Nothing really specific to check (only for a disaster). You can load the aparc+aseg with it as they should mostly agree (but not perfectly)
On 3/31/2020 5:03 AM, Ferraro, Pilar wrote:
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Dear Freesurfer experts,
I’m performing an analysis using PETSurfer and, after processing all the T1 images with the Freesurfer analysis, I’m now creating the segmentation for the GTM. I’ve run the gtmseg —s command on a first subject. I was surprised though, cause I’ve read the process should have taken about an hour or two, but it actually took only 25 minutes, so, even if at the end of the process it was reported “gtmseg done”, I’ve checked the resulting gtmseg.mgz image using the command:
tkmeditfv subject/ nu.mgz -seg gtmseg.mgz gtmseg.ctab -opacity 1
And this is how it looked like:
My question is, is there something specific I should check in this image to be sure everything has been done correctly?
Sorry, I’m new to this type of analysis, so I’d rather be sure about everything before further proceeding.
Many thanks,
Pilar Maria Ferraro
Il giorno 26 mar 2020, alle ore 2:44 PM, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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Today's Topics:
1. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Mason Wells) 2. Re: VM_setup (fsbuild) 3. Re: mri_deface download link not found (Hoopes, Andrew) 4. Registration file types confusion (Xiaojiang Yang) 5. Freeview CLI feature request (VINCENT KOPPELMANS) 6. Re: Freeview CLI feature request (Ruopeng Wang) 7. Re: Freeview CLI feature request (VINCENT KOPPELMANS) 8. Re: training set (javier quilis) 9. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Mason Wells) 10. Re: Hippocampal Volume Extraction (Devika K) 11. Re: training set (Bruce Fischl) 12. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Bruce Fischl)
Message: 1 Date: Wed, 25 Mar 2020 18:38:34 +0000 From: Mason Wells WellsMT1@cardiff.ac.uk Subject: Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 5BD22FFC-C541-42CB-964B-AA3B2186428F@cardiff.ac.uk Content-Type: text/plain; charset="utf-8"
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HI Bruce,
Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post?
Best wishes, Mason
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU
E-bost: WellsMT1@caerdydd.ac.uk Ff?n: 02920 879628
?On 25/03/2020, 17:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Mason
I can't tell from those images except that it looks reasonable cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote:
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Hi again Bruce,
I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think?
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU
E-bost: WellsMT1@caerdydd.ac.uk Ff?n: 02920 879628
On 25/03/2020, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:
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Hi Bruce,
I get the following error message when I try to load freeview
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl masontwells@masontwells-VIG800S:~$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU
E-bost: WellsMT1@caerdydd.ac.uk Ff?n: 02920 879628
On 25/03/2020, 16:19, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
something like
freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \ -f $SUBJECTS_DIR/<subject name>/surf/?h.white
cheers Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:
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Hi Bruce,
Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here. Could you please explain how I would check this?
Thanks again for your help. Mason
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU
E-bost: WellsMT1@caerdydd.ac.uk Ff?n: 02920 879628
On 25/03/2020, 16:11, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Mason
can you confirm that things look ok within FreeSurfer if you look at the surface over the volume in freeview?
cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote:
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Hello Freesurfer developers,
I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis:
- Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
- Ran Feat
? Distortion correction of the EPI
? Motion correction
? No smoothing
? Highpass filter
? No registration to whole brain
? Register to T1_biascorr_brain
? Register to standard space
- Ran recon-all on T1_biascorr
- Convert T1/T1_brain/orig(001) from mgz to nii
- Check registration (using the SurfaceProjection command from
the SamSrf package) which leads to the attached images named S1 and S1.
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: Linux 5.3.0-40-generic x86_64
Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
As you can see, the registration is significantly misaligned.
Can anyone offer any advice on this/suggest a way to rectify it?
Thanks in advance,
Mason
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
Email: WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau?r Golwg
& Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: WellsMT1@caerdydd.ac.uk
Ff?n: 02920 879628
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