Re: [Freesurfer] niiRead: error opening file, through mri_convert

2021-08-02 Thread Fischl, Bruce 
I’m glad to hear it worked out. We have all done this….
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andrew
Sent: Monday, August 2, 2021 12:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] niiRead: error opening file, through mri_convert


External Email - Use Caution
Bruce, thank you for this response. In fact I had the T1 path wrong despite 
having read it over and over 20 times.. listing directory contents indeed 
revealed my error…
-andrew


On Jul 30, 2021, at 13:38, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:

Can you load 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in 
freeview? Maybe run ls -l on it?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew
Sent: Friday, July 30, 2021 1:44 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] niiRead: error opening file, through mri_convert

External Email - Use Caution
Hello,
I’m trying to reconstruct an old pipeline that I don’t completely understand 
(so sorry if this is very elementary or out of date), and one step is to 
convert the freesurfer T1 segmentation ribbon.mgz to .nii format using 
mri_convert.

Through freesurfer interface I see the T1 and the segmentation are fine; but 
mri_convert seems to fail on looking for the T1:

The command (from inside Matlab) is:
mri_convert  --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
Output looks like:
mri_convert --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
reading template info from volume 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...
error: niiRead(): error opening file 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*

It is failing to read the T1 and then it does not save the output file.
But the input files (T1.nii and ribbon.mgz) are all where they should be.
What could I be doing wrong?

thanks,
-Andrew
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Re: [Freesurfer] niiRead: error opening file, through mri_convert

2021-08-02 Thread Andrew 
External Email - Use Caution

Bruce, thank you for this response. In fact I had the T1 path wrong despite 
having read it over and over 20 times.. listing directory contents indeed 
revealed my error…
-andrew

> On Jul 30, 2021, at 13:38, Fischl, Bruce  wrote:
> 
> Can you load 
> /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in 
> freeview? Maybe run ls -l on it?
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Andrew
> Sent: Friday, July 30, 2021 1:44 PM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] niiRead: error opening file, through mri_convert
>  
> External Email - Use Caution
> 
> Hello,
> I’m trying to reconstruct an old pipeline that I don’t completely understand 
> (so sorry if this is very elementary or out of date), and one step is to 
> convert the freesurfer T1 segmentation ribbon.mgz to .nii format using 
> mri_convert.
>  
> Through freesurfer interface I see the T1 and the segmentation are fine; but 
> mri_convert seems to fail on looking for the T1:
>  
> The command (from inside Matlab) is:
> mri_convert  --reslice_like 
> /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
> nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
> /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
> 
> Output looks like:
> mri_convert --reslice_like 
> /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
> nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
> /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii 
> reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> reading template info from volume 
> /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...
> error: niiRead(): error opening file 
> /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*
>  
> It is failing to read the T1 and then it does not save the output file. 
> But the input files (T1.nii and ribbon.mgz) are all where they should be. 
> What could I be doing wrong?
>  
> thanks,
> -Andrew
> ___
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>  
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Re: [Freesurfer] niiRead: error opening file, through mri_convert

2021-07-30 Thread Fischl, Bruce 
Can you load 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in 
freeview? Maybe run ls -l on it?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andrew
Sent: Friday, July 30, 2021 1:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] niiRead: error opening file, through mri_convert


External Email - Use Caution
Hello,
I’m trying to reconstruct an old pipeline that I don’t completely understand 
(so sorry if this is very elementary or out of date), and one step is to 
convert the freesurfer T1 segmentation ribbon.mgz to .nii format using 
mri_convert.

Through freesurfer interface I see the T1 and the segmentation are fine; but 
mri_convert seems to fail on looking for the T1:

The command (from inside Matlab) is:
mri_convert  --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
Output looks like:
mri_convert --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii
reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
reading template info from volume 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...
error: niiRead(): error opening file 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*

It is failing to read the T1 and then it does not save the output file.
But the input files (T1.nii and ribbon.mgz) are all where they should be.
What could I be doing wrong?

thanks,
-Andrew
___
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[Freesurfer] niiRead: error opening file, through mri_convert

2021-07-30 Thread Andrew 
External Email - Use Caution

Hello,
I’m trying to reconstruct an old pipeline that I don’t completely understand 
(so sorry if this is very elementary or out of date), and one step is to 
convert the freesurfer T1 segmentation ribbon.mgz to .nii format using 
mri_convert.

Through freesurfer interface I see the T1 and the segmentation are fine; but 
mri_convert seems to fail on looking for the T1:

The command (from inside Matlab) is:
mri_convert  --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii

Output looks like:
mri_convert --reslice_like 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt 
nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz 
/Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii 
reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
reading template info from volume 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...
error: niiRead(): error opening file 
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*

It is failing to read the T1 and then it does not save the output file. 
But the input files (T1.nii and ribbon.mgz) are all where they should be. 
What could I be doing wrong?

thanks,
-Andrew___
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Re: [Freesurfer] niiRead error

2017-08-01 Thread Francesca Strappini 
It does work with 6.0, thank you!

2017-07-31 20:59 GMT+03:00 Douglas Greve :

> I think this may be fixed in 6.0
>
> On 7/31/17 12:43 PM, Francesca Strappini wrote:
>
> Thanks for the reply.
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.
>
> I opened it with fslview and it looks like a normal 3-dimentional file.
>
> Thanks
> Francesca
>
> 2017-07-31 16:38 GMT+02:00 Douglas Greve :
>
>> what version of FS are you running?
>>
>>
>> On 7/30/17 12:37 PM, Bruce Fischl wrote:
>> > Hi Francesca
>> >
>> > why is the nifti 5-dimensional? The code is complaining that it doesn't
>> > know how to intepret the input volume
>> >
>> > cheers
>> > Bruce
>> > On Sun, 30 Jul 2017, Francesca
>> > Strappini wrote:
>> >
>> >> Hi, I'm trying to register to the surface a t-test map created with
>> afni
>> >> (3dttest++) but I got this error message:
>> >>
>> >> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage
>> --surf-fwhm 3
>> >> --hemi lh --o movierestTest_lh.nii.gz
>> >>
>> >> srcvol = movierestTest.nii.gz
>> >> srcreg unspecified
>> >> srcregold = 0
>> >> srcwarp unspecified
>> >> surf = white
>> >> hemi = lh
>> >> reshape = 0
>> >> interp = nearest
>> >> float2int = round
>> >> GetProjMax = 0
>> >> INFO: float2int code = 0
>> >> niiRead(): 5 dimensions in/media/francesca/DATA/Shared
>> /fmri-experiments/fc_categories/searchlight/tes
>> >> rest/movierestTest.nii.gz; unsupported
>> >> Invalid argument
>> >> ERROR: could not read movierestTest.nii.gz as type 24
>> >>
>> >> Thanks
>> >> Francesca
>> >>
>> >>
>> >> --
>> >> Francesca Strappini, Ph.D.
>> >> Neurobiology Department
>> >> Weizmann Institute of Science
>> >> 234 Herzl Street, Rehovot 7610001 Israel
>> >> Tel.: +972 58 444 2584 <+972%2058-444-2584>
>> >> E-mail: francesca.strapp...@weizmann.ac.il
>> >>
>> >>
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>>
>> ___
>> 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.
>>
>>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584 <+972%2058-444-2584>
> E-mail: francesca.strapp...@weizmann.ac.il
>
>
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>
>
>
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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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> error
> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] niiRead error

2017-07-31 Thread Douglas Greve 

I think this may be fixed in 6.0


On 7/31/17 12:43 PM, Francesca Strappini wrote:

Thanks for the reply.

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.

I opened it with fslview and it looks like a normal 3-dimentional file.

Thanks
Francesca

2017-07-31 16:38 GMT+02:00 Douglas Greve >:


what version of FS are you running?


On 7/30/17 12:37 PM, Bruce Fischl wrote:
> Hi Francesca
>
> why is the nifti 5-dimensional? The code is complaining that it
doesn't
> know how to intepret the input volume
>
> cheers
> Bruce
> On Sun, 30 Jul 2017, Francesca
> Strappini wrote:
>
>> Hi, I'm trying to register to the surface a t-test map created
with afni
>> (3dttest++) but I got this error message:
>>
>> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage
--surf-fwhm 3
>> --hemi lh --o movierestTest_lh.nii.gz
>>
>> srcvol = movierestTest.nii.gz
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> niiRead(): 5 dimensions

in/media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tes
>> rest/movierestTest.nii.gz; unsupported
>> Invalid argument
>> ERROR: could not read movierestTest.nii.gz as type 24
>>
>> Thanks
>> Francesca
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il

>>
>>
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Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il 




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Re: [Freesurfer] niiRead error

2017-07-31 Thread Francesca Strappini 
Thanks for the reply.

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.

I opened it with fslview and it looks like a normal 3-dimentional file.

Thanks
Francesca

2017-07-31 16:38 GMT+02:00 Douglas Greve :

> what version of FS are you running?
>
>
> On 7/30/17 12:37 PM, Bruce Fischl wrote:
> > Hi Francesca
> >
> > why is the nifti 5-dimensional? The code is complaining that it doesn't
> > know how to intepret the input volume
> >
> > cheers
> > Bruce
> > On Sun, 30 Jul 2017, Francesca
> > Strappini wrote:
> >
> >> Hi, I'm trying to register to the surface a t-test map created with afni
> >> (3dttest++) but I got this error message:
> >>
> >> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage
> --surf-fwhm 3
> >> --hemi lh --o movierestTest_lh.nii.gz
> >>
> >> srcvol = movierestTest.nii.gz
> >> srcreg unspecified
> >> srcregold = 0
> >> srcwarp unspecified
> >> surf = white
> >> hemi = lh
> >> reshape = 0
> >> interp = nearest
> >> float2int = round
> >> GetProjMax = 0
> >> INFO: float2int code = 0
> >> niiRead(): 5 dimensions in/media/francesca/DATA/
> Shared/fmri-experiments/fc_categories/searchlight/tes
> >> rest/movierestTest.nii.gz; unsupported
> >> Invalid argument
> >> ERROR: could not read movierestTest.nii.gz as type 24
> >>
> >> Thanks
> >> Francesca
> >>
> >>
> >> --
> >> Francesca Strappini, Ph.D.
> >> Neurobiology Department
> >> Weizmann Institute of Science
> >> 234 Herzl Street, Rehovot 7610001 Israel
> >> Tel.: +972 58 444 2584
> >> E-mail: francesca.strapp...@weizmann.ac.il
> >>
> >>
> > ___
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> >
> >
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-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] niiRead error

2017-07-31 Thread Douglas Greve 
what version of FS are you running?


On 7/30/17 12:37 PM, Bruce Fischl wrote:
> Hi Francesca
>
> why is the nifti 5-dimensional? The code is complaining that it doesn't
> know how to intepret the input volume
>
> cheers
> Bruce
> On Sun, 30 Jul 2017, Francesca
> Strappini wrote:
>
>> Hi, I'm trying to register to the surface a t-test map created with afni
>> (3dttest++) but I got this error message:
>>
>> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3
>> --hemi lh --o movierestTest_lh.nii.gz
>>
>> srcvol = movierestTest.nii.gz
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> niiRead(): 5 dimensions 
>> in/media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tes
>> rest/movierestTest.nii.gz; unsupported
>> Invalid argument
>> ERROR: could not read movierestTest.nii.gz as type 24
>>
>> Thanks
>> Francesca
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strapp...@weizmann.ac.il
>>
>>
> ___
> Freesurfer mailing list
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>
>

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Re: [Freesurfer] niiRead error

2017-07-30 Thread Bruce Fischl 
Hi Francesca

why is the nifti 5-dimensional? The code is complaining that it doesn't 
know how to intepret the input volume

cheers
Bruce
On Sun, 30 Jul 2017, Francesca 
Strappini wrote:

> Hi, I'm trying to register to the surface a t-test map created with afni
> (3dttest++) but I got this error message:
> 
> mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3
> --hemi lh --o movierestTest_lh.nii.gz
> 
> srcvol = movierestTest.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> niiRead(): 5 dimensions 
> in/media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tes
> rest/movierestTest.nii.gz; unsupported
> Invalid argument
> ERROR: could not read movierestTest.nii.gz as type 24
> 
> Thanks
> Francesca
> 
> 
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
> 
>
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[Freesurfer] niiRead error

2017-07-30 Thread Francesca Strappini 
Hi, I'm trying to register to the surface a *t*-test map created with afni
(3dttest++) but I got this error message:

mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3
--hemi lh --o movierestTest_lh.nii.gz

srcvol = movierestTest.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): 5 dimensions in
/media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tesrest/movierestTest.nii.gz;
unsupported
Invalid argument
ERROR: could not read movierestTest.nii.gz as type 24

Thanks
Francesca


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

2015-10-01 Thread andrea cristina Lima 
Em 30/09/2015 11:30, "andrea cristina Lima" 
escreveu:

> I got the error below. Could you help me? I've already check the dti file
> and it seems Ok. Tks
>
> macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
> /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt
>
> INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer
>
> INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
> -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd
>
> #-
>
> /Applications/freesurfer/bin/trac-preproc
>
> #-
>
> #@# Image corrections Wed Sep 30 11:27:28 BRT 2015
>
> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>
> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>
> niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...
>
> Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
> 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015
>
> --
> Andrea Cristina de Lima Pardini
> CV: http://lattes.cnpq.br/0921194840474573
>
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[Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

2015-10-01 Thread andrea cristina Lima 
I got the error below. Could you help me? I've already check the dti file
and it seems Ok. Tks

macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
/Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt

INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer

INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
-log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-

#@# Image corrections Wed Sep 30 11:27:28 BRT 2015

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...

Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015

-- 
Andrea Cristina de Lima Pardini
CV: http://lattes.cnpq.br/0921194840474573
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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

2015-10-01 Thread andrea cristina Lima 
Ok! Thank you! I will try again!

2015-09-30 19:16 GMT-03:00 andrea cristina Lima :

> Em 30/09/2015 11:30, "andrea cristina Lima" 
> escreveu:
>
>> I got the error below. Could you help me? I've already check the dti file
>> and it seems Ok. Tks
>>
>> macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
>> /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt
>>
>> INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer
>>
>> INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1
>>
>> Actual FREESURFER_HOME /Applications/freesurfer
>>
>> trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local
>> -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd
>>
>> #-
>>
>> /Applications/freesurfer/bin/trac-preproc
>>
>> #-
>>
>> #@# Image corrections Wed Sep 30 11:27:28 BRT 2015
>>
>> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>>
>> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii
>> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz
>>
>> niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
>>
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>
>> reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...
>>
>> Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29
>> 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>>
>>
>> trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015
>>
>> --
>> Andrea Cristina de Lima Pardini
>> CV: http://lattes.cnpq.br/0921194840474573
>>
>


-- 
Andrea Cristina de Lima Pardini
CV: http://lattes.cnpq.br/0921194840474573
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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

2015-10-01 Thread Anastasia Yendiki 


It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This 
is a relative path, i.e., it's trying to find it under the directory where 
you are currently cd'd.


This seems like a problem with defining paths properly for unix, rather 
than a tracula problem per se.


On Wed, 30 Sep 2015, andrea cristina Lima wrote:


I got the error below. Could you help me? I've already check the dti file and 
it seems Ok. Tks 

macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c
/Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt

INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer

INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc 

#-

#@# Image corrections Wed Sep 30 11:27:28 BRT 2015

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz

mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii 
SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz 

niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from SUBJECTS_DIR/Enzo_recon1/dti.nii...

Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 
02:26:53 PDT 2015;
root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015


--
Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573

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Re: [Freesurfer] niiRead error

2015-08-31 Thread Bruce Fischl 

Hi Katarina

it looks like that file might be corrupted. Where did you get it from? 
Can you view it in freeview? Maybe that partition was full when you copied 
it there or something similar?


cheers
Bruce

On Mon, 31 Aug 2015, Katarina Trojacanec wrote:



Dear experts,


After running recon-all I got this output: 

---


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux

/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD


 
mri_convert/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri/orig/001.mgz


mri_convert/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri/orig/001.mgz

INFO: using NIfTI-1 qform

niiRead(): error reading 
from/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading 
from/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii...

ERROR: Read 70, expected 256

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon
Aug 31 13:10:05 CEST 2015


For more details, see the log 
file/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

-rw-rw-r-- 1 katarina.trojachanec margi 17946 Aug 31 
13:10/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux

#

#@# MotionCor Mon Aug 31 13:10:10 CEST 2015

ERROR: no run data found 
in/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri. Make sure to

have a volume called 001.mgz in 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S2933
9_I89671_1.5T_AD/mri/orig.

If you have a second run of data call it 002.mgz, etc.

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon
Aug 31 13:10:10 CEST 2015


For more details, see the log 
file/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

---
---
-

This is happening only for one file (from multiple that I have tried with). 
Would you please be able to answer me what might be the problem?

Thank you in advance.
Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia  

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[Freesurfer] niiRead error

2015-08-31 Thread Katarina Trojacanec 
Dear experts,


After running recon-all I got this output:

---

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux

/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD


 mri_convert 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii
 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz


mri_convert 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii
 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz

INFO: using NIfTI-1 qform

niiRead(): error reading from 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii...

ERROR: Read 70, expected 256

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon 
Aug 31 13:10:05 CEST 2015


For more details, see the log file 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

-rw-rw-r-- 1 katarina.trojachanec margi 17946 Aug 31 13:10 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux

#

#@# MotionCor Mon Aug 31 13:10:10 CEST 2015

ERROR: no run data found in 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri.
 Make sure to

have a volume called 001.mgz in  
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig.

If you have a second run of data call it 002.mgz, etc.

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon 
Aug 31 13:10:10 CEST 2015


For more details, see the log file 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

---

This is happening only for one file (from multiple that I have tried with).
Would you please be able to answer me what might be the problem?

Thank you in advance.
Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

___
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.