Hi Daniele,
as others commented, the stream is unbiased so the order does not affect results, so you are fine. That said, if you switch the order around you will get slightly different results due to numerical reasons (small differences affected by the order that accumulate to produce noticeable differences).
Best, Martin
On 16. Jun 2017, at 18:01, Daniele Orlandi dorlandi@fatebenefratelli.eu wrote:
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:
- Re: viewing 3D surfaces (Michael Davies)
- Freesurfer parcelations of cortical regions in TrackVis (Leyton Moscoso, Cristian Eduardo)
- Re: viewing 3D surfaces (Bruce Fischl)
- Re: mris_anatomical_stats and cortical thickness {Disarmed} {Disarmed} (Hilton, Benjamin Taylor)
- bvals and bvecs for tracula v6 (Marissa Pifer)
- Re: bvals and bvecs for tracula v6 (Yendiki, Anastasia)
- Re: viewing 3D surfaces (Michael Davies)
- Re: viewing 3D surfaces (Bruce Fischl)
- substract images (John Anderson)
- Re: substract images (Bruce Fischl)
- Re: substract images (John Anderson)
- Re: viewing 3D surfaces (Michael Davies)
- Re: substract images (Bruce Fischl)
- Re: viewing 3D surfaces (Bruce Fischl)
- Re: Freesurfer parcelations of cortical regions in TrackVis (Lilla Zollei)
- Re: substract images (John Anderson)
- Re: substract images (Bruce Fischl)
- Re: substract images (John Anderson)
- Cropping of slices during recon-all (Jerry Jeyachandra)
- When running mkcontrast-sess: A fatal error has been detected by the Java Runtime Environment (???)
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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