Re: [Freesurfer] Recon-all Error: _FindFacePath

[Daniel Ferreira Padilla]

Hello Khoa,

 

Thank you very much for your suggestion. I checked both brainmask.mgz and
wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope
something can be done.

 

Cheers!

 

Daniel Ferreira

 

 

 

2011/9/13 Khoa Nguyen 

Hi Daniel,

Usually when I get the FindFacePath error, the wm.mgz is very bad. You can
try placing control points on the wm and rerun -autorecon2 and -autorecon3.
That worked for me.

-Khoa



On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote:

Dear Bruce and experts,



I would really appreciate if you can help me with my scans.



I have successfully processed all my sample but got this same FindFacePath
error with 2 subjects.



I checked the brainmask and wm files and for me they look ok. So I do not
know how can I fix this error.



Thank you very much in advance





ERROR: _FindFacePath: could not find path!
Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC
2011 x86_64 GNU/Linux

recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011













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contains patient information, please contact the Partners Compliance
HelpLine at
 
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properly
dispose of the e-mail.

 

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Re: [Freesurfer] Recon-all Error: _FindFacePath

[Ahmed, F, Me]

Hi Daniel,

How did you send your scans to Bruce?

Thanks,
Fatima

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Daniel Ferreira 
Padilla
Sent: 14 September 2011 09:19
To: 'Khoa Nguyen'
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello Khoa,

Thank you very much for your suggestion. I checked both brainmask.mgz and 
wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope 
something can be done.

Cheers!

Daniel Ferreira



2011/9/13 Khoa Nguyen 
mailto:k...@nmr.mgh.harvard.edu>>
Hi Daniel,

Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try 
placing control points on the wm and rerun -autorecon2 and -autorecon3. That 
worked for me.

-Khoa


On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote:
Dear Bruce and experts,



I would really appreciate if you can help me with my scans.



I have successfully processed all my sample but got this same FindFacePath
error with 2 subjects.



I checked the brainmask and wm files and for me they look ok. So I do not
know how can I fix this error.



Thank you very much in advance





ERROR: _FindFacePath: could not find path!
Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC
2011 x86_64 GNU/Linux

recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011










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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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Re: [Freesurfer] Recon-all Error: _FindFacePath

[Daniel Ferreira Padilla]

Hi Fatima,

 

I used the Martinos Center File drop (

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html).

 

Daniel

 

 

 

 


2011/9/14 Ahmed, F, Me  

 

Hi Daniel,

 

How did you send your scans to Bruce?

 

Thanks,

Fatima

 

From:  
freesurfer-boun...@nmr.mgh.harvard.edu [mailto:

freesurfer-boun...@nmr.mgh.harvard.edu]On Behalf Of Daniel Ferreira Padilla
Sent: 14 September 2011 09:19
To: 'Khoa Nguyen'
Cc:   freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath

 

Hello Khoa,

 

Thank you very much for your suggestion. I checked both brainmask.mgz and
wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope
something can be done.

 

Cheers!

 

Daniel Ferreira

- Ocultar texto citado -

 

 

 

2011/9/13 Khoa Nguyen < 
k...@nmr.mgh.harvard.edu>

Hi Daniel,

Usually when I get the FindFacePath error, the wm.mgz is very bad. You can
try placing control points on the wm and rerun -autorecon2 and -autorecon3.
That worked for me.

-Khoa



On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote:

Dear Bruce and experts,



I would really appreciate if you can help me with my scans.



I have successfully processed all my sample but got this same FindFacePath
error with 2 subjects.



I checked the brainmask and wm files and for me they look ok. So I do not
know how can I fix this error.



Thank you very much in advance





ERROR: _FindFacePath: could not find path!
Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC
2011 x86_64 GNU/Linux

recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011











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] Recon-all Error: _FindFacePath

[Ahmed, F, Me]

Thanks Daniel! That's great!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Daniel Ferreira 
Padilla
Sent: 14 September 2011 10:25
To: Ahmed, F, Me 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath

Hi Fatima,

I used the Martinos Center File drop 
(https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html).

Daniel





2011/9/14 Ahmed, F, Me  

Hi Daniel,

How did you send your scans to Bruce?

Thanks,
Fatima

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]On
 Behalf Of Daniel Ferreira Padilla
Sent: 14 September 2011 09:19
To: 'Khoa Nguyen'
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello Khoa,

Thank you very much for your suggestion. I checked both brainmask.mgz and 
wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope 
something can be done.

Cheers!

Daniel Ferreira
- Ocultar texto citado -



2011/9/13 Khoa Nguyen 
mailto:k...@nmr.mgh.harvard.edu>>
Hi Daniel,

Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try 
placing control points on the wm and rerun -autorecon2 and -autorecon3. That 
worked for me.

-Khoa


On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote:
Dear Bruce and experts,



I would really appreciate if you can help me with my scans.



I have successfully processed all my sample but got this same FindFacePath
error with 2 subjects.



I checked the brainmask and wm files and for me they look ok. So I do not
know how can I fix this error.



Thank you very much in advance





ERROR: _FindFacePath: could not find path!
Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC
2011 x86_64 GNU/Linux

recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011








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[Freesurfer] Segmentation fault during -autorecon1

[Palzes, Vanessa]

Hello,

 

I am continuously getting a "Segmentation fault" error during
-autorecon1 when it's running mri_binarize. I have been running
Freesurfer on a Mac, but now I am trying to implement it using Linux. I
am running this version:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux
2.6.9-89.0.20.ELsmp x86_64.

 

I this a memory issue, or can there be another explanation? I've tried
multiple times and with different subjects.

 

Here is my log output:

 

home/harshad/data5/Freesurfer/PATHD/process/P2608/mri/] [2011-09-13
16:08:43] running:

  /usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3
./tmp.mri_nu_correct.mni.31037/nu1.mnc
./tmp.mri_nu_correct.mni.31037/1//template.mnc

 

Transforming
slices:.
.Done

Transforming
slices:.
.Done

 

mri_binarize --i ./tmp.mri_nu_correct.mni.31037/nu2.mnc --min -1 --o
./tmp.mri_nu_correct.mni.31037/ones.mgz

Segmentation fault 

Linux vhasfcapp21 2.6.9-89.0.20.ELsmp #1 SMP Mon Jan 18 12:19:33 EST
2010 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s P2608 exited with ERRORS at Tue Sep 13 16:10:11 PDT 2011

 

 

Any help would be greatly appreciated.

 

Thanks,

 

Vanessa Palzes

Research Assistant

Brain Imaging & EEG Lab

San Francisco VA Medical Center

4150 Clement Street

San Francisco, CA 94121

Tel: 415-221-4810 ext. 6155

 

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Re: [Freesurfer] Reference

[Louis Nicholas Vinke]

Hi,
On the pages below there are some links to articles describing how the FS 
cortical and sub-cortical atlases were created.

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

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

-Louis

On Wed, 14 Sep 2011, Anne Bailey wrote:

> Hi,
>
>
> I am a PhD student currently using Freesurfer for analyses and I was
> wondering if you could provide me with the reference for the original brains
> that were used as the basis for the automatic parcellation of cortical and
> subcortical structures.
>
> If I have contacted the wrong person, could you please forward my inquiry to
> someone who can point me to this information?
>
> Thank you!
>
> Anne Bailey
>
>
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[Freesurfer] time course within ROI

[YUMI MAEDA]

HI,
I am trying to get timecourse from each subject within a ROI
with GUI as follows,
in tksurfer GUI,
Tools > timecourse > Write summary of marked vetices/label,

I would like to do it command line, would you tell me what line I can use?

I tried to use mri_segstats
 --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf
test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img

the output has 7 columns and does not seems to be timecourse and also it
is different from the one that I get when I use GUI as I described above.

thank you very much.
YUMI
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[Freesurfer] tksurfer sliver problem

[Michael Harms]

Hi guys,
So, the infamous tksurfer "sliver" display problem has reared its ugly
head on some of the systems that I'm accessing, but in a manner that I
can't make any sense of across the systems.  

Machine 1: CentOS 5.5, 64 bit, FS versions 4.5.0 and 5.0.0 installed
Sliver problem is present for v4.5.0, but not 5.0.0

Machine 2: RHEL Server 5.7, 64 bit, FS versions 4.5.0, 5.0.0, and 5.1.0
installed.  Sliver problem is present for all 3 FS versions.

For both machines, I'm viewing the results in a VNC server, and
'glxgears' works fine in each.  

The results of 'glxinfo' in a terminal within the VNC Server on each
machine indicates that the same rendering is being used on each.
i.e,. 
direct rendering: No
OpenGL renderer string: Mesa GLX Indirect
OpenGL version string: 1.2 (1.5 Mesa 6.5.1)

What I find particularly puzzling is that tksurfer works fine on FS
v5.0.0 on Machine 1, but not FS 4.5.0 on the same machine.  Yet the
sliver problem is present for v5.0.0 on Machine 2, indicating that it
isn't simply an FS version issue either.

I was wondering if the above behavior makes sense to someone, so that I
can have something more concrete to take to the admins of each system.

thanks,
-MH

-- 
Michael Harms, Ph.D.

Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604   Tel: 314-747-6173
660 South Euclid Ave.Fax: 314-747-2182
St. Louis, MO 63110  Email: mha...@wustl.edu


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Re: [Freesurfer] time course within ROI

[Douglas N Greve]

You have specified two segmentations (an annotation and a segmentation). 
Just use one (probably the annot). There will be a column for each label 
in the annot. Use the --ctab-out to get a color table that indicates 
which column belongs to which region.
doug

YUMI MAEDA wrote:
> HI,
> I am trying to get timecourse from each subject within a ROI
> with GUI as follows,
> in tksurfer GUI,
> Tools > timecourse > Write summary of marked vetices/label,
>
> I would like to do it command line, would you tell me what line I can use?
>
> I tried to use mri_segstats
>  --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf
> test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img
>
> the output has 7 columns and does not seems to be timecourse and also it
> is different from the one that I get when I use GUI as I described above.
>
> thank you very much.
> YUMI
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>
>
>   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] tksurfer sliver problem

[Nick Schmansky]

hi mike,

this problem has been a real pain for years, and i've never been able to
debug it.  it would seem its some interaction with the shared gl libs,
and the static glut libs compiled into tksurfer, as indicated by the
combinations you list below.

fyi, if you havent seen this page already, its the known workarounds:

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

n.



On Wed, 2011-09-14 at 15:30 -0500, Michael Harms wrote:
> Hi guys,
> So, the infamous tksurfer "sliver" display problem has reared its ugly
> head on some of the systems that I'm accessing, but in a manner that I
> can't make any sense of across the systems.  
> 
> Machine 1: CentOS 5.5, 64 bit, FS versions 4.5.0 and 5.0.0 installed
> Sliver problem is present for v4.5.0, but not 5.0.0
> 
> Machine 2: RHEL Server 5.7, 64 bit, FS versions 4.5.0, 5.0.0, and 5.1.0
> installed.  Sliver problem is present for all 3 FS versions.
> 
> For both machines, I'm viewing the results in a VNC server, and
> 'glxgears' works fine in each.  
> 
> The results of 'glxinfo' in a terminal within the VNC Server on each
> machine indicates that the same rendering is being used on each.
> i.e,. 
> direct rendering: No
> OpenGL renderer string: Mesa GLX Indirect
> OpenGL version string: 1.2 (1.5 Mesa 6.5.1)
> 
> What I find particularly puzzling is that tksurfer works fine on FS
> v5.0.0 on Machine 1, but not FS 4.5.0 on the same machine.  Yet the
> sliver problem is present for v5.0.0 on Machine 2, indicating that it
> isn't simply an FS version issue either.
> 
> I was wondering if the above behavior makes sense to someone, so that I
> can have something more concrete to take to the admins of each system.
> 
> thanks,
> -MH
> 

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Re: [Freesurfer] mean and stdev group-wise

[Douglas N Greve]

You can run mris_preproc on each group separately. Then run mri_glmfit 
with the --osgm flag. The rstd will be the group std, and the 
osgm/gamma.mgh will be the group mean. You can also call mri_concat on 
the group files with --mean and again with --std
doug

Tetiana Dadakova wrote:
> Dear list,
>
> I would like to calculate mean and stdev of thickness group-wise.
> Could you please give me a hint how to do it?
>
> Thank you,
> Tanja.
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>
>
>   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] flipped orientation in tksurfer and tkmedit

[Douglas N Greve]

When you say on the "right hemi in tkmedit" do you mean on the right 
side of the image (which is the left side of the brain)?
doug

Ilana Hairston wrote:
> Hi there,
> We recently had a problem that tksurfer and tkmedit were flipped 
> relative to each other.  Basically, when saving a point in the left 
> hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit.
> Any ideas how this could have happened?
> Thanks
> ilana
>
>
>
> -- 
>> **
>> Ilana Hairston ,PhD
>> Research Assistant Professor
>> 4250 Plymouth Rd. (rm 2439)
>> Psychiatry Department, Addiction Research Center
>> University of Michigan, Ann Arbor MI 48109-2700
>> Tel: 734-232-0232; Mobile: 650-906-8449
>>
>> 
>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, 
>> and own 1% of the world's property
>
>
>
> 
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] .img extension read as analyze even though hdr says nifti1

[Douglas N Greve]

If it happens with one, it will happen with all of them. We never got 
around to having our code look in the .img header to see if it is really 
nifti. Why not use the single-file nifti with nii extension?
doug

Satrajit Ghosh wrote:
> hi all,
>
> when a .img extension file is passed to freesurfer routines, it is 
> read in as analyze even if the header says it's a nifti image. we have 
> observed that this causes a left-right flip in some cases. since a 
> .img cannot exist without a header to be meaningful, shouldn't the 
> appropriate type be detected from the header?
>
> also it would be good to know if this behavior is consistent across 
> all of freesurfer or restricted to certain binaries.
>
> see below for mri_info output
>
> cheers,
>
> satra
>
> $ mri_info con_0001.img
> Volume information for con_0001.img
>   type: analyze4d
> dimensions: 79 x 95 x 68
>voxel sizes: 2., 2., 2.
>   type: FLOAT (3)
>fov: 79.000
>dof: 0
> xstart: -39.5, xend: 39.5
> ystart: -47.5, yend: 47.5
> zstart: -34.0, zend: 34.0
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r 
> =-1.
>   : x_a =   0., y_a =   1., z_a =   0., c_a 
> =   -17.
>   : x_s =   0., y_s =   0., z_s =   1., c_s 
> =18.
> Orientation   : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.   0.   0.78.
> 0.   2.   0.  -112.
> 0.   0.   2.   -50.
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>-0.5000   0.   0.39.
>-0.   0.5000  -0.56.
>-0.  -0.   0.500025.
> 0.   0.   0. 1.
>
> $ mri_info con_0001.hdr
> Volume information for con_0001.hdr
>   type: nifti1
> dimensions: 79 x 95 x 68
>voxel sizes: 2., 2., 2.
>   type: FLOAT (3)
>fov: 79.000
>dof: 0
> xstart: -39.5, xend: 39.5
> ystart: -47.5, yend: 47.5
> zstart: -34.0, zend: 34.0
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r 
> =-1.
>   : x_a =   0., y_a =   1., z_a =   0., c_a 
> =   -17.
>   : x_s =   0., y_s =   0., z_s =   1., c_s 
> =18.
> Orientation   : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.   0.   0.78.
> 0.   2.   0.  -112.
> 0.   0.   2.   -50.
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>-0.5000   0.   0.39.
>-0.   0.5000  -0.56.
>-0.  -0.   0.500025.
> 0.   0.   0. 1.
>
> 
>
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Fax: 617-726-7422

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Re: [Freesurfer] statical question recon-all -qcache -s (subject) ?

[Douglas N Greve]

I think that is ok.
doug

Knut J Bjuland wrote:
> Hi
>
> Can I use a different version of Freesurfer to run recon-all -qcache -s
> (subject) than the version used for recon-all -all -s (subject)?
>
> Knut J
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Converting a cluster to a ROI without manually drawing

[Douglas N Greve]

You can also do it from the command line with mri_surfcluster.
doug

Nasim Maleki wrote:
> Hi all,
>
> I figured it out. This is easily doable using TkSurfer.
>
> Thanks,
> Nasim
> On Sep 13, 2011, at 12:37 PM, Nasim Maleki wrote:
>
>   
>> Hi all,
>>
>> In qdec, is there a way to convert a cluster to an ROI without
>> manually drawing the ROI? I'm talking about selecting clusters on the
>> mc-z maps.
>>
>> Thanks,
>> Nasim
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] mri_mcsim and mri_glmfit-sim

[Douglas N Greve]

mri_mcsim just runs the monte carlo simulation that mri_glmfit runs (but 
more efficiently). Either way, you still need a FWHM to do a 
cluster-wise correction. You can probably run mri_glmfit (and 
mri_glmfit-sim) on the data that you use as input to your GLM software. 
Alternatively, you can have your software produce a file of residuals 
which you then run mris_fwhm to compute the FWHM. If you can't use the 
smoothing kernel size if you did volume smoothing. If you did surface 
smoothing, then the FWHM will be underestimated (I often find by a lot 
for functional data).
doug

MCLAREN, Donald wrote:
> I am trying to figure out how to cluster some data on the cortical
> surface; however, I've run into a few issues:
>
> (1) I can't seem to find a description or examples for running
> mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST
> to create my statistical maps.
>
> (2) A previous email suggested that there are stored values that I
> could lookup, but I can't seem to locate the files anywhere.
>
> (3) With respect to the fwhm values used in the simulations, it was
> suggested that this be matched to the fwhm.dat file output from
> mri_glmfit; however, since I didn't use mri_glmfit, I don't have
> fwhm.data file. Should I just use the smoothing used on the surfaces?
>
> Any thoughts would be appreciated.
>
> Best Regards, Donald McLaren
> =
> D.G. McLaren, Ph.D.
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Office: (773) 406-2464
> =
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] TRACULA: how to implement DTI repeat sequence?

[Ansgar Furst]

Dear Anastasia and Team FreeSurfer,
First of all thanks so much for developing TRACULA. I think it has a lot of
potential!
Here is my question: I'm trying to modify "dmrirc_single_subject" file in
order to reflect our local sequence and wondered how you are dealing with
DTI repeat sequences for the same subject.
We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion
bvalue Table would look like this:
==
*   0  0  0  0  0  1000  1000  1000  1000  1000  1000  1000  1000  1000
1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000
1000  1000  1000  1000  1000  1000  1000  1000  0  0  0  0  0  1000  1000
1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000
1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000  1000
1000  1000
Now I wonder how I would modify the below default settings from the tutorial
data to reflect this:
=
set subjlist = (Diff001)

set runlist = (1)

# Input diffusion DICOMs (file names relative to dcmroot)

set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/

set dcmlist = (Diff001/orig/6-1.dcm)

=

Oh also, I noticed that in the wiki you have the following settings:
===

set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt

===
In the latest version of the freesurfer distribution I counted 33
subjects for the training algorithm and therefore use:

"subj,train,difftutorial33.txt" pointing to

/usr/local/freesurfer/trctrain/trc001
/usr/local/freesurfer/trctrain/trc002
/usr/local/freesurfer/trctrain/trc003
/usr/local/freesurfer/trctrain/trc004
/usr/local/freesurfer/trctrain/trc005
/usr/local/freesurfer/trctrain/trc006
/usr/local/freesurfer/trctrain/trc007
/usr/local/freesurfer/trctrain/trc008
/usr/local/freesurfer/trctrain/trc009
/usr/local/freesurfer/trctrain/trc010
/usr/local/freesurfer/trctrain/trc011
/usr/local/freesurfer/trctrain/trc012
/usr/local/freesurfer/trctrain/trc013
/usr/local/freesurfer/trctrain/trc014
/usr/local/freesurfer/trctrain/trc015
/usr/local/freesurfer/trctrain/trc016
/usr/local/freesurfer/trctrain/trc017
/usr/local/freesurfer/trctrain/trc018
/usr/local/freesurfer/trctrain/trc019
/usr/local/freesurfer/trctrain/trc020
/usr/local/freesurfer/trctrain/trc021
/usr/local/freesurfer/trctrain/trc022
/usr/local/freesurfer/trctrain/trc023
/usr/local/freesurfer/trctrain/trc024
/usr/local/freesurfer/trctrain/trc025
/usr/local/freesurfer/trctrain/trc026
/usr/local/freesurfer/trctrain/trc027
/usr/local/freesurfer/trctrain/trc028
/usr/local/freesurfer/trctrain/trc029
/usr/local/freesurfer/trctrain/trc030
/usr/local/freesurfer/trctrain/trc031
/usr/local/freesurfer/trctrain/trc032
/usr/local/freesurfer/trctrain/trc033

Does that make sense?

Thanks so much for your help!

Ansgar
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[Freesurfer] pial surface file format

[Jeff Eriksen]

I wish to extract the pial and GW surfaces from their surface files to
manipulate in Matlab. As far as I can determine, these are the files
l&Rh.white and l&rh.pial. Can someone please confirm this, and also
confirm that these are in the "triangle surface file" binary format? If
this is all true, I can proceed to opening and reading the meshes. Thanks,
-Jeff Eriksen


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Re: [Freesurfer] pial surface file format

[Bruce Fischl]

Yes, and we provide m files for reading them
Cheers
Bruce



On Sep 14, 2011, at 9:46 PM, Jeff Eriksen  wrote:

> I wish to extract the pial and GW surfaces from their surface files to
> manipulate in Matlab. As far as I can determine, these are the files
> l&Rh.white and l&rh.pial. Can someone please confirm this, and also
> confirm that these are in the "triangle surface file" binary format? If
> this is all true, I can proceed to opening and reading the meshes. Thanks,
> -Jeff Eriksen
> 
> 
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Re: [Freesurfer] pial surface file format

[Jeff Eriksen]

Super! Please tell me how to obtain the m-files.
-Jeff

On 9/14/11 6:49 PM, "Bruce Fischl"  wrote:

>Yes, and we provide m files for reading them
>Cheers
>Bruce
>
>
>
>On Sep 14, 2011, at 9:46 PM, Jeff Eriksen  wrote:
>
>> I wish to extract the pial and GW surfaces from their surface files to
>> manipulate in Matlab. As far as I can determine, these are the files
>> l&Rh.white and l&rh.pial. Can someone please confirm this, and also
>> confirm that these are in the "triangle surface file" binary format? If
>> this is all true, I can proceed to opening and reading the meshes.
>>Thanks,
>> -Jeff Eriksen
>> 
>> 
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>
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