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
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: 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 (???)
----------------------------------------------------------------------
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
The information in this e-mail is intended only for the person to whom it is addressed. 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 http://www.partners.org/complianceline . 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear experts, any suggestion about my question? (see below) Thank you in advance! Daniele
----- Messaggio originale ----- \Da: "Daniele Orlandi" dorlandi@fatebenefratelli.eu \A: freesurfer@nmr.mgh.harvard.edu \Inviato: Venerdì, 16 giugno 2017 18:01:59 \Oggetto: Freesurfer Template Creation \ \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
Hi Daniele - A main feature of the freesurfer longitudinal stream is that it is unbiased, i.e., it treats all the time points in the same way, regardless of their order in time.
a.y
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Daniele Orlandi [dorlandi@fatebenefratelli.eu] Sent: Tuesday, June 20, 2017 7:07 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Template Creation
Dear experts, any suggestion about my question? (see below) Thank you in advance! Daniele
----- Messaggio originale ----- \Da: "Daniele Orlandi" dorlandi@fatebenefratelli.eu \A: freesurfer@nmr.mgh.harvard.edu \Inviato: Venerdì, 16 giugno 2017 18:01:59 \Oggetto: Freesurfer Template Creation \ \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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, the longitudinal anlaysis is be design insensitive (and unbiased!) w.r.t. the order of the timepoints
cheers Bruce On Tue, 20 Jun 2017, Daniele Orlandi wrote:
Dear experts, any suggestion about my question? (see below) Thank you in advance! Daniele
----- Messaggio originale ----- \Da: "Daniele Orlandi" dorlandi@fatebenefratelli.eu \A: freesurfer@nmr.mgh.harvard.edu \Inviato: Venerdì, 16 giugno 2017 18:01:59 \Oggetto: Freesurfer Template Creation \ \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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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:
- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
The information in this e-mail is intended only for the person to whom it is addressed. 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 http://www.partners.org/complianceline . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Daniele Orlandi -
Martin Reuter -
Yendiki, Anastasia