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] 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] mkbrainmask-sess: couldn't find register.dof6.lta

[Douglas N Greve]

Yes, it does. Prior to v6, the brain mask was created by the FSL BET 
program, which did not depend on the registration. V6 now maps the 
brainmask from the FS analysis into the subject space, which does depend 
on the registration


On 07/11/2017 02:36 PM, Li Guo wrote:
> Dear freesurfer developers,
>
> I’d like to ask about an error I encountered in Freesurfer v6.0 with 
> mkbrainmask-sess. I am using macOS Sierra.
> Here is the error:
>
> error:"ERROR: cannot find 
> /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, 
> you might need to run register-sess”
>
> The error goes away if I run register-sess before mkbrainmask-sess. 
> However, my lab mates use v5.3 and ran the exact same preprocess 
> pipeline without this error. The order for them is mkbrainmask-sess 
> first and register-sess later.
>
> I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess 
> now depends on register-sess to generate the register.dof6.lta file? 
> Or how should I interpret this? Does running registration and masks 
> have some fixed order at all or it doesn’t matter?
>
> Best,
> Li
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] mkbrainmask-sess: couldn't find register.dof6.lta

[Li Guo]

Dear freesurfer developers,

I’d like to ask about an error I encountered in Freesurfer v6.0 with 
mkbrainmask-sess. I am using macOS Sierra.
Here is the error:

error:"ERROR: cannot find 
/Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you 
might need to run register-sess”

The error goes away if I run register-sess before mkbrainmask-sess. However, my 
lab mates use v5.3 and ran the exact same preprocess pipeline without this 
error. The order for them is mkbrainmask-sess first and register-sess later.

I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess now 
depends on register-sess to generate the register.dof6.lta file? Or how should 
I interpret this? Does running registration and masks have some fixed order at 
all or it doesn’t matter?

Best,
Li
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Re: [Freesurfer] mkbrainmask-sess and inorm-sess

[Douglas N Greve]

Run preproc-sess instead. inorm-sess is no longer used

On 03/04/2016 05:18 PM, Ji Won Bang wrote:
> Thanks for your help!
>
> I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
>
> What I used to run are:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd 
> bold_retino
> inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd 
> bold_retino
>
> However, since version 5.3.0 changed a lot, I tried:
> mkbrainmask-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
> inorm-sess -s $SUBJECT -motioncor -df sessdirfile -fsd bold_retino
>
> It gives me an error:
> ERROR: could not determine file for 
> /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc
> ERROR: inorm failed
>
> Which part am I doing wrong?
>
> Thank you so much.
>
> Best,
> Ji Won
>
>
> 2016-03-04 17:13 GMT-05:00 Douglas N Greve  >:
>
> The functional stream changed a lot from version 4 to version 5. The
> commands and workflow are very different now
>
> On 03/04/2016 04:31 PM, Ji Won Bang wrote:
> > Dear. Freesurfer experts.
> >
> > Hi. How are you?
> >
> > It might be very naive question.
> >
> > When using version 4.5.0 I used the command:
> > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
> > bold_retino
> >
> > However under the version 5.3.0, mkbrainmask-sess does not have
> -funcstem.
> >
> > May I use -maskstem instead of -funcstem?
> >
> > If so, after that, I tried:
> > inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
> > bold_retino
> >
> > However, it complains that:
> > ERROR: cannot find
> > /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
> > You may need to run preproc-sess or mkbrainmask-sess to create a
> brain
> > mask
> >
> > Could you please help?
> >
> > Thank you very much.
> >
> > Best,
> > Ji Won
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> 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
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> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] mkbrainmask-sess and inorm-sess

[Ji Won Bang]

Thanks for your help!

I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0

What I used to run are:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
bold_retino

However, since version 5.3.0 changed a lot, I tried:
mkbrainmask-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
inorm-sess -s $SUBJECT -motioncor -df sessdirfile -fsd bold_retino

It gives me an error:
ERROR: could not determine file for
/home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc
ERROR: inorm failed

Which part am I doing wrong?

Thank you so much.

Best,
Ji Won


2016-03-04 17:13 GMT-05:00 Douglas N Greve :

> The functional stream changed a lot from version 4 to version 5. The
> commands and workflow are very different now
>
> On 03/04/2016 04:31 PM, Ji Won Bang wrote:
> > Dear. Freesurfer experts.
> >
> > Hi. How are you?
> >
> > It might be very naive question.
> >
> > When using version 4.5.0 I used the command:
> > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
> > bold_retino
> >
> > However under the version 5.3.0, mkbrainmask-sess does not have
> -funcstem.
> >
> > May I use -maskstem instead of -funcstem?
> >
> > If so, after that, I tried:
> > inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
> > bold_retino
> >
> > However, it complains that:
> > ERROR: cannot find
> > /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
> > You may need to run preproc-sess or mkbrainmask-sess to create a brain
> > mask
> >
> > Could you please help?
> >
> > Thank you very much.
> >
> > Best,
> > Ji Won
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] mkbrainmask-sess and inorm-sess

[Douglas N Greve]

You specify it when you run mkanalysis-sess

On 03/04/2016 04:36 PM, Ji Won Bang wrote:
> In a simple word, my question is:
>
> under version 5.3.0, how can I specify funcstem (stem of functional 
> volume)? I don't see any argument for that..
>
> Thanks a lot.
>
> Best,
> Ji Won
>
> 2016-03-04 16:31 GMT-05:00 Ji Won Bang  >:
>
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive question.
>
> When using version 4.5.0 I used the command:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
> bold_retino
>
> However under the version 5.3.0, mkbrainmask-sess does not have
> -funcstem.
>
> May I use -maskstem instead of -funcstem?
>
> If so, after that, I tried:
> inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile
> -fsd bold_retino
>
> However, it complains that:
> ERROR: cannot find
> /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
> You may need to run preproc-sess or mkbrainmask-sess to create a
> brain mask
>
> Could you please help?
>
> Thank you very much.
>
> Best,
> Ji Won
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

[Douglas N Greve]

The functional stream changed a lot from version 4 to version 5. The 
commands and workflow are very different now

On 03/04/2016 04:31 PM, Ji Won Bang wrote:
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive question.
>
> When using version 4.5.0 I used the command:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd 
> bold_retino
>
> However under the version 5.3.0, mkbrainmask-sess does not have -funcstem.
>
> May I use -maskstem instead of -funcstem?
>
> If so, after that, I tried:
> inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd 
> bold_retino
>
> However, it complains that:
> ERROR: cannot find 
> /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
> You may need to run preproc-sess or mkbrainmask-sess to create a brain 
> mask
>
> Could you please help?
>
> Thank you very much.
>
> Best,
> Ji Won
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

[Ji Won Bang]

In a simple word, my question is:

under version 5.3.0, how can I specify funcstem (stem of functional
volume)? I don't see any argument for that..

Thanks a lot.

Best,
Ji Won

2016-03-04 16:31 GMT-05:00 Ji Won Bang :

> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive question.
>
> When using version 4.5.0 I used the command:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
>
> However under the version 5.3.0, mkbrainmask-sess does not have -funcstem.
>
> May I use -maskstem instead of -funcstem?
>
> If so, after that, I tried:
> inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
> bold_retino
>
> However, it complains that:
> ERROR: cannot find
> /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
> You may need to run preproc-sess or mkbrainmask-sess to create a brain mask
>
> Could you please help?
>
> Thank you very much.
>
> Best,
> Ji Won
>
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[Freesurfer] mkbrainmask-sess and inorm-sess

[Ji Won Bang]

Dear. Freesurfer experts.

Hi. How are you?

It might be very naive question.

When using version 4.5.0 I used the command:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino

However under the version 5.3.0, mkbrainmask-sess does not have -funcstem.

May I use -maskstem instead of -funcstem?

If so, after that, I tried:
inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
bold_retino

However, it complains that:
ERROR: cannot find
/home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain
You may need to run preproc-sess or mkbrainmask-sess to create a brain mask

Could you please help?

Thank you very much.

Best,
Ji Won
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Re: [Freesurfer] mkbrainmask-sess

[Joseph Dien]

I imagine this issue has been solved by now but just for the record I ran into 
a similar issue.  In my case the problem turned out to be that FSL installs by 
default in /usr/local/fsl/bin but FSFAST was looking for it in /bin

This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesurfer 
5.2.0.

Is there some way to set up Freesurfer so it'll look in the correct directory?  
For now I'm copying the critical files to /bin but am hoping there is a better 
solution.

Thanks!

Joe


 It could be. It uses fsl only to create a mask of the brain, so it probably 
 does not need a full fsl install, but it might need more than you have.
 doug
 
 On 3/25/12 7:05 AM, Kiley Seymour wrote:
 Hi again,
 Could this error be due to the fact that I don't have a full version
 of fsl installed and configured on my ubuntu virtual machine? i.e.
 does fsfast require fsl to be installed?
 
 Thanks
 
 K
 
 
 *From:* Kiley Seymour kiley_seym...@yahoo.com.au
 *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 *Sent:* Friday, 23 March 2012 3:04 PM
 *Subject:* mkbrainmask-sess
 
 Dear Freesurfers,
 
 I am currently trying to do some retinotopic mapping. I have been successful 
 in running the reconstruction commands and setting everything up for the 
 analysis, but I have run into problems when using the selxavg3-sess command. 
 i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc 
 since I have co-registered and motion corrected my files in SPM).
 I was unable to run this command as freesurfer could not 
 find/media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat
 So I ran mktemplate - sess, which was successfully completed. And then I ran 
 mkbrainmask-sess (see below).
 Any help with this would be much appreciated.
 
 Thanks
 
 Kiley
 
 FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 
 -d~/data1/RETINOTOPY
 
 /media/sf_DATA1/RETINOTOPY/IFEE2211
 Fri Mar 23 09:42:26 EDT 2012
 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_7930
 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
 mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
 mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
 reading from template.nii.gz...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-0.998558, -0.0534653, -0.00482299)
 j_ras = (-0.0536701, 0.992375, 0.110955)
 k_ras = (0.00114604, -0.111054, 0.993814)
 writing to /tmp/mkbrainmask_7930/in.nii...
 # -- Using FSL's BET to Extract Brain-- #
 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
 bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
 /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
 /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
 [: 158: =: unexpected operator
 /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
 mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 
 --o/tmp/mkbrainmask_7930/brain_mask.nii
 niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii
 
 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
 cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
 cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
 /tmp/mkbrainmask_7930/brain_mask.nii
 sysname  Linux
 hostname FreeSurfer
 machine  i686
 user virtualuser
 
 input  /tmp/mkbrainmask_7930/brain_mask.nii
 frame  0
 nErode3d   0
 nErode2d   0
 output /tmp/mkbrainmask_7930/brain_mask.nii
 Binarizing based on threshold
 min0.01
 max+infinity
 binval1
 binvalnot 0
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 ___
 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.




Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//











___

Re: [Freesurfer] mkbrainmask-sess

[Kiley Seymour]

Hi again,

Could this error be due to the fact that I don't have a full version
of fsl installed and configured on my ubuntu virtual machine? i.e.
does fsfast require fsl to be installed?

Thanks

K




 From: Kiley Seymour kiley_seym...@yahoo.com.au
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu 
Sent: Friday, 23 March 2012 3:04 PM
Subject: mkbrainmask-sess 
 

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in 
running the reconstruction commands and setting everything up for the analysis, 
but I have run into problems when using the selxavg3-sess command. i.e. 
selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc (  -no-preproc since I 
have co-registered and motion corrected my files in SPM). 

I was unable to run this command as freesurfer could not 
find  /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran 
mkbrainmask-sess (see below). 

Any help with this would be much appreciated.

Thanks

Kiley

 
FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d 
~/data1/RETINOTOPY

/media/sf_DATA1/RETINOTOPY/IFEE2211 
Fri Mar 23 09:42:26 EDT 2012
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_7930
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii 
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from template.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998558, -0.0534653, -0.00482299)
j_ras = (-0.0536701, 0.992375, 0.110955)
k_ras = (0.00114604, -0.111054, 0.993814)
writing to /tmp/mkbrainmask_7930/in.nii...
# -- Using FSL's BET to Extract Brain-- #
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
/home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
[: 158: =: unexpected operator
/home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_7930/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_7930/brain_mask.nii 
sysname  Linux
hostname FreeSurfer
machine  i686
user     virtualuser

input      /tmp/mkbrainmask_7930/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_7930/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mkbrainmask-sess

[Douglas Greve]

It could be. It uses fsl only to create a mask of the brain, so it 
probably does not need a full fsl install, but it might need more than 
you have.

doug

On 3/25/12 7:05 AM, Kiley Seymour wrote:

Hi again,

Could this error be due to the fact that I don't have a full version
of fsl installed and configured on my ubuntu virtual machine? i.e.
does fsfast require fsl to be installed?

Thanks

K


*From:* Kiley Seymour kiley_seym...@yahoo.com.au
*To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
*Sent:* Friday, 23 March 2012 3:04 PM
*Subject:* mkbrainmask-sess

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been 
successful in running the reconstruction commands and setting 
everything up for the analysis, but I have run into problems when 
using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh 
-s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and 
motion corrected my files in SPM).


I was unable to run this command as freesurfer could not find 
 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat


So I ran mktemplate - sess, which was successfully completed. And then 
I ran mkbrainmask-sess (see below).


Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d 
~/data1/RETINOTOPY


/media/sf_DATA1/RETINOTOPY/IFEE2211
Fri Mar 23 09:42:26 EDT 2012
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_7930
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from template.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998558, -0.0534653, -0.00482299)
j_ras = (-0.0536701, 0.992375, 0.110955)
k_ras = (0.00114604, -0.111054, 0.993814)
writing to /tmp/mkbrainmask_7930/in.nii...
# -- Using FSL's BET to Extract Brain-- #
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
/home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
[: 158: =: unexpected operator
/home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_7930/brain_mask.nii

niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min 
.01 --o /tmp/mkbrainmask_7930/brain_mask.nii

sysname  Linux
hostname FreeSurfer
machine  i686
user virtualuser

input  /tmp/mkbrainmask_7930/brain_mask.nii
frame  0
nErode3d   0
nErode2d   0
output /tmp/mkbrainmask_7930/brain_mask.nii
Binarizing based on threshold
min0.01
max+infinity
binval1
binvalnot 0





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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mkbrainmask-sess

[Kiley Seymour]

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in 
running the reconstruction commands and setting everything up for the analysis, 
but I have run into problems when using the selxavg3-sess command. i.e. 
selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc (  -no-preproc since I 
have co-registered and motion corrected my files in SPM). 

I was unable to run this command as freesurfer could not 
find  /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran 
mkbrainmask-sess (see below). 

Any help with this would be much appreciated.

Thanks

Kiley

 
FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d 
~/data1/RETINOTOPY

/media/sf_DATA1/RETINOTOPY/IFEE2211 
Fri Mar 23 09:42:26 EDT 2012
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 
-nerode 0
FSLMATHSfslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_7930
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii 
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from template.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998558, -0.0534653, -0.00482299)
j_ras = (-0.0536701, 0.992375, 0.110955)
k_ras = (0.00114604, -0.111054, 0.993814)
writing to /tmp/mkbrainmask_7930/in.nii...
# -- Using FSL's BET to Extract Brain-- #
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
/home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
[: 158: =: unexpected operator
/home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_7930/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
cmdlinemri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_7930/brain_mask.nii 
sysname  Linux
hostnameFreeSurfer
machine  i686
user     virtualuser

input      /tmp/mkbrainmask_7930/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_7930/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0
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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.

Re: [Freesurfer] mkbrainmask-sess

[Doug Greve]

HI Sebastian,

I made a mod to this in development version, but it operates slightly 
differently in that you set the nth run with -run. Eg, -run 2 would 
mean to use the 2nd run. Otherwise, if you run it on more than one 
session, the run that you specify might not exist. Would this work for you?


doug


Sebastian Moeller wrote:


Hi List,

to follow up my mail from several days ago, all mkbrainmask-sess 
(v3.0.2 centos4 x86_64) really needs to be able to select the run from 
which to take the run-number are the following lines:

case -run
set run = $argv[1]; shift;
breaksw

somewhere between the label parse_args: and the command goto 
parse_args_return.


Ahoi
Sebastian



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] mkbrainmask-sess

[Sebastian Moeller]

Hi Doug,

On 26. Jun 2006, at 21:19 Uhr, Doug Greve wrote:



HI Sebastian,

I made a mod to this in development version, but it operates slightly 
differently in that you set the nth run with -run. Eg, -run 2 would 
mean to use the 2nd run. Otherwise, if you run it on more than one 
session, the run that you specify might not exist. Would this work for 
you?
	Ah great, I did not think about this. All I wanted to assure is that 
the brain mask was from the same run as my moco reference volume (and 
this only because it feels right to do so ;)).


ahoi
Sebastian



doug


Sebastian Moeller wrote:


Hi List,

to follow up my mail from several days ago, all mkbrainmask-sess 
(v3.0.2 centos4 x86_64) really needs to be able to select the run 
from which to take the run-number are the following lines:

case -run
set run = $argv[1]; shift;
breaksw

somewhere between the label parse_args: and the command goto 
parse_args_return.


Ahoi
Sebastian



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





--
Sebastian Moeller

Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM:  01 62 - 3 25 45 59
[EMAIL PROTECTED]

AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen


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[Freesurfer] mkbrainmask-sess

[Sebastian Moeller]

Hi List,

to follow up my mail from several days ago, all mkbrainmask-sess 
(v3.0.2 centos4 x86_64) really needs to be able to select the run from 
which to take the run-number are the following lines:

case -run
set run = $argv[1]; shift;
breaksw

somewhere between the label parse_args: and the command goto 
parse_args_return.


Ahoi
Sebastian
--
Sebastian Moeller

Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM:  01 62 - 3 25 45 59
[EMAIL PROTECTED]

AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen


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[Freesurfer] mkbrainmask-sess

[Sebastian Moeller]

Hi All,

just a quick note to let you know that 3.0.2's (centos4 x86_64) 
mkbrainmask-sess does not really parse the -run nth parameter it 
specifies in its help text. Haven't found time to implement a fix yet, 
but it is a minor issue anyway...


Ahoi
Sebastian
--
Sebastian Moeller

Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM:  01 62 - 3 25 45 59
[EMAIL PROTECTED]

AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen


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[Freesurfer] mkbrainmask-sess failed

[Jia Liu]

Dear all,



When I used mkbrainmask-sess, an error occurred shown
below. I am using the latest FreeSurfer, and the bet command is included in the
distribution. Could anyone tell me how to fix it? thanks,



Jia



++begin of error
message+

mkbrainmask-sess

20041007syhu

$Id: mkbrainmask-sess,v 1.2 2003/10/01 21:54:43 greve
Exp $

Linux zion 2.4.22-1.zion #5 SMP
Sun Dec 21 12:35:17 CST 2003 i686 i686 i386 GNU/Linux

Tue Nov 23 20:23:19 CST 2004

/nfs/home/jliu/data/scramface/mystudy

-sf sessid_syhu -df sesspar

ProjectDir /nfs/home/jliu/data/scramface/mystudy





/nfs/home/jliu/data/scramface/20041007syhu 

Tue Nov 23 20:23:19 CST 2004

/nfs/home/jliu/data/scramface/20041007syhu/bold

mkbrainmask -i 005/f -o masks/brain -thresh 0.1 -umask
2

Scratch Dir is /tmp/mkbrainmask_4734

# -- Converting bvolume to .img
-- #

mri_convert 005/f_000.bshort
/tmp/mkbrainmask_4734/f.img 

Reading 005/f_000.bshort ... 

Reading 005/f_001.bshort ... 

Reading 005/f_002.bshort ... 

Reading 005/f_003.bshort ... 

Reading 005/f_004.bshort ... 

Reading 005/f_005.bshort ... 

Reading 005/f_006.bshort ... 

Reading 005/f_007.bshort ... 

Reading 005/f_008.bshort ... 

Reading 005/f_009.bshort ... 

Reading 005/f_010.bshort ... 

Reading 005/f_011.bshort ... 

Reading 005/f_012.bshort ... 

Reading 005/f_013.bshort ... 

Reading 005/f_014.bshort ... 

Reading 005/f_015.bshort ... 

reading from 005/f_000.bshort...

INFO: bvolumeRead: min = 0, max = 885

TR=1.50, TE=30.00, TI=30.00, flip angle=90.00

i_ras = (-1, 0, 0)

j_ras = (0, -0.996195, 0.0871557)

k_ras = (-0, 0.087156, 0.996195)

writing to /tmp/mkbrainmask_4734/f.img...

Analyze Output Matrix

-3.125 0.000 -0.000
100.229;

0.000 -3.113 0.418
99.376;

0.000 0.272 4.782
-50.897;

0.000 0.000
0.000 1.000;



INFO: set hdr.hist.orient to 3

# -- Using FSL's BET to Extract
Brain-- #

This program has not been compiled for this data type

/nfs/home/jliu/data/scramface/20041007syhu/bold

bet /tmp/mkbrainmask_4734/f
/tmp/mkbrainmask_4734/brain -m -f 0.1

ERROR: bet failed

ERROR: mkbrainmask failed



+end of error message






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