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
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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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
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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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> 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.
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>
>
>
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-- 
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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
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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
> error
> 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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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
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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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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 
> *To:* "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
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> ___
> 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 
> 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

[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 
*To:* "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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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 
To: "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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contains patient information, please contact the Partners Compliance HelpLine at
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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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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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