[Freesurfer] bbregister --init-spm with Freesurfer 6.0

[Ajay Kurani]

Hi Freesurfer Experts,
   I was running bbregister and came across an issue.  I have used previous
versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it
worked perfectly for a specific subject.

I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
option with the same resting state scan, and it did not move at all.  When
looking at the terminal I saw that when matlab started up within
bbregister, the command fs_spmreg was not found.  I also installed spm8 and
reran the subject with the same issue.  When I changed the option to
--init-fsl everything worked. I checked the matlab installation and
everything looks fine, so I think the issue may be the fs_spmreg function
not being found.  I am not sure if there is an easy fix for this, but any
help would be appreciated.

Thanks,
Ajay
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Re: [Freesurfer] dt_recon image inputs -i flag

[Anastasia Yendiki]

Hi Bryan - It'll convert whatever input you give it to nifti, so it's fine 
if your input is already nifti.


Best,
a.y

On Wed, 6 Apr 2016, Chiu, Bryan (PHTH) wrote:


Hi,

I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI 
images in par/rec. I ran dcm2nii
and have retrieved the associated *bval, *bvec and *nii.gz files that come out.

In the tutorial it mentions the -i flag requiring a dcm image. Is it possible 
to pass a *.nii.gz file ?

Regards,

___
Bryan Chiu
Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia


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Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

Hi Dr. Fischl

I have a mixture - some of the labels were painted in the MNI305 space
(older ones) and the more recent ones are registered to the ICBM152
nonlinear symmetric VI (2006) template.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> what space are your labels in?
>
> cheers
> Bruce
> On Tue, 5 Apr 2016, Trisanna Sprung-Much
> wrote:
>
> > Hi Freesurfer
> >
> > I have some labels (.mnc) that are painted voxels generated from a
> Montreal
> > Neurological Institute software. I am trying to project the labels onto
> the
> > surfaces generated from recon-all that I applied to the corresponding MRI
> > volumes.
> >
> > I used mri_vol2surf:
> >
> > mri_vol2surf --src labels.mnc --out test.mgz --srcreg talairach.auto.xfm
> > --hemi lh
> >
> > and got the following error:
> >
> > Error reading inplaneres from talairach.auto.xfm
> >
> >
> > Do I need a .dat file? If so, how can I attain it? Essentially, what is
> the
> > registration file that I am supposed to be using?
> >
> > Many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> ___
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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
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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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[Freesurfer] dt_recon image inputs -i flag

[Chiu, Bryan (PHTH)]

Hi,

I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI 
images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec 
and *nii.gz files that come out.

In the tutorial it mentions the -i flag requiring a dcm image. Is it possible 
to pass a *.nii.gz file ?

Regards,

___
Bryan Chiu
Research Assistant
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy
Faculty of Medicine
University of British Columbia
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Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Eugenio Iglesias]

Almost correct!
recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
subj1_hipp/I0001.dcm T2hipp
Also, this is assuming that you have defined the environment variable 
SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd .
Cheers,
/Eugenio


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Lara Foland-Ross" 
To: "Freesurfer support list" 
Sent: Wednesday, April 6, 2016 12:29:09 AM
Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Hi Eugenio,

Thank you so much for the quick and helpful reply.  I checked the images in 
Freeview and they actually line up quite nicely!

Can you provide further guidance on how to run recon-all once with both the 
-all and the hippocampal-subfields-T1T2 flags?

For example, in my rawdata directory, I have two folders: subj1_T1 and 
subj1_hipp. I cd'd into the rawdata folder and ran the following with no 
success:

recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
subj1_hipp T2hipp

Is this directory setup correct? And can you please point out the errors in the 
above recon-all command?

Many thanks again for your help!
Lara

Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Tuesday, April 5, 2016 2:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Dear Lara,
Two things:
1. You don't need to recon the T2 scan. The recon-all stream only works for T1 
data anyway.
2. The registration between the T1 and T2 scans happens internally (with a 
mri_register command similar to the one you wrote) during the hippocampal 
subfield segmentation. You only need to coarsely align the T1 and T2 scans 
manually if the initial alignment between the two is terrible. What happens 
when you open them both in Freeview?
3. If the alignment is decent, just run recon-all once, with both the -all and 
the -hippocampal-subfields-T1T2 flags.
Feel free to send me the T1 and T2 scans if you are not sure whether they are 
sufficiently well aligned or not.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Lara Foland-Ross" 
To: "Freesurfer support list" 
Sent: Tuesday, April 5, 2016 11:14:39 PM
Subject: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Hello,

I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 
6.0. I have a whole brain T1-weighted image as well as a high-resolution 
T2-weighted image of the hippocampus. The T2 weighted image covers the entire 
hippocampus, but not the whole brain.

My understanding (and please correct me if I'm wrong) is that I should first 
run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted 
scan using the -hippocampal-subfields-T1T2 flag, but that I must first make 
sure that the two scans are roughly aligned.

I was able to successfully register the T1-weighted scan to the T2-weighted 
scan using mri_robust_register using the following commands:

mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta 
wholebrain_to_hippocampus.lta -satit --noinit --nosym

mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz 
wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz

My plan was then to run recon-all on the newly upsampled, registered 
wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the 
T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the 
resampled whole brain T1-weighted image now has only a partial FOV.

Is there a way that I can preserve the full field of view in the T1-weighted 
scan? I've experimented with mri_coreg and flirt and am at a loss.

Many thanks in advance,
Lara


Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


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Re: [Freesurfer] mri_vol2surf after recon-all

[Bruce Fischl]

Hi Trisanna

what space are your labels in?

cheers
Bruce
On Tue, 5 Apr 2016, Trisanna Sprung-Much 
wrote:

> Hi Freesurfer
> 
> I have some labels (.mnc) that are painted voxels generated from a Montreal
> Neurological Institute software. I am trying to project the labels onto the
> surfaces generated from recon-all that I applied to the corresponding MRI
> volumes.
> 
> I used mri_vol2surf:
> 
> mri_vol2surf --src labels.mnc --out test.mgz --srcreg talairach.auto.xfm
> --hemi lh
> 
> and got the following error:
> 
> Error reading inplaneres from talairach.auto.xfm
> 
> 
> Do I need a .dat file? If so, how can I attain it? Essentially, what is the
> registration file that I am supposed to be using?
> 
> Many thanks!
> 
> Trisanna
> 
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
>
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Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Lara Foland-Ross]

Hi Eugenio,

Thank you so much for the quick and helpful reply.  I checked the images in 
Freeview and they actually line up quite nicely!

Can you provide further guidance on how to run recon-all once with both the 
-all and the hippocampal-subfields-T1T2 flags?

For example, in my rawdata directory, I have two folders: subj1_T1 and 
subj1_hipp. I cd'd into the rawdata folder and ran the following with no 
success:

recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
subj1_hipp T2hipp

Is this directory setup correct? And can you please point out the errors in the 
above recon-all command?

Many thanks again for your help!
Lara

Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Eugenio Iglesias 

Sent: Tuesday, April 5, 2016 2:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Dear Lara,
Two things:
1. You don't need to recon the T2 scan. The recon-all stream only works for T1 
data anyway.
2. The registration between the T1 and T2 scans happens internally (with a 
mri_register command similar to the one you wrote) during the hippocampal 
subfield segmentation. You only need to coarsely align the T1 and T2 scans 
manually if the initial alignment between the two is terrible. What happens 
when you open them both in Freeview?
3. If the alignment is decent, just run recon-all once, with both the -all and 
the -hippocampal-subfields-T1T2 flags.
Feel free to send me the T1 and T2 scans if you are not sure whether they are 
sufficiently well aligned or not.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Lara Foland-Ross" 
To: "Freesurfer support list" 
Sent: Tuesday, April 5, 2016 11:14:39 PM
Subject: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Hello,

I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 
6.0. I have a whole brain T1-weighted image as well as a high-resolution 
T2-weighted image of the hippocampus. The T2 weighted image covers the entire 
hippocampus, but not the whole brain.

My understanding (and please correct me if I'm wrong) is that I should first 
run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted 
scan using the -hippocampal-subfields-T1T2 flag, but that I must first make 
sure that the two scans are roughly aligned.

I was able to successfully register the T1-weighted scan to the T2-weighted 
scan using mri_robust_register using the following commands:

mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta 
wholebrain_to_hippocampus.lta -satit --noinit --nosym

mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz 
wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz

My plan was then to run recon-all on the newly upsampled, registered 
wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the 
T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the 
resampled whole brain T1-weighted image now has only a partial FOV.

Is there a way that I can preserve the full field of view in the T1-weighted 
scan? I've experimented with mri_coreg and flirt and am at a loss.

Many thanks in advance,
Lara


Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


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[Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

Hi Freesurfer

I have some labels (.mnc) that are painted voxels generated from a Montreal
Neurological Institute software. I am trying to project the labels onto the
surfaces generated from recon-all that I applied to the corresponding MRI
volumes.

*I used mri_vol2surf: *

mri_vol2surf --src labels.mnc --out test.mgz --srcreg talairach.auto.xfm
--hemi lh

*and got the following error:*

Error reading inplaneres from talairach.auto.xfm


Do I need a .dat file? If so, how can I attain it? Essentially, what is the
registration file that I am supposed to be using?

Many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] mixed models and longitudinal streaming

[Angela Favaro]

Hi Martin, thank you for your help.
I still have problems in running mixed models analyses. Do I need some
additional toolbox in matlab? (I did not find this information in the
web)
I tried to run the module in two versions of matlab, but the same
problem occurr.

I used these commands:
[M,Y,ni] = sortData(M,1,Y,sID)
X = [ones(length(M),1) M M(:,1).*M(:,2)]

[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)

this is the error message:
Undefined function 'matlabpool' for input
arguments of type 'char'.

Error in lme_mass_fit_init (line 74)
if (prs==1) || (matlabpool('size') ~= prs)

Error in lme_mass_fit_EMinit (line 69)
[Theta1,Re1] =
lme_mass_fit_init(X,Zcols,Y,ni,[],prs);

What can it be the problem?
the matrices seem to be OK (and M has the same number of rows as Y
(and as the sID)).

thank you for any help!

Angela




Martin Reuter  ha scritto:

> Hi Angela,
>
> the smooth function seems to be part of the curve fitting toolbox
> http://www.mathworks.com/help/curvefit/smooth.html
> so either that is missing, or your version is too old.
> You can skip the lowess Plot (it is just for initially checking the data).
>
>
> Make sure your M has the same number of rows as your Y (and as the sID).
> Also make sure you are computing the ni (and sorted M and Y) like this
> (if your first column in M is the time, else specify the column with the
> time as the second parameter):
>
> [M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
>
>
> Best, Martin
>
>
>
> On 03/20/2016 04:38 PM, Angela Favaro wrote:
>> Dear Freesurfer experts,
>> I need some help with the longitudinal streaming and the use of mixed
>> models in matlab.
>> I followed all the instructions and tried to use the following
>> commands in matlab:
>>
>> lme_timePlot(M(:,1),Y,ni)
>> and this worked well
>>
>> However, when I tried this:
>> lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
>>
>> matlab gave the following error message:
>>
>> Undefined function 'smooth' for input arguments of type 'double'.
>> Error in lme_lowessPlot (line 49)
>>   ybw = smooth(st,dat(ix),bw,'rlowess')
>>
>> I checked in my version of matlab (R2012b) and the command 'smooth'
>> does not exist
>>
>> Further, when I tried this:
>>
>> lhstats  = lme_fit_FS(X,[1 2],Y,ni)
>>
>> Error using  -
>> Matrix dimensions must agree.
>>
>> Error in lme_fit_init (line 42)
>>   ri = yi-Xi*Bhat;
>>
>> Error in lme_fit_FS (line 71)
>> [D,phisq] = lme_fit_init(X,Zcols,y,ni);
>>
>> Looking into the matlab code, I observed that in line 42 there is no
>> command.
>> and I am sure that matrix dimensions are correct.
>>
>> So, I have problems in solving these issues... Any help is greatly
>> appreciated!
>> Is it a problem of Matlab version?
>> Thank you!
>>
>> Angela
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu
>
> ___
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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] Installation issue

[dgw]

Try following the mac os install directions.

On Tue, Apr 5, 2016 at 1:57 PM,   wrote:
> Hi list,
>
> I'm reinstalling FS on my PC (iMac end of 2012).
> This error occur:
>
> freeview
>
> /Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file
> not executable.
>
>
>
> Please take in account:
>
> freesurfer &   [1] 1818
>
> [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano%
>
> FreeSurfer is a set of tools for analysis and visualization
>
> of structural and functional brain imaging data. FreeSurfer
>
> also refers to the structural imaging stream within the
>
> FreeSurfer suite.
>
>
> Users should consult the online documentation available at:
>
>
>   https://surfer.nmr.mgh.harvard.edu
>
>
> Alternatively, the 'recon-all' command help-text provides
>
> adequate information to begin processing subject data, such
>
> as the sample subject 'bert' found in the 'freesurfer/subjects'
>
> directory.  Type 'recon-all --help' to view this help-text.
>
>
> Direct comments and questions to:
>
>
>   freesurfer@nmr.mgh.harvard.edu
>
>
> You are running this version of FreeSurfer:
>
>
>   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
>
>
> Thanks
>
>
> Stefano
>
>
> ___
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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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Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Eugenio Iglesias]

Dear Lara,
Two things:
1. You don't need to recon the T2 scan. The recon-all stream only works for T1 
data anyway.
2. The registration between the T1 and T2 scans happens internally (with a 
mri_register command similar to the one you wrote) during the hippocampal 
subfield segmentation. You only need to coarsely align the T1 and T2 scans 
manually if the initial alignment between the two is terrible. What happens 
when you open them both in Freeview?
3. If the alignment is decent, just run recon-all once, with both the -all and 
the -hippocampal-subfields-T1T2 flags.
Feel free to send me the T1 and T2 scans if you are not sure whether they are 
sufficiently well aligned or not.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Lara Foland-Ross" 
To: "Freesurfer support list" 
Sent: Tuesday, April 5, 2016 11:14:39 PM
Subject: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Hello, 

I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 
6.0. I have a whole brain T1-weighted image as well as a high-resolution 
T2-weighted image of the hippocampus. The T2 weighted image covers the entire 
hippocampus, but not the whole brain.

My understanding (and please correct me if I'm wrong) is that I should first 
run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted 
scan using the -hippocampal-subfields-T1T2 flag, but that I must first make 
sure that the two scans are roughly aligned.

I was able to successfully register the T1-weighted scan to the T2-weighted 
scan using mri_robust_register using the following commands:

mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta 
wholebrain_to_hippocampus.lta -satit --noinit --nosym

mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz 
wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz

My plan was then to run recon-all on the newly upsampled, registered 
wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the 
T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the 
resampled whole brain T1-weighted image now has only a partial FOV.

Is there a way that I can preserve the full field of view in the T1-weighted 
scan? I've experimented with mri_coreg and flirt and am at a loss.

Many thanks in advance,
Lara


Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


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[Freesurfer] octave fast_selxavg3() failed\n

[stdp82]

Hi listthis error occurs using octave in FS-FAST.Thanks,
Stefano
--- octave output 
LD_LIBRARY_PATH :/usr/local/octave/3.8.0/lib
/usr/local/octave/3.8.0/bin: Permission denied.
--
ERROR: fast_selxavg3() failed\n

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[Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Lara Foland-Ross]

Hello, 

I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 
6.0. I have a whole brain T1-weighted image as well as a high-resolution 
T2-weighted image of the hippocampus. The T2 weighted image covers the entire 
hippocampus, but not the whole brain.

My understanding (and please correct me if I'm wrong) is that I should first 
run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted 
scan using the -hippocampal-subfields-T1T2 flag, but that I must first make 
sure that the two scans are roughly aligned.

I was able to successfully register the T1-weighted scan to the T2-weighted 
scan using mri_robust_register using the following commands:

mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta 
wholebrain_to_hippocampus.lta -satit --noinit --nosym

mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz 
wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz

My plan was then to run recon-all on the newly upsampled, registered 
wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the 
T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the 
resampled whole brain T1-weighted image now has only a partial FOV.

Is there a way that I can preserve the full field of view in the T1-weighted 
scan? I've experimented with mri_coreg and flirt and am at a loss.

Many thanks in advance,
Lara


Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


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[Freesurfer] Installation issue

[stdp82]

Hi list,
I'm reinstalling FS on my PC (iMac end of 2012).This error occur:
freeview
/Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file not 
executable.

Please take in account:freesurfer[1] 1818
[iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% 
FreeSurfer is a set of tools for analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.


Users should consult the online documentation available at:


  https://surfer.nmr.mgh.harvard.edu


Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.


Direct comments and questions to:


  freesurfer@nmr.mgh.harvard.edu


You are running this version of FreeSurfer:


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

Thanks
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[Freesurfer] Preprocessing task data with multiple B0-corrected runs

[Shea, Conor]

Dear Doug,

I'm trying to use FSFAST to analyze task data with multiple runs.  Before using 
the preproc-sess pipeline, I ran B0 correction on each of the runs, so I have 3 
different b0dcmap files.  I'm trying to figure out the best way to run 
preprocessing on the three runs simultaneously using preproc-sess, but I don't 
know how to get FSFAST to use each run's specific b0dcmap in the preprocessing 
of each run's data.  FSFAST wants the b0dcmap files to be in the task folder, 
but how can it differentiate between the three b0dcmap files if they're not in 
the run folders?

Thanks,
Conor
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Re: [Freesurfer] longitudinal pipeline surface error

[Martin Reuter]

Hi Mihaela,

you can use our BrainPrint tool (after running FS) to see how closely 
the brain shape matches:


http://reuter.mit.edu/publications/pid/wachinger-brainprint15
http://reuter.mit.edu/software/brainprint/

Best, Martin


On 04/05/2016 12:49 PM, Mihaela Stefan wrote:

Hi Martin,
Just an update on this. It turned out that there was just a DICOM 
mismatch for this subject but now that you mentioned it, I wonder what 
people do to make sure that the same person returns for follow-up in a 
longitudinal study. Even when there is one study coordinator for the 
entire length of the study, it's quite difficult for that person to 
remember hundred of faces and asking for an ID is not always doable.


Thanks!
Mihaela

On Thu, Mar 31, 2016 at 1:50 PM, Mihaela Stefan 
> wrote:


Wow! I haven't thought about that but it's possible since we had a
few study coordinators along the way. So it could be the case that
the study coordinator didn't know the subject who came at
follow-up. Hopefully it will be just a DICOM mismatch. Will see
how it goes.. :)

On Thu, Mar 31, 2016 at 10:38 AM, Martin Reuter
>
wrote:

I have seen cases where annonymization messed up ID's and
individual time points came from a different subject. That
could mess things up quite bad. (Also if the person sends
their sibling or friend, because they don't have time to come
to the follow up themselves, has also happened - not to me
though ).

Best, Martin


On 03/31/2016 10:21 AM, Mihaela Stefan wrote:

Hi Martin,

We ran this subject twice but we got the same error. The norm
is not aligned. They almost look like two different brains. I
double checked the exam numbers to make sure that these three
exams belong to the same person. They indeed seem to belong
to the same person but I will re-run recon cross from scratch
for MRI3 just to make sure that I started with the right
DICOMs. I will let you know how it worked.

Thanks!
Mihaela

On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter
> wrote:

Hi Mihaela,

does the cross sectional run of that time point, and the
base look OK? Also check if this time point is aligned
correctly to the base (e.g. open norm.mgz from the long
and the base, they should be aligned).  If all this is
OK, then I would recommend to re-run this long run again,
but make sure you are removing the longitudinal directory
first so that it re-runs from scratch. If that does not
fix it, we would need to get the data for debugging.

Thanks, Martin


On 03/30/2016 03:19 PM, Mihaela Stefan wrote:

Dear FreeSurfers,

We are doing a longitudinal analysis with three time
points (MRI1, MRI2, MRI3). All the subjects were
processed well except for one. The MRI3.long of that
subject has very bad surfaces (see attachment - I am
also attaching the log file). The cross, the template
and the first two long runs were reconned well, though.
We can't figure out why this third run is so bad.

As a note, we processed all the cross runs on an Ubuntu
machine but we ran the longitudinal pipeline on a
computer cluster (both with freesurfer v5.3). We ran the
long twice for that subject thinking that the pipeline
crashed somehow the first time. However, the results
were the same.

Any help would be appreciated.

Thanks!
Mihaela


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-- 
Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  



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Re: [Freesurfer] longitudinal pipeline surface error

[Mihaela Stefan]

Hi Martin,
Just an update on this. It turned out that there was just a DICOM mismatch
for this subject but now that you mentioned it, I wonder what people do to
make sure that the same person returns for follow-up in a longitudinal
study. Even when there is one study coordinator for the entire length of
the study, it's quite difficult for that person to remember hundred of
faces and asking for an ID is not always doable.

Thanks!
Mihaela

On Thu, Mar 31, 2016 at 1:50 PM, Mihaela Stefan 
wrote:

> Wow! I haven't thought about that but it's possible since we had a few
> study coordinators along the way. So it could be the case that the study
> coordinator didn't know the subject who came at follow-up. Hopefully it
> will be just a DICOM mismatch. Will see how it goes.. :)
>
> On Thu, Mar 31, 2016 at 10:38 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> I have seen cases where annonymization messed up ID's and individual time
>> points came from a different subject. That could mess things up quite bad.
>> (Also if the person sends their sibling or friend, because they don't have
>> time to come to the follow up themselves, has also happened - not to me
>> though ).
>>
>> Best, Martin
>>
>>
>> On 03/31/2016 10:21 AM, Mihaela Stefan wrote:
>>
>> Hi Martin,
>>
>> We ran this subject twice but we got the same error. The norm is not
>> aligned. They almost look like two different brains. I double checked the
>> exam numbers to make sure that these three exams belong to the same person.
>> They indeed seem to belong to the same person but I will re-run recon cross
>> from scratch for MRI3 just to make sure that I started with the right
>> DICOMs. I will let you know how it worked.
>>
>> Thanks!
>> Mihaela
>>
>> On Wed, Mar 30, 2016 at 4:12 PM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Mihaela,
>>>
>>> does the cross sectional run of that time point, and the base look OK?
>>> Also check if this time point is aligned correctly to the base (e.g. open
>>> norm.mgz from the long and the base, they should be aligned).  If all this
>>> is OK, then I would recommend to re-run this long run again, but make sure
>>> you are removing the longitudinal directory first so that it re-runs from
>>> scratch. If that does not fix it, we would need to get the data for
>>> debugging.
>>>
>>> Thanks, Martin
>>>
>>>
>>> On 03/30/2016 03:19 PM, Mihaela Stefan wrote:
>>>
>>> Dear FreeSurfers,
>>>
>>> We are doing a longitudinal analysis with three time points (MRI1, MRI2,
>>> MRI3). All the subjects were processed well except for one. The MRI3.long
>>> of that subject has very bad surfaces (see attachment - I am also attaching
>>> the log file). The cross, the template and the first two long runs were
>>> reconned well, though. We can't figure out why this third run is so bad.
>>>
>>> As a note, we processed all the cross runs on an Ubuntu machine but we
>>> ran the longitudinal pipeline on a computer cluster (both with freesurfer
>>> v5.3). We ran the long twice for that subject thinking that the pipeline
>>> crashed somehow the first time. However, the results were the same.
>>>
>>> Any help would be appreciated.
>>>
>>> Thanks!
>>> Mihaela
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> --
>>> Martin Reuter, PhD
>>> Assistant Professor of Radiology, Harvard Medical School
>>> Assistant Professor of Neurology, Harvard Medical School
>>> A.A.Martinos Center for Biomedical Imaging
>>> Massachusetts General Hospital
>>> Research Affiliate, CSAIL, MIT
>>> Phone: +1-617-724-5652
>>> Web  : http://reuter.mit.edu
>>>
>>>
>>> ___
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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.
>>>
>>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  : http://reuter.mit.edu
>>
>>
>> ___
>> Freesurfer 

[Freesurfer] White matter parcellation based on ROIs from fMRI

[Beyh, Ahmad]

Hello Freesurfers,

I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s. 
I want to use the ROIs for tractography, and therefore need them to include the 
underlying white matter.


I I am aware that freesurfer can do this after running the subjects through 
recon-all using freesurfer's own atlas. But is there a way to do this using the 
cortical ROIs defined in native space? So can I give freesurfer the T1 and the 
cortical ROIs as input and get the volumetric ROIs (that include white matter) 
as output in each subject's native space? This is important because the ROIs 
come from fMRI and are not based on the anatomy.


A detailed answer would be highly appreciated.

Many thanks,

Ahmad
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Re: [Freesurfer] License invalid for Development Version

[Z K]

Hello Ben,

The license file should still work. Please send me your .license file to MY 
PERSONAL EMAIL ADDRESS so I can test it. Also, please send me your 
build-stamp.txt file as well. Thanks. 

-Zeke

> On Apr 5, 2016, at 7:31 AM, Jeurissen Ben  wrote:
> 
> Dear Freesurfer experts,
> 
> I am affected by the PERL incompatibility described in 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043504.html
>  . To get around this issue, I switched to the newest development version as 
> suggested in that post. However, my license file (which worked fine with the 
> stable version) is not recognised:
> 
> "ERROR: Invalid FreeSurfer license key found in license file 
> /home/ben/freesurfer/license.txt”
> 
> Do I need a special license for the development version? How can I obtain it?
> 
> Cheers,
> Ben
> 
> -
> Ben Jeurissen, Ph.D.
> Post-doctoral researcher
> Vision Lab, Dept. of Physics
> University of Antwerp
> Universiteitsplein 1, N.1.18
> B-2610 Wilrijk, Belgium
> Phone: +32 3 265 24 77
> Email: ben.jeuris...@uantwerpen.be
> Url: http://visielab.uantwerpen.be/people/ben-jeurissen
> 
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Re: [Freesurfer] Tracula problems (creating symbolic link)

[Anastasia Yendiki]

Hi Efrat - You could just use cp instead of ln -s. This will duplicate the 
file, instead of creating a link to it.


a.y

On Tue, 5 Apr 2016, Efrat Kliper wrote:



Dear Anastasia,

 

Thank you for the fast replay.

I have tried both suggestions, however it still reports:  Operation not 
supported

Also, I have used the links that you have sent me but non work. This time 
(after changing according to the
links), I got the message: operation denied


I don’t know how to resolve the issue of virtual machine, as not much is 
written about that and the links are
not helping with that issue.


Do you have other suggestions regarding how to change the script, so it will 
create the data.nii without the
symbolic link (there are plenty "ln" commands uses in the script)?


Many thanks,

Efrat


On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki 
 wrote:

  Hi Efrat - This appears to be a virtual machine problem:

  https://communities.vmware.com/thread/312591?tstart=0

  There are some solutions suggested in that thread. I'm wondering if using 
a relative instead of an
  absolute path for the symlink works, i.e.,

  ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  instead of:

  ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
  /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

  Can you please try it both ways and let me know if the former works on a 
computer where the latter
  doesn't?

  And yes, if you fix error #1 it'll fix error #2 as well.

  Thanks,
  a.y


  On Tue, 29 Mar 2016, Efrat Kliper wrote:


Dear Freesurfer experts,


I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the 
preprocessing has already
been completed in Freesurfer 5.1) in order to run some new functions
of Tracula (I have also installed the latest Tracula update
(tracula.update.centos4_x86_64.5.3.2014_05_26).


I am using:

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 5.3 (Final)

Kernel info: Linux 2.6.18-128.1.6.el5 x86_64

 

 I encountered two problems:


1.  When I run the initial code of Tracula: trac-all –prep code:

/home/fsl/

usr/local/freesurfer/bin/trac-all -prep -c
/mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt

Subject TB_480

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message: ln -sf
/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz

 

ln: creating symbolic link 
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
`/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation 
not
supported

 

2.  If I run the trac-all –bedp command of Tracula (on already 
trac-all data which
was preproc on Freesurfer version 5.1. /home/fsl

/usr/local/freesurfer/bin/trac-all

-bedp -c /home/fsl/Desktop/xxx.txt

Subject TB_201

SUBJECTS_DIR /mnt/hgfs/linux_share/subjects

FREESURFER_HOME /usr/local/freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer

build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

fsl

localhost.localdomain

Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 
09:10:25 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

 

I am getting the following message:

Program versions:

$Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $

mri_convert --all-info

ProgramName: mri_convert  ProgramArguments: --all-info  
ProgramVersion: $Name:  $ 
TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014 
05:13:24 
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  
User: fsl  Machine:
localhost.localdomain  Platform: Linux  PlatformVersion:
2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400

FLIRT version 6.0

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $

$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 

[Freesurfer] License invalid for Development Version

[Jeurissen Ben]

Dear Freesurfer experts,

I am affected by the PERL incompatibility described in 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043504.html 
. To get around this issue, I switched to the newest development version as 
suggested in that post. However, my license file (which worked fine with the 
stable version) is not recognised:

"ERROR: Invalid FreeSurfer license key found in license file 
/home/ben/freesurfer/license.txt”

Do I need a special license for the development version? How can I obtain it?

Cheers,
Ben

-
Ben Jeurissen, Ph.D.
Post-doctoral researcher
Vision Lab, Dept. of Physics
University of Antwerp
Universiteitsplein 1, N.1.18
B-2610 Wilrijk, Belgium
Phone: +32 3 265 24 77
Email: ben.jeuris...@uantwerpen.be
Url: 
http://visielab.uantwerpen.be/people/ben-jeurissen

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[Freesurfer] Postdoctoral research fellows, University of Oslo, Norway

[Lars Tjelta Westlye]

2 three-year positions as Postdoctoral Research Fellow at the Norwegian Centre 
for Mental Disorders Research, University of Oslo are currently available.

http://uio.easycruit.com/vacancy/1599437/65775?iso=no

NORMENT is a Norwegian Centre of Excellence, and coordinates a translational 
multicenter study involving all University hospitals in Oslo and several groups 
at the Universities of Oslo and Bergen. The main aims are to disentangle the 
mechanisms of severe mental illness. NORMENT Multimodal Imaging group includes 
eight postdoctoral fellows and several PhD and graduate students, and is 
directly involved in various international collaborations.

* Job description

The postdoctoral fellows will play a central role in the analysis and 
dissemination of a large imaging genetics database, in particular focusing on 
methods for integrating multimodal imaging (sMRI, ASL, DTI, fMRI) and genetic 
data.

* Qualifications

The ideal candidate is ambitious and highly motivated for pursuing a career in 
science, hold a PhD in psychology, neuroimaging, computational or cognitive 
neuroscience, biomedical engineering, biostatistics, or equivalent, have a 
strong background and interest in neuroscience, genetics, and an excellent 
publication record. Experience with MRI analysis tools including Freesurfer and 
FSL, and expertise in brain network and connectivity analysis, or multivariate 
pattern recognition or machine learning techniques is an advantage.

* Applying for the positions

The application is to be submitted electronically and must include application 
letter, CV, copies of educational certificates and letters of recommendation, 
list of publications, up to five published papers that the applicant wishes to 
be considered by the evaluation committee, references.

Yearly salary: NOK 483 700-560 700, depending on qualifications and experience.

Application deadline: April 21 2016.

For any informal enquiries, please contact Lars T. Westlye 
(l.t.west...@psykologi.uio.no).

http://uio.easycruit.com/vacancy/1599437/65775?iso=no?





Lars T. Westlye, PhD

Senior Researcher, Head of Multimodal Imaging Group
NORMENT CoE, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, 
Oslo, Norway

Associate Professor II, Department of Psychology, University of Oslo

Email: l.t.west...@psykologi.uio.no | Phone: +47 971 63 221
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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.

[Freesurfer] Qdec DOSS

[tom parker]

Hi Freesurfers,

I posted this question a few days ago but didn't get any replies.
Would you mind answering this for me?

I compared 2 groups, while controlling for 1 covariate in qdec using
freesurfer 5.1.

There were no significant interactions with the covariate so I need to use
DOSS.

I read on several post that DOSS has some bugs related to the generation of
contrasts in qdec and that mri_glmfit should be used to run a DOSS analysis.

However, when I ran my analysis with DOSS in qdec I saw that the C.mat file
looked like this: 1 -1 0, which seems correct to me.

My question is can I use DOSS in qdec in this case? Or are there other bugs
related to using it in qdec?

Thank you so much!
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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] Tracula problems (creating symbolic link)

[Efrat Kliper]

Dear Anastasia,



Thank you for the fast replay.

I have tried both suggestions, however it still reports:  Operation not
supported

Also, I have used the links that you have sent me but non work. This time
(after changing according to the links), I got the message: operation denied


I don’t know how to resolve the issue of virtual machine, as not much is
written about that and the links are not helping with that issue.


Do you have other suggestions regarding how to change the script, so it
will create the data.nii without the symbolic link (there are plenty "ln"
commands uses in the script)?


Many thanks,

Efrat

On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Efrat - This appears to be a virtual machine problem:
>
> https://communities.vmware.com/thread/312591?tstart=0
>
> There are some solutions suggested in that thread. I'm wondering if using
> a relative instead of an absolute path for the symlink works, i.e.,
>
> ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>
> instead of:
>
> ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
> /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>
> Can you please try it both ways and let me know if the former works on a
> computer where the latter doesn't?
>
> And yes, if you fix error #1 it'll fix error #2 as well.
>
> Thanks,
> a.y
>
>
>
> On Tue, 29 Mar 2016, Efrat Kliper wrote:
>
>
>> Dear Freesurfer experts,
>>
>>
>> I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the
>> preprocessing has already been completed in Freesurfer 5.1) in order to run
>> some new functions
>> of Tracula (I have also installed the latest Tracula update
>> (tracula.update.centos4_x86_64.5.3.2014_05_26).
>>
>>
>> I am using:
>>
>> FREESURFER_HOME: /usr/local/freesurfer
>>
>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> RedHat release: CentOS release 5.3 (Final)
>>
>> Kernel info: Linux 2.6.18-128.1.6.el5 x86_64
>>
>>
>>
>>  I encountered two problems:
>>
>>
>> 1.  When I run the initial code of Tracula: trac-all –prep code:
>>
>> /home/fsl/
>>
>> usr/local/freesurfer/bin/trac-all -prep -c
>> /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt
>>
>> Subject TB_480
>>
>> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
>>
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Actual FREESURFER_HOME /usr/local/freesurfer
>>
>> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> fsl
>>
>> localhost.localdomain
>>
>> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
>> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>>
>> I am getting the following message: ln -sf
>> /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz
>> /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz
>>
>>
>>
>> ln: creating symbolic link
>> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to
>> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not
>> supported
>>
>>
>>
>> 2.  If I run the trac-all –bedp command of Tracula (on already
>> trac-all data which was preproc on Freesurfer version 5.1. /home/fsl
>>
>> /usr/local/freesurfer/bin/trac-all
>>
>> -bedp -c /home/fsl/Desktop/xxx.txt
>>
>> Subject TB_201
>>
>> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects
>>
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Actual FREESURFER_HOME /usr/local/freesurfer
>>
>> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>>
>> fsl
>>
>> localhost.localdomain
>>
>> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25
>> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>>
>> I am getting the following message:
>>
>> Program versions:
>>
>> $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $
>>
>> mri_convert --all-info
>>
>> ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Aug 16 2014
>> 05:13:24
>> CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User:
>> fsl  Machine: localhost.localdomain  Platform: Linux  PlatformVersion:
>> 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion: 30400
>>
>> FLIRT version 6.0
>>
>> $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
>>
>> $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
>>
>> ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: Feb  2 2013
>> 22:46:06
>> CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux
>> PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion:
>> 30400
>>
>> ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion:
>> $Name:  $  TimeStamp: 2016/03/29-13:00:54-GMT  BuildTimeStamp: May 23 2014
>> 05:15:35
>> CVS:   User: fsl  Machine: localhost.localdomain  Platform: Linux
>> PlatformVersion: 2.6.18-128.1.6.el5  CompilerName: GCC  CompilerVersion:
>> 30400
>>
>>