:
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@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@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@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner@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@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