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....@gmail.com
Skype: daniele.orlandi.skype
----- Original Message -----
From: freesurfer-requ...@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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When replying, please edit your Subject line so it is more specific
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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 (???)
----------------------------------------------------------------------
Message: 1
Date: Thu, 15 Jun 2017 16:01:58 +0000
From: Michael Davies <michael.davie...@hotmail.com>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<mm1p123mb1372c65604fabcbcfc7372df89...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang
<rpw...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu><mailto:fis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> on behalf of Bruce Fischl
> <fis...@nmr.mgh.harvard.edu><mailto:fis...@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.edu<mailto: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
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> error
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>
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Message: 2
Date: Thu, 15 Jun 2017 16:02:22 +0000
From: "Leyton Moscoso, Cristian Eduardo" <cley...@mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer parcelations of cortical regions in
TrackVis
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <96f2fcdd-3894-4570-a4f1-afd58866f...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Freesurfer?s and TrackVis experts
I am wondering if there is a way to import cortical parcelations mapped on a T1
image in TrackVis. I tried loading segmentation in TrackVis, but this does not
allow me to see all parcelations in T1 as I can be done in Freeview. In
TrackVis I need to upload them one by one.
Thank you
Cris
Dr Cristian Leyton M
Research Fellow in Neurology
Department of Neurology
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129
This email plus any attachments to it are confidential. Any unauthorised use is
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Message: 3
Date: Thu, 15 Jun 2017 12:11:53 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151211010.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hi Michael
I think you need to do a Unix tutorial. That path is wrong.
cheers
Bruce
On Thu, 15 Jun
2017, 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=inflat
> ed_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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@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=infla
> t
> > 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-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fis...@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=ap
> a
> > r
> > > c.annot:name=pial_aparc:visible=0 \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over
> l
> > a
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi
> b
> > 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.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.
> >
> >
> >
>
>
------------------------------
Message: 4
Date: Thu, 15 Jun 2017 16:15:50 +0000
From: "Hilton, Benjamin Taylor" <bt...@pitt.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
{Disarmed} {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<blupr04mb786f3ba119d51f11a27a3b9c7...@blupr04mb786.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
Okay I think I found a fix, but wanted to run it by you to see if it makes
sense and for anyone else who might have this problem. I ran it with the
thickness file specified under the -t argument, which I think makes it so that
the program doesn't pick up anything that is subcortical when calculating the
thickness average. Now the values seem reasonable, and look similar to when I
use the thickness as an overlay in freeview. I'll post a sample of one of the
commands I am running below.
mris_anatomical_stats -l s71765/label/rh.cluster-001.label -t
s71765/surf/rh.thickness -b s71765 rh
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Tuesday, June 13, 2017 1:52:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
{Disarmed}
how did you do the test of the group diffs?
On 6/12/17 7:37 PM, Hilton, Benjamin Taylor wrote:
I just loaded up the label on a single subject, looks like it is fine, it's in
the same position and squarely on the surface, it's a little skinnier but I'm
guessing that's the difference of overlaying it on the subject. We tried
looking at the ocn.dat file earlier and didn't find a significant difference
between groups despite the output of mri_glmfit-sim (see this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53380.html<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg53380.html&data=01%7C01%7CBTH22%40pitt.edu%7Cab6a52bd6f10440a55f108d4b22084d1%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=OwkZjONYT96jUWeigQL63zsmiPOK0ybiX%2BmSuVK%2Bldk%3D&reserved=0>)
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>
Sent: Friday, June 9, 2017 9:48:50 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you tried to view your label on the individual subject? If your original
analysis was on cortical thickness, then there will be a *ocn*.dat file in the
output with the values for each input subject and each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I?m trying to extract individual cortical thickness values using the output of
the annotation file from mri_glmfit-sim. This worked well for the left
hemisphere, we got values that were significantly different between groups we
had specified in mri_glmfit, but for the right hemisphere we get all values of
0 for the cortical thickness and mean curvature. I?ll post the commands I?m
running below. Essentially I?m attempting to take the annot file from
mri_glmfit-sim, convert it to a label, then put that label onto a subject
(which may or may not be necessary), and pull out the anatomical stats using
that label. Below is the example code for one subject. I did also confirm
that the initial annot file, and the final subject label both sit on the right
hemisphere when loading them up in freeview. I?ll also attach the summary file
from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H.
Lab Data Coordinator
LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts
--annotation
archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label
--trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh
--regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >>
s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc
Total face volume 228346
Total vertex volume 224557 (mask=0)
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1
s72064/label/rh.cluster-001.label
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Message: 5
Date: Thu, 15 Jun 2017 12:20:45 -0400
From: Marissa Pifer <marissapi...@gmail.com>
Subject: [Freesurfer] bvals and bvecs for tracula v6
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<caehkf7ae0wsdelx4vta+cypzax9vqn0pzzjv6oe5rrjur+q...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi freesurfers,
I recently updated my freesurfer version from 5.3 to 6, and I'm running
into a problem with the tracula dmrirc.example file. In the dmrirc.example
file for v5.3, it required just the bvals and bvecs in a text file in the
correct format. For v6, it now requires a bval files, bval list, bvec file
and bvec list. Could you give me an example of what the bval list and bvec
list would look like? I'm not sure what the difference is, and I've tried a
few different things but cannot get tracula to run correctly due to there
being an error with these inputs.
Marissa
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Message: 6
Date: Thu, 15 Jun 2017 16:26:42 +0000
From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu>
Subject: Re: [Freesurfer] bvals and bvecs for tracula v6
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <d5682cc1.10ae7%ayend...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Hi Marissa ? Those things are not all required simultaneously. You should
either specify a single file (if it?s the same for all scans you?re processing)
or a list of files, but not both at the same time.
As far as errors go, there?s no way of guessing what?s going on without seeing
the error. Please send the trac-all.log file and your config file if you want
help troubleshooting. Thanks!
a.y
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Marissa Pifer
<marissapi...@gmail.com<mailto:marissapi...@gmail.com>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, June 15, 2017 at 12:20 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] bvals and bvecs for tracula v6
Hi freesurfers,
I recently updated my freesurfer version from 5.3 to 6, and I'm running into a
problem with the tracula dmrirc.example file. In the dmrirc.example file for
v5.3, it required just the bvals and bvecs in a text file in the correct
format. For v6, it now requires a bval files, bval list, bvec file and bvec
list. Could you give me an example of what the bval list and bvec list would
look like? I'm not sure what the difference is, and I've tried a few different
things but cannot get tracula to run correctly due to there being an error with
these inputs.
Marissa
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Message: 7
Date: Thu, 15 Jun 2017 17:00:14 +0000
From: Michael Davies <michael.davie...@hotmail.com>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<mm1p123mb1372b1d0bbd06c79ec908aa089...@mm1p123mb1372.gbrp123.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello Bruce, how do you mean the path is wrong? I am curious as the data loaded
just.
Kind regards, Michael
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Sent: 15 June 2017 16:11:53
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
Hi Michael
I think you need to do a Unix tutorial. That path is wrong.
cheers
Bruce
On Thu, 15 Jun
2017, 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=inflat
> ed_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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@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=infla
> t
> > 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-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fis...@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=ap
> a
> > r
> > > c.annot:name=pial_aparc:visible=0 \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over
> l
> > a
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi
> b
> > 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.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.
> >
> >
> >
>
>
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------------------------------
Message: 8
Date: Thu, 15 Jun 2017 13:03:19 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151302310.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
I mean the /surf/lh.pial path has to be wrong, as that points to the root
where you wouldn't be allowed to put data. I guess surf/ worked for you,
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
issued the freeview command.
cheers
Bruce
On Thu, 15 Jun 2017, Michael
Davies wrote:
>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
> ____________________________________________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>
> Sent: 15 June 2017 16:11:53
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces ?
> Hi Michael
>
> I think you need to do a Unix tutorial. That path is wrong.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun
> 2017, 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=infla
> t
> > ed_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-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fis...@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=infl
> a
> > t
> > > 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-boun...@nmr.mgh.harvard.edu
> > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > > <fis...@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=a
> p
> > a
> > > r
> > > > c.annot:name=pial_aparc:visible=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ove
> r
> > l
> > > a
> > > >
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > > \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:vis
> i
> > b
> > > l
> > > > e=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visibl
> e
> > =
> > > 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.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.
> > >
> > >
> > >
> >
> >
>
>
------------------------------
Message: 9
Date: Thu, 15 Jun 2017 19:13:15 +0200
From: "John Anderson" <j.ander...@publicist.com>
Subject: [Freesurfer] substract images
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<trinity-98d8dd77-a163-4a7e-954c-19f6cd9da950-1497546795584@3capp-mailcom-lxa13>
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Message: 10
Date: Thu, 15 Jun 2017 13:19:50 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] substract images
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151319420.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Jon
mri_mask should do the trick
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> Dear experts,
> I have image and mask and I want to subtract the mask from the image.
> Meaning I want to get image free of?specific anatomical region. For example,
>
> I have image T1.nii for the brain and mask for the thalamus. How can I
> remove the thalamus from the T1 image to get T1 image free of the thalamus.
> Thanks you for any help
> Jon
>
>
------------------------------
Message: 11
Date: Thu, 15 Jun 2017 19:29:19 +0200
From: "John Anderson" <j.ander...@publicist.com>
Subject: Re: [Freesurfer] substract images
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-94466195-e126-474a-ae23-72ba25818e1c-1497547759661@3capp-mailcom-lxa16>
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Message: 12
Date: Thu, 15 Jun 2017 17:30:55 +0000
From: Michael Davies <michael.davie...@hotmail.com>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<mm1p123mb137235cf430ea9bbf2a865e789...@mm1p123mb1372.gbrp123.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is
there any others you could recommend?
Michael
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Sent: 15 June 2017 17:03:19
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces
I mean the /surf/lh.pial path has to be wrong, as that points to the root
where you wouldn't be allowed to put data. I guess surf/ worked for you,
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
issued the freeview command.
cheers
Bruce
On Thu, 15 Jun 2017, Michael
Davies wrote:
>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
> ____________________________________________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>
> Sent: 15 June 2017 16:11:53
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> I think you need to do a Unix tutorial. That path is wrong.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun
> 2017, 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=infla
> t
> > ed_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-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fis...@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=infl
> a
> > t
> > > 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-boun...@nmr.mgh.harvard.edu
> > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > > <fis...@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=a
> p
> > a
> > > r
> > > > c.annot:name=pial_aparc:visible=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ove
> r
> > l
> > > a
> > > >
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > > \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:vis
> i
> > b
> > > l
> > > > e=0 \
> >>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visibl
> e
> > =
> > > 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.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.
> > >
> > >
> > >
> >
> >
>
>
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------------------------------
Message: 13
Date: Thu, 15 Jun 2017 13:32:30 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] substract images
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151331120.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Jon
use mri_binarize on your initial mask to create a new one for mri_mask (use
--min and --max to specify the input mask intensity ranges that you want to
be "on"), then give that to mri_mask
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> Thank you Dr Bruce
>
> mri_mask removes everything and leaves the areas behind the mask. And what I
> want is the opposite.
> For example with mri_mask if I have?brain with skull and mask for skull
> stripped brain then the output is skull stripped brain. What I want is the
> opposite, the skull without the brain. I highly aprreciate any suggestion.?
> ? Sent:?Thursday, June 15, 2017 at 1:19 PM
> From:?"Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To:?"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject:?Re: [Freesurfer] substract images
> Hi Jon
>
> mri_mask should do the trick
>
> cheers
> Bruce
> On Thu, 15 Jun 2017, John Anderson wrote:
>
> > Dear experts,
> > I have image and mask and I want to subtract the mask from the image.
> > Meaning I want to get image free of?specific anatomical region. For
> example,
> >
> > I have image T1.nii for the brain and mask for the thalamus. How can I
> > remove the thalamus from the T1 image to get T1 image free of the
> thalamus.
> > Thanks you for any help
> > Jon
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
------------------------------
Message: 14
Date: Thu, 15 Jun 2017 13:32:46 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] viewing 3D surfaces
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151332390.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
seems like that is a good start
On Thu, 15 Jun 2017, Michael Davies wrote:
>
> Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is
> there any others you could recommend?
>
>
> Michael
>
>
>
>
> ____________________________________________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>
> Sent: 15 June 2017 17:03:19
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces ?
> I mean the /surf/lh.pial path has to be wrong, as that points to the root
> where you wouldn't be allowed to put data. I guess surf/ worked for you,
> but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
> issued the freeview command.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael
> Davies wrote:
>
> >
> > Hello Bruce, how do you mean the path is wrong? I am curious as the data
> > loaded just.
> >
> >
> > Kind regards, Michael
> >
> >___________________________________________________________________________
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu>
> > Sent: 15 June 2017 16:11:53
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces ?
> > Hi Michael
> >
> > I think you need to do a Unix tutorial. That path is wrong.
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 15 Jun
> > 2017, 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=infl
> a
> > t
> > > ed_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-boun...@nmr.mgh.harvard.edu
> > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > > <fis...@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=inf
> l
> > a
> > > t
> > > > 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-boun...@nmr.mgh.harvard.edu
> > > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
> > > > <fis...@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=
> a
> > p
> > > a
> > > > r
> > > > > c.annot:name=pial_aparc:visible=0 \
> >>>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ov
> e
> > r
> > > l
> > > > a
> > > > >
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > > > \
> >>>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:vi
> s
> > i
> > > b
> > > > l
> > > > > e=0 \
> >>>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visib
> l
> > e
> > > =
> > > > 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.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.
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>
------------------------------
Message: 15
Date: Thu, 15 Jun 2017 13:35:57 -0400 (EDT)
From: Lilla Zollei <lzol...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer parcelations of cortical regions
in TrackVis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151334340.16...@semmelweis.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Cris,
As long as your parcellation file gets resampled into the diffusion space,
you should not have any trouble reading it into TrackVis. When defining
ROIs you can just select individual label values afterwards.
Lilla
On Thu, 15 Jun 2017, Leyton Moscoso, Cristian Eduardo wrote:
> Hi Freesurfer?s and TrackVis experts
>
> I am wondering if there is a way to import cortical parcelations mapped on a
> T1 image in TrackVis. ?I tried loading segmentation in TrackVis, but this
> does not allow me to see all parcelations in T1 as I can be done in Freeview.
> In TrackVis I need to upload them one by one.?
>
> Thank you
>
> Cris
>
>
> Dr Cristian Leyton M Research Fellow in Neurology
> Department of Neurology
> Massachusetts General Hospital
> Harvard Medical School
> 149 ?13th Street
> Charlestown, MA 02129
>
> This email plus any attachments to it are confidential. Any unauthorised use
> is strictly prohibited. If you receive this email in error, please delete it
> and any attachments.
> Please think of our environment and only print this e-mail if necessary.
>
>
>
------------------------------
Message: 16
Date: Thu, 15 Jun 2017 19:47:11 +0200
From: "John Anderson" <j.ander...@publicist.com>
Subject: Re: [Freesurfer] substract images
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-c52483b4-e5cb-4d21-93a6-ba564579ac30-1497548831519@3capp-mailcom-lxa08>
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Message: 17
Date: Thu, 15 Jun 2017 13:51:26 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] substract images
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1706151348500.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"
try:
mri_binarize mask.nii --min 0 --max .1 --o mask.rev.nii --binval 1
mri_mask T1.nii mask.rev.nii T1.masked.nii
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> Hi Bruce, the mask is already binariz (min=0 ; max=1)
> I tried
> mri_mask T1.nii mask.nii output.nii
> ?
> The output is a maked image meaning the structure behind the mask
> ?
> I tried mri_binarize mask.nii --min 0 --max 1 output mask.nii then?
> mri_mask T1.nii output_mask.nii output.nii
> ?
> And I still get the same output. What in behind the mask and what I want is
> T1 free of what in the mask. I am not sure what I am doing wrong. My
> appologies for asking to many times.
> ?
> ?
> ?
> ? Sent:?Thursday, June 15, 2017 at 1:32 PM
> From:?"Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To:?"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject:?Re: [Freesurfer] substract images
> Hi Jon
>
> use mri_binarize on your initial mask to create a new one for mri_mask (use
> --min and --max to specify the input mask intensity ranges that you want to
> be "on"), then give that to mri_mask
>
> cheers
> Bruce
> On Thu, 15 Jun 2017, John Anderson wrote:
>
> > Thank you Dr Bruce
> >
> > mri_mask removes everything and leaves the areas behind the mask. And what
> I
> > want is the opposite.
> > For example with mri_mask if I have?brain with skull and mask for skull
> > stripped brain then the output is skull stripped brain. What I want is the
> > opposite, the skull without the brain. I highly aprreciate any
> suggestion.?
> > ? Sent:?Thursday, June 15, 2017 at 1:19 PM
> > From:?"Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> > To:?"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> > Subject:?Re: [Freesurfer] substract images
> > Hi Jon
> >
> > mri_mask should do the trick
> >
> > cheers
> > Bruce
> > On Thu, 15 Jun 2017, John Anderson wrote:
> >
> > > Dear experts,
> > > I have image and mask and I want to subtract the mask from the image.
> > > Meaning I want to get image free of?specific anatomical region. For
> > example,
> > >
> > > I have image T1.nii for the brain and mask for the thalamus. How can I
> > > remove the thalamus from the T1 image to get T1 image free of the
> > thalamus.
> > > Thanks you for any help
> > > Jon
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
------------------------------
Message: 18
Date: Thu, 15 Jun 2017 19:54:28 +0200
From: "John Anderson" <j.ander...@publicist.com>
Subject: Re: [Freesurfer] substract images
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-3e7469b7-ee97-41ff-af3f-e73b7ce92cbb-1497549268681@3capp-mailcom-lxa08>
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------------------------------
Message: 19
Date: Thu, 15 Jun 2017 20:23:17 +0000
From: Jerry Jeyachandra <jerrold.jeyachan...@queensu.ca>
Subject: [Freesurfer] Cropping of slices during recon-all
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<dm5pr07mb2891477a5151542bcb79078298...@dm5pr07mb2891.namprd07.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi Freesurfer team,
I have a compressed nifti file converted from DICOM that I am running through
recon-all. From my understanding first mri_convert is run on the original nifti
file in order to generate 001.mgz which is then averaged across multiple runs
to make rawavg.mgz. Since I'm only using 1 run, rawavg.mgz should be equivalent
to 001.mgz. Now I've noticed that compared to simply loading in the original
NIFTI image, loading in rawavg.mgz produces a cropped version of the image
where the bottom section (neck region and below) is cropped out. In addition
the SI axis which used to be 255 voxels in height, is now shorter (different
across individuals run through recon-all). With a set of voxel indices in the
original NIFTI image, I'd like to find a corresponding set of voxel indices in
the cropped rawavg.mgz. Does FreeSurfer store any information related to the
cropping that is done, I expect that there is only a translational shift in the
SI axis but I'd like to automatically extract this value for e
ach individual I've run through recon-all.
Thanks,
Jerrold Jeyachandra
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------------------------------
Message: 20
Date: Fri, 16 Jun 2017 05:17:18 +0800 (GMT+08:00)
From: ??? <yan...@psych.ac.cn>
Subject: [Freesurfer] When running mkcontrast-sess: A fatal error has
been detected by the Java Runtime Environment
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1ccf97e.40ed.15cad9e187a.coremail.yan...@psych.ac.cn>
Content-Type: text/plain; charset="gbk"
Hello FreeSurfer Developers,
I'm attempting to run 1st-level analysis with FS-FAST, following the tutorial
here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel. I
could run
mkanalysis-sess successfully:
mkanalysis-sess \
-fsd bold -surface fsaverage lh -fwhm 6 \
-event-related -paradigm onset_cond.par -nconditions 5 \
-spmhrf 0 -TR 2 -refeventdur 2 -nskip 0 -polyfit 2 \
-analysis fmcpr.sm6.fsaverage.lh -per-run -force
But when I run mkmkcontrast-sess with the following parameters:
mkmkcontrast-sess -analysis fmcpr.sm6.fsaverage.lh -contrast vSSI-v-vSSC -a 2
-c 1
it failed and reported error:
------------------------------------------Error------------------------------------------------------------------------
INFO: Found 5 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: -1.00000000000000000000 1.00000000000000000000 0 0 0
mkcontrast2 -config fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.config -anadir
fmcpr.sm6.fsaverage.lh -wcond -1.00000000000000000000 1.00000000000000000000 0
0 0 -sumconds -o fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat -wdelay 1 -no-octave
$Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $
cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat
nconds 5, wcond -1.00000000000000000000 1.00000000000000000000 0 0 0
ndelays 1, wdelay 1
ndelays 1, wpsa
sumconds 1
sumdelays 0
nircorr 0
TER 0.050000
rdelta
rtau
cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat
monly 0
NCond 5
WCond -1.00000000000000000000 1.00000000000000000000 0 0 0
NDelay 1
WDelay 1
TER 0.050000
sumconds 1
sumdelays 0
nircorr 0
TPreStim 0
RmPreStim 0
rdelta 0 0
rtau 0 0
ndelays 1
CNorm 1
setwdelay 0
setwcond 0
Matlab file is /tmp/mkcontrast2.4735.m
#
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007f9d60d795ac, pid=4928, tid=140313822955264
#
# JRE version: Java(TM) SE Runtime Environment (7.0_60-b19) (build 1.7.0_60-b19)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode linux-amd64
compressed oops)
# Problematic frame:
# C [libmwuix.so+0x455ac] uixDisplayInformation::getTopWindow() const+0xc
#
# Core dump written. Default location:
/home/amazinger/Public/share/fMRI/CrossModal/Imges/freesurfer/my-functional/core
or core.4928
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
matlab: javainit.cpp:1389: void {anonymous}::mwJavaAbort(): Assertion `Fatal
Java Exception. See Java Crash Report for details.' failed.
------------------------------------------------------------------------
Assertion detected at Thu Jun 15 15:57:34 2017
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Crash Mode : continue (default)
Current Visual : None
Default Encoding : UTF-8
GNU C Library : 2.23 stable
Host Name : X1
Java Crash Report : /home/amazinger/hs_error_pid4928.log
MATLAB Architecture : glnxa64
MATLAB Root : /usr/local/MATLAB/R2016a
MATLAB Version : 9.0.0.341360 (R2016a)
Operating System : Linux 4.4.0-79-generic #100-Ubuntu SMP Wed May 17
19:58:14 UTC 2017 x86_64
Processor ID : x86 Family 6 Model 78 Stepping 3, GenuineIntel
Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Assertion in void {anonymous}::mwJavaAbort() at javainit.cpp line 1389:
Fatal Java Exception. See Java Crash Report for details.
Register State (captured):
RAX = 00007f9d5b92bf60 RBX = 00007f9d751b8878
RCX = 000000000000000a RDX = 00007f9d75198c20
RSP = 00007f9d5b92bd70 RBP = 00007f9d5b92c130
RSI = 00007f9d74f4f3b8 RDI = 00007f9d5b92bd80
R8 = 0000000000000000 R9 = 00007f9d5aa0b8e0
R10 = 00007f9d74dc70b8 R11 = 00007f9d5b92bdf4
R12 = 00007f9d5aa0b1bb R13 = 00007f9d5aa0b8e0
R14 = 00007f9d751a87e8 R15 = 00007f9d5b92c9a0
RIP = 00007f9d74ebc59e EFL = 00007f9d5b92bf88
CS = b94f FS = 7b24 GS = 7f9d
Stack Trace (captured):
[ 0] 0x00007f9d74ebc59e
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01082782
_ZN2fl4diag5linux6x86_6412context_base12capture_dataEv+00000030
[ 1] 0x00007f9d74eb8541
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01066305
[ 2] 0x00007f9d74eb9bd0
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072080
[ 3] 0x00007f9d74eb9c42
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072194
[ 4] 0x00007f9d5a9cc75a
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01099610
[ 5] 0x00007f9d5960f8bb
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08513723
[ 6] 0x00007f9d5978fbc7
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+10087367
[ 7] 0x00007f9d596147cf
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08533967
JVM_handle_linux_signal+00000335
[ 8] 0x00007f9d7919b390
/lib/x86_64-linux-gnu/libpthread.so.0+00070544
[ 9] 0x00007f9d60d795ac
/usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00284076
_ZNK21uixDisplayInformation12getTopWindowEv+00000012
[ 10] 0x00007f9d60d66425
/usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00205861
[ 11] 0x00007f9d60d667a5
/usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00206757
[ 12] 0x00007f9d6a34cd71
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00650609
[ 13] 0x00007f9d6a353d7b
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00679291
[ 14] 0x00007f9d6a39c39e
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00975774
[ 15] 0x00007f9d7a4ae656
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwservices.so+02451030
_Z18svWS_PostUserEventil+00000038
[ 16] 0x00007f9d470c54e7
/usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01000679
_ZN5boost6detail8function26void_function_obj_invoker3INS_3_bi6bind_tIvPFvP7JNIEnv_P8_jobjectENS3_5list2INS_3argILi1EEENSC_ILi2EEEEEEEvS6_S8_lE6invokeERNS1_15function_bufferES6_S8_l+00000023
[ 17] 0x00007f9d470d13cc
/usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01049548
_ZNK5boost9function3IvP7JNIEnv_P8_jobjectlEclES2_S4_l+00000028
[ 18] 0x00007f9d470c456e
/usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+00996718
_Z17PostMatlabMessageP7JNIEnv_P8_jobjectS2_l+00000222
[ 19] 0x00007f9d4e3c9d98
<unknown-module>+00000000
[ 20] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 21] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 22] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 23] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 24] 0x00007f9d4e3bd233
<unknown-module>+00000000
[ 25] 0x00007f9d4e3bd233
<unknown-module>+00000000
[ 26] 0x00007f9d4e3b74e7
<unknown-module>+00000000
[ 27] 0x00007f9d593f08f5
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 28] 0x00007f9d593ef358
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 29] 0x00007f9d593b37ca
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498
[ 30] 0x00007f9d593b3a24
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06040100
[ 31] 0x00007f9d593b3e7a
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210
[ 32] 0x00007f9d59535b0e
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621390
[ 33] 0x00007f9d59535c76
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621750
[ 34] 0x00007f9d593e8d1f
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06257951
[ 35] 0x00007f9d4e3d4e88
<unknown-module>+00000000
[ 36] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 37] 0x00007f9d4e3b74e7
<unknown-module>+00000000
[ 38] 0x00007f9d593f08f5
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 39] 0x00007f9d593ef358
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 40] 0x00007f9d593b37ca
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498
[ 41] 0x00007f9d593b3a24
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06040100
[ 42] 0x00007f9d593b3e7a
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210
[ 43] 0x00007f9d59467d26
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06778150
[ 44] 0x00007f9d5947835a
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06845274
JVM_FindClassFromClassLoader+00000490
[ 45] 0x00007f9d515df68c
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/libjava.so+00054924
Java_java_lang_Class_forName0+00000300
[ 46] 0x00007f9d4e3c9d98
<unknown-module>+00000000
[ 47] 0x00007f9d4e3bd233
<unknown-module>+00000000
[ 48] 0x00007f9d4e3bd233
<unknown-module>+00000000
[ 49] 0x00007f9d4e3bd058
<unknown-module>+00000000
[ 50] 0x00007f9d4e3b74e7
<unknown-module>+00000000
[ 51] 0x00007f9d593f08f5
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653
[ 52] 0x00007f9d593ef358
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120
[ 53] 0x00007f9d59429099
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06520985
[ 54] 0x00007f9d59431a1d
/usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06556189
[ 55] 0x00007f9d5a9d3b91
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01129361
[ 56] 0x00007f9d5a9cd9f4
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01104372
[ 57] 0x00007f9d5a9d3174
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01126772
[ 58] 0x00007f9d5a9d3300
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01127168
[ 59] 0x00007f9d5a99961b
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00890395
[ 60] 0x00007f9d5a996bc5
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00879557
_ZN3jmi3jmi23JmiMethodsUsedByRuntime4initERKN8services6config14JmiInitOptionsE+00000021
[ 61] 0x00007f9d6a03d5c1
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00783809
[ 62] 0x00007f9d6a0380ab
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00762027
[ 63] 0x00007f9d6a028196
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00696726
[ 64] 0x00007f9d6a014cfd
/usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00617725
[ 65] 0x00007f9d791916ba
/lib/x86_64-linux-gnu/libpthread.so.0+00030394
[ 66] 0x00007f9d78ec782d
/lib/x86_64-linux-gnu/libc.so.6+01075245 clone+00000109
[ 67] 0x0000000000000000
<unknown-module>+00000000
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as
/home/amazinger/matlab_crash_dump.4928-1 **
MATLAB is exiting because of fatal error
Killed
-----------------------------------------END-------------------------------------------------------------------------
It also created an error log and a matlab crash file, which I attached to this
email.
I've searched the list and no similar errors have been reported. Does anyone
have any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.
log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu Kylin 16.04 LTS
3) uname -a: Linux X1 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log and error logs: see attached
Best Regards
Guochun Yang
Institute of Psychology, Chinese Academy of Sciences
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End of Freesurfer Digest, Vol 160, Issue 27
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