12 Jul
2017
12 Jul
'17
12:32 p.m.
Hi Johnmark, sorry, I can't reconstruct the thread from the earlier emails. Can you resubmit with just the thread from your email and not all 29 threads from July 5?
thanks
doug
On 07/06/2017 02:00 PM, Taylor, Johnmark wrote:
The subject name when I call tksurfer, the subject name when I call tkmedit, and the subject name in the registration file are all exactly the same: red_badger. One thing I noticed is that in the left hemisphere everything seems normal (the activation is in the expected location); things only look weird in the right hemisphere. There's no possibility that the surface reconstruction could have been off the mark? Though it seems implausible that it would take the IPS and somehow warp it all the way onto the medial surface of the brain...
Here are pictures of both the volume and surface views of the activation in question (it's the medial patch on the surface view, the patch with the red cursor in the volume view), in case they didn't load before for some reason.
https://ibb.co/b8HFCv https://ibb.co/cWYcQF
On Thu, Jul 6, 2017 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto: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: error message while using autorecon1 (Hoopes, Andrew) 2. Re: error message while using autorecon1 (Buckless, Colleen) 3. Re: Additional surface area (Bruce Fischl) 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) 5. Re: error message while using autorecon1 (Hoopes, Andrew) 6. Re: error message while using autorecon1 (Buckless, Colleen) 7. Re: error message while using autorecon1 (Hoopes, Andrew) 8. Re: recon-all on newborn (Lilla Zollei) 9. Re: recon-all on newborn (Das S.) 10. Re: Still confused by group analysis.. (Douglas Greve) 11. Re: Raw Cortical thickness values (Douglas Greve) 12. Re: Average myelination within ROI (Douglas Greve) 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) 14. Re: Recon-all: too many ('s (Douglas Greve) 15. Re: Using multimodal slab input for hippocampus subfield segmentation in FS6 (Douglas Greve) 16. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas Greve) 17. Re: negative header after preproc-sess (Douglas Greve) 18. Re: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> (Douglas Greve) 19. Re: Building your own fsaverage (Douglas Greve) 20. Re: Qdec error in analysis (Douglas Greve) 21. Re: mri_glmfit error (mri_reshape number of elements) (Douglas Greve) 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) 23. Re: GLM fitting for the cortical volume (Douglas Greve) 24. Re: Subject with missing fMRI data (Douglas Greve) 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) 27. Re: content of "subjects_dir" (Douglas Greve) 28. Re: Qdec error in analysis (AYUSHI SHUKLA) 29. asegstats2table error (Elizabeth Dao) 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz@gmail.com <mailto:miracooloz@gmail.com>) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 17:29:23 +0000 From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu <mailto:AHOOPES@mgh.harvard.edu>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com <mailto:BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="Windows-1252" Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all ?autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ------------------------------ Message: 2 Date: Wed, 5 Jul 2017 17:36:47 +0000 From: "Buckless, Colleen" <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org <mailto:6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>> Content-Type: text/plain; charset="us-ascii" Hi Andrew, The output list includes nu_correct. Thanks, Colleen -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: Re: [Freesurfer] error message while using autorecon1 Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. 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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=> . 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. ------------------------------ Message: 3 Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) From: Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Additional surface area To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu <mailto:alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Michael you need to look in the volume to see what is causing it. I would guess some dura that is being incorrectly included, but you will be able to tell in the slice view cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > > Hello, when inspecting a subject i discovered an anomaly on top of the 3D > surface i have not previously encountered on other subjects i have > inspected. Could you please let me know if this would be problematic when at > the analysing group data please? > > > Kind regards, Michael > > > ------------------------------ Message: 4 Date: Wed, 5 Jul 2017 13:53:57 -0400 From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg@mail.gmail.com <mailto:54nuLg@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" ---------- Forwarded message ---------- From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Date: Tue, Jul 4, 2017 at 10:23 AM Subject: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Hello Freesurfer, After running the first step of PETsurfer (https://surfer.nmr.mgh. harvard.edu/fswiki/PetSurfer <http://harvard.edu/fswiki/PetSurfer>). I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks. Please, see attached image Best, Paul