Re: [Freesurfer] Preproc-sess Error

[Douglas Greve]

it is not in $FREESURFER_HOME/bin ? If not, you can copy it from 5.3


On 10/25/17 4:59 PM, Hsu, Eugene wrote:


Hi FreeSurfer Experts,


We're trying to run preproc-sess on FreeSurfer 6, but we're 
encountering an error when motion correcting:



    ERROR: cannot find AFNI command 3dvolreg.afni


When we tried Freesurfer 5.3 the preproc-sess ran to completion.


Thanks for your help!

--Eugene





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[Freesurfer] Preproc-sess Error

[Hsu, Eugene]

Hi FreeSurfer Experts,


We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an 
error when motion correcting:


ERROR: cannot find AFNI command 3dvolreg.afni


When we tried Freesurfer 5.3 the preproc-sess ran to completion.


Thanks for your help!

--Eugene


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Re: [Freesurfer] segmentHA znzread failed error

[Iglesias Gonzalez, Eugenio]

Dear Arkadiy
Andrew Hoopes just pinpointed that they have tracked down these warnings to a 
recent code change. It’s happening for everyone using dev. You can ignore these 
znz error statements, they are completely innocuous. It’s just caused by a 
print statement that shouldn’t have been added.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of "Maksimovskiy, 
Arkadiy" 
Reply-To: Freesurfer support list 
Date: Tuesday, 24 October 2017 at 14:31
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA znzread failed error

Dear Hipp. Segmentation experts,

I keep getting the following error when running the segmentHA script from the 
Dev. Version. Wondering if this is serious or something that can be ignored, as 
the process keeps running to the end:

Transforming points
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
threshold mask volume at 0.5
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed
No such file or directory
threshold mask volume at 0.5
znzreadInt: znzread failed
No such file or directory
znzreadInt: znzread failed


Thank  you for your help,
Arkadiy

--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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Re: [Freesurfer] smoothing a surface map

[Douglas Greve]

if it is a group map in fsaverage space, then specify fsaverage as the 
subject



On 10/25/17 1:12 PM, Eryilmaz, H. Hamdi wrote:


Hello all,


How can I simply smooth a surface map (constructed using MRIwrite) 
using a specific FWHM? mri_surf2surf requires source subject as an 
input but all I want to do is to smooth a single group map.



Thanks in advance for your help!


Best,

Hamdi





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Re: [Freesurfer] Freesurfer mkbrainmask-sess

[Rebecca Sheley]

Never mind, I believe I fixed the issue. Just missed a step. Thanks!

--Rebecca Sheley

On Wed, Oct 25, 2017 at 12:14 PM, Rebecca Sheley 
wrote:

> Hello Freesurfer Team,
>
> I'm having trouble running preproc-sess, but only with the
> mkbrainmask-sess step. I tried just running this step and got this output.
> Do you have any insights on why this might be happening?
>
> My tmp folder is empty.
> The cwd directory is the folder where my data are located.
> Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> OS: Ubuntu
>
> Here is the command I ran:
>
> mkbrainmask-sess -s FS_0184 -d `pwd`
>
> Here is the output:
>
> /home/rebecca/SC/FS_0184
> Wed Oct 25 11:59:31 EDT 2017
> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1
> -nerode 0
> FSLMATHS fslmaths.fsl
> Scratch Dir is /tmp/mkbrainmask_29130
> /home/rebecca/SC/FS_0184/bold
> mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
> mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from template.nii.gz...
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to /tmp/mkbrainmask_29130/in.nii...
> # -- Using FSL's BET to Extract Brain-- #
> /home/rebecca/SC/FS_0184/bold
> bet.fsl /tmp/mkbrainmask_29130/in.nii /tmp/mkbrainmask_29130/brain -m -f
> 0.1
> Segmentation fault (core dumped)
> mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01 --o
> /tmp/mkbrainmask_29130/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_29130/brain_mask.nii
>
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> cwd /home/rebecca/SC/FS_0184/bold
> cmdline mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01
> --o /tmp/mkbrainmask_29130/brain_mask.nii
> sysname  Linux
> hostname wernickesarea
> machine  x86_64
> user rebecca
>
> input  /tmp/mkbrainmask_29130/brain_mask.nii
> frame  0
> nErode3d   0
> nErode2d   0
> output /tmp/mkbrainmask_29130/brain_mask.nii
> Binarizing based on threshold
> min0.01
> max+infinity
> binval1
> binvalnot 0
>
> Thanks!
> --Rebecca Sheley
>
>
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[Freesurfer] smoothing a surface map

[Eryilmaz, H. Hamdi]

Hello all,


How can I simply smooth a surface map (constructed using MRIwrite) using a 
specific FWHM? mri_surf2surf requires source subject as an input but all I want 
to do is to smooth a single group map.


Thanks in advance for your help!


Best,

Hamdi


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[Freesurfer] Freesurfer mkbrainmask-sess

[Rebecca Sheley]

Hello Freesurfer Team,

I'm having trouble running preproc-sess, but only with the mkbrainmask-sess
step. I tried just running this step and got this output. Do you have any
insights on why this might be happening?

My tmp folder is empty.
The cwd directory is the folder where my data are located.
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
OS: Ubuntu

Here is the command I ran:

mkbrainmask-sess -s FS_0184 -d `pwd`

Here is the output:

/home/rebecca/SC/FS_0184
Wed Oct 25 11:59:31 EDT 2017
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1
-nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_29130
/home/rebecca/SC/FS_0184/bold
mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_29130/in.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from template.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /tmp/mkbrainmask_29130/in.nii...
# -- Using FSL's BET to Extract Brain-- #
/home/rebecca/SC/FS_0184/bold
bet.fsl /tmp/mkbrainmask_29130/in.nii /tmp/mkbrainmask_29130/brain -m -f 0.1
Segmentation fault (core dumped)
mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01 --o
/tmp/mkbrainmask_29130/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_29130/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/rebecca/SC/FS_0184/bold
cmdline mri_binarize --i /tmp/mkbrainmask_29130/brain_mask.nii --min .01
--o /tmp/mkbrainmask_29130/brain_mask.nii
sysname  Linux
hostname wernickesarea
machine  x86_64
user rebecca

input  /tmp/mkbrainmask_29130/brain_mask.nii
frame  0
nErode3d   0
nErode2d   0
output /tmp/mkbrainmask_29130/brain_mask.nii
Binarizing based on threshold
min0.01
max+infinity
binval1
binvalnot 0

Thanks!
--Rebecca Sheley
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Re: [Freesurfer] Fwd: Adding control points to aparc+aseg

[Nicholas Goh]

Hello,

I have tried fixing the image using the topical defects page. However,
because it uses recon-edit the affected area does not seem to be recognized
as white matter. Is it okay to do free editing for the same results, or is
there something else that I should try for implementation?
Thank you for the help,

Nicholas Goh

On Mon, Oct 23, 2017 at 4:10 PM, Douglas N Greve 
wrote:

> I think you have an incorrectly fixed defect at that location. Follow
> the instructions on fixing defects on our wiki.
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
> TopologicalDefect_freeview
>
>
> On 10/23/2017 09:18 AM, Nicholas Goh wrote:
> > Sorry for the delay, I was hoping to get some input from another on
> > why my numbers seemed off.
> > I have attached a screenshot which I believe has an image of an
> > example which needs to be fixed, along with the coordinates.
> > Please let me know if you need anything else,
> >
> > Nicholas Goh
> >
> > On Mon, Oct 16, 2017 at 1:08 PM, Douglas Greve
> > > wrote:
> >
> > I don't know what coordinates those are. Can you give indices?
> > indices are non-neg
> >
> >
> > On 10/16/17 12:59 PM, Nicholas Goh wrote:
> >> An example of the aparc+aseg not covering all that it needs to
> >> can be found around [-7, 114, 133]
> >>
> >> On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve
> >> >
> wrote:
> >>
> >> what is the index (ie, col, row, slice) where you are seeing
> >> a problem?
> >>
> >>
> >> On 10/16/17 11:44 AM, Nicholas Goh wrote:
> >>> Hi,
> >>>
> >>> I am not sure if this email got lost in the process or is
> >>> still awaiting approval, but I was asked to tar and gzip the
> >>> images that I was having no luck with fixing the white
> >>> matter for.
> >>> Any help would be appreciated.
> >>> Thank you,
> >>>
> >>> Nicholas Goh
> >>> -- Forwarded message --
> >>> From: *Nicholas Goh*  >>> >
> >>> Date: Mon, Oct 2, 2017 at 12:33 PM
> >>> Subject: Re: [Freesurfer] Adding control points to aparc+aseg
> >>> To: Freesurfer support list  >>> >
> >>>
> >>>
> >>> I have still been having trouble with fixing the white
> >>> matter of the aparc+aseg.mgz file for a subject.
> >>> I have tried using
> >>>
> >>> recon-all -autorecon2-cp -autorecon3 -subjid 
> >>> recon-all -autorecon2-wm -subjid 
> >>> recon-all -autorecon2-wm -autorecon3 -subjid 
> >>>
> >>> None of these have solved the issue, and I was hoping for
> >>> help in finding a way to fix this? There are other more
> >>> extreme examples, but this one seems to have an error at
> >>> [-7, 114, 133]
> >>> Thank you for the help,
> >>>
> >>> Nicholas Goh
> >>>
> >>> On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh
> >>> > wrote:
> >>>
> >>> Ping, is this okay to do? I Think it is but wanted to
> >>> check before sending
> >>> -- Forwarded message --
> >>> From: *Bruce Fischl*  >>> >
> >>> Date: Thu, Sep 28, 2017 at 5:23 PM
> >>> Subject: Re: [Freesurfer] Adding control points to
> >>> aparc+aseg
> >>> To: Freesurfer support list
> >>>  >>> >
> >>>
> >>>
> >>> Hi Nicholas
> >>>
> >>> why don't you tar, gzip and upload your subject and we
> >>> will take a look. Make sure to tell us the coordinates
> >>> of where you are trying to fix things
> >>>
> >>> cheers
> >>> Bruce
> >>>
> >>>
> >>> On Thu, 28 Sep 2017, Nicholas Goh wrote:
> >>>
> >>> I am still having trouble with getting the
> >>> aparc+aseg to recognize sections
> >>> that should be white matter as such. Using the
> >>> control points paired
> >>> withrecon-all -autorecon2-cp -autorecon3 -subjid 
> >>>
> >>> did not work, after 4 or 5 attempts with different
> >>> control points, and using
> >>> recon-all -autorecon2-wm -s 
> >>> also did not yield appreciable results. Is there
> >>> anything else that I might
> >>> be able to try to fix this?
> >>> Thank you for all the help,
> >>>
> >>>