Dear experts,
I'm running the Fresurfer Longitudinal Stream and I didn't realize that creating the Template file, some time points were not in the right order:
recon-all -base <templateid> -tp <tp3id> -tp <tp1id> -tp <tp4id> -tp <tp2id> -all
instead of:
recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -tp <tp3id> -tp <tp4id> -all
Does it affect the creation of the Template?
Thank you again!
Best
Daniele
_____________________________________________________________
Daniele Orlandi, PsyD Laboratory of Alzheimer's Neuroimaging and Epidemiology IRCCS Fatebenefratelli,Via Pilastroni 4,25125 Brescia - Italy T: +39 030 35 01 563 - M: +39 346 50 90 531 daniele.orlandi.psy@gmail.com Skype: daniele.orlandi.skype
----- Original Message ----- From: freesurfer-request@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 15, 2017 11:33:01 PM Subject: Freesurfer Digest, Vol 160, Issue 27
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Today's Topics:
1. Re: viewing 3D surfaces (Michael Davies) 2. Freesurfer parcelations of cortical regions in TrackVis (Leyton Moscoso, Cristian Eduardo) 3. Re: viewing 3D surfaces (Bruce Fischl) 4. Re: mris_anatomical_stats and cortical thickness {Disarmed} {Disarmed} (Hilton, Benjamin Taylor) 5. bvals and bvecs for tracula v6 (Marissa Pifer) 6. Re: bvals and bvecs for tracula v6 (Yendiki, Anastasia) 7. Re: viewing 3D surfaces (Michael Davies) 8. Re: viewing 3D surfaces (Bruce Fischl) 9. substract images (John Anderson) 10. Re: substract images (Bruce Fischl) 11. Re: substract images (John Anderson) 12. Re: viewing 3D surfaces (Michael Davies) 13. Re: substract images (Bruce Fischl) 14. Re: viewing 3D surfaces (Bruce Fischl) 15. Re: Freesurfer parcelations of cortical regions in TrackVis (Lilla Zollei) 16. Re: substract images (John Anderson) 17. Re: substract images (Bruce Fischl) 18. Re: substract images (John Anderson) 19. Cropping of slices during recon-all (Jerry Jeyachandra) 20. When running mkcontrast-sess: A fatal error has been detected by the Java Runtime Environment (???)
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Message: 1 Date: Thu, 15 Jun 2017 16:01:58 +0000 From: Michael Davies Michael.Davies30@hotmail.com Subject: Re: [Freesurfer] viewing 3D surfaces To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: MM1P123MB1372C65604FABCBCFC7372DF89C00@MM1P123MB1372.GBRP123.PROD.OUTLOOK.COM Content-Type: text/plain; charset="windows-1252"
That did it :) thank you so much for your help!!
Kind regards, Michael
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: 15 June 2017 15:48:31 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] viewing 3D surfaces
Remove the '/' in front of "surf".
On 06/15/2017 11:45 AM, Michael Davies wrote:
Hi Bruce, i'm getting closer to opening it now. But the final command /surf/lh.pial \ didnt work this time. Any further suggestions?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ freeview -f \
/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ /surf/lh.inflated:visible=0 \ /surf/lh.white:visible=0 \ /surf/lh.pial \ --viewport 3d
MRISread(/surf/lh.pial): could not open file No such file or directory MRISread failed No such file or directory ould not open file bash-4.1$
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu Sent: 15 June 2017 15:19:21 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces
you are not calling freeview in this command. Try putting freeview at the start On Thu, 15 Jun 2017, Michael Davies wrote:
Hi Bruce, i am still getting error messages. is there anything else i could try doing?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer_v6.0.0 FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects MNI_DIR /usr/local/freesurfer_v6.0.0/mni FSL_DIR /usr/local/fsl bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
ed_thickness:visible=0 \
/surf/lh.inflated:visible=0 \ /surf/lh.white:visible=0 \ /surf/lh.pial \ --viewport 3d
bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file or directory bash-4.1$
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu Sent: 15 June 2017 14:11 To: Freesurfer support list Subject: Re: [Freesurfer] viewing 3D surfaces Hi Michael
you need to have FreeSurfer in your path or nothing will work. Have you sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the environment?
cheers Bruce
On Thu, 15 Jun 2017, Michael Davies wrote:
Hello, i am having problems accessing the 3D surfaces of my data. Is there any advice you could provide for me please? bash-4.1$ freeview -f \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
r
c.annot:name=pial_aparc:visible=0 \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
a
y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
\
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
l
e=0 \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
0
\
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ --viewport 3d
bash: freeview: command not found
Kind regards, Michael
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