date:20160226

[Freesurfer] Freesurfer course in Tours, France, 26-27 May 2016

2016-02-26 Thread Christophe Destrieux

Dear colleagues, 
It is our pleasure to host a FreeSurfer course in Tours, Loire Valley, France, 
26-27 may.

This event is coorganized by the brain and imaging laboratory, INSERM 
U930-Université François Rabelais of Tours (France) and by the Martinos Center.

It will be limited to 64 participants and will focus on surface-based analysis 
of individual and group morphological data and on tractographic analysis using 
FreeSurfer tools.

See you in Tours next May!

Registration and information : http://freesurfer2016.sciencesconf.org/?lang=en


— 
Christophe Destrieux, 
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours 
Service de Neurochirurgie 
Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - 
France 
Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: 
christophe.destri...@univ-tours.fr
Web : http://www.u930.tours.inserm.fr/  









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[Freesurfer] FS on Macaque

2016-02-26 Thread Narkhede, Atul

Hi FS Experts,

I am relatively new to FS and have been trying to analyze macaque brains 
recently.
I used the following tutorial:

Freesurfer on Macaque
There are hardly any good tutorials or references on how one could generate a 
freesurfer surface using freesurfer. There are many problems to following the 
standard human analysis that simply does not work well for the macaque brain. 
Below is a work-in-progress tutorial on how to generate freesurfer surfaces. 
This tutorial requires FSL and it's associated tools, as well as a working 
installation of freesurfer. The easiest way of getting all this is to download 
the VirtualBox image of FreeSurfer from the MGH website and voila!

Anyways, here goes the rough draft:

1. You should have a high-contrast, low noise MPRAGE of your monkey's brain. We 
typically use 0.35 mm isotropic voxel resolution, and scan between 9 to 12 
times (each scan runs for 15 minutes) to generate a good mean image.

2. You should also aquire a T2 image while you acquire your MPRAGEs, as this 
will make skull extraction (a BIG deal with monkeys) much easier.

3. You must get your images in the orientation that FSL likes (nifti files, 
with very particular dimension ordering). You can use fslswapdim function for 
this. If you are converting dicoms from the scanner to nifti's using the 
mri_convert command (from the FreeSurfer distribution), make sure to pass the 
"--sphinx" argument to it. After this, run

fslswapdim inputvol.nii LR PA IS outputvol.nii

to correct the dimension directions as FSL likes it. Check with fsl_view.

4. If the images are properly aligned, you can now use the FSL Brain Extraction 
Tool (BET) to rip out the brain. Here, you can pass the T2 image for a much 
better skull stripping. Alternatively (haven't tried it, but in theory should 
work), you can generate a brain mask using the T2 by thresholding it, then 
filling the volume and cutting the brain out of the hi-res anatomical with this.

5. Once you have a nice clean skull-stripped brain, you'll have to correct for 
the non-uniform intensity across the image. This can be achieved easily by 
FreeSurfer's implementation of the MNI's N3 correction tool. Apply this using 
"mri_nu_correct", as follows:

mri_nu_correct --i skulStrippedBrain.nii --o skull_stripped_nu.nii --distance 24

The distance factor may need to be adjusted, depending on what type of coil you 
used, and how big your monkey is, etc. Increasing the distance factor makes the 
program look for lower-frequency modulations of the intensity, whereas smaller 
numbers (better for phased-array coils) look for higher spatial frequency 
modulations.

6. You can then use the FSL FAST tool to segment your volume into white, gray, 
and csf. Output the white matter image for FreeSurfer, and leave the rest alone.

7. Make a new subject directory in keeping with the FreeSurfer system by using 
mksubjdirs.

8. Now comes the fun part: FreeSurfer wants 1mm isotropic voxels, but your 
images are 0.35 mm iso, so if you ask FreeSurfer to work with them, it will 
have to downsample them to 1mm. That's no fun, so we play a trick.

8a. Start Matlab. Make sure to download the NIFTI toolbox from the NIFTI 
website. Using load_nii, load the image you want to prep, like this:

nii = load_nii('mynifti.nii');

Make sure the nifti file is not compress (not "niil.gz"). Then modify 
nii.hdr.pixeldim to reflect 1 mm voxel ( = [1 1 1 1 0 0 0], or just replace the 
0.35 in the size vector by 1's).

nii.hdr.pixeldim = [1 1 1 1 0 0 0];

Now save the volume, keeping track of what you did:

save_nii(nii, 'newNiftiName.nii');

8b. Finally, convert to MGZ format, and make sure to tell it to CONFORM:

mri_convert -c invol_fake1mm.nii outvol_fake1mm.mgz

Now, do this for all your volumes. Then they'll be ready for FreeSurfer.

9. Fill in your white matter surface:
9a. load in tkmedit, like this:

tkmedit -f /directory/brain.mgz

9b. In tkmedit, make note of the VOXEL coordinates (bottom left of window, top 
row) for the corpus calosum and the pons.

9c. Go back to the command prompt and exceute the following on the white matter 
image:

mri_fill -CV 192 172 214 -PV 192 249 194 /subj/mri/wm/wm.mgz 
../filled/filled.mgz

where CV and PV reflect the corpus callosum VOXEL coordinates, and PV that of 
the pons.

9d. Check the results in tkmedit. Should be cute.

10. Now, we follow the recon-all dev table, which uses mri_pretess as follows:

mri_pretess ../filled/filled.mgz 255 ../brain/nu.mgz ../filled-pretess255.mgz

Then,

mri_tessellate ../filled-pretess255.mgz 255 ../lh.orig.nofix

Then,

mris_extract_main_component ../lh.orig.nofix ../lh.orig.nofix

mris_smooth -nw ../lh.orig.nofix ../lh.smoothwm.nofix

mris_inflate -no-save-sulc ../lh.smoothwm.nofix ../lh.inflated.nofix

mris_sphere -q ../lh.inflated.nofix ../lh.qsphere.nofix
And now, repeat this for the righ hemisphere (rh.orig)
posted by brainmeister

I have the following questions:


1)   What steps would follow after the

Re: [Freesurfer] (no subject)

2016-02-26 Thread Maheen Siddiqui

Thanks very much, I'll have a look!

On Fri, Feb 26, 2016 at 4:13 PM, Bruce Fischl 
wrote:

> yes, they are documented pretty extensively on our wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> On Fri, 26 Feb 2016, Maheen Siddiqui wrote:
>
> Hi,
>> Thanks for your reply. I have sought advice from someone who is
>> experienced
>> in Homer2 atlas viewer.
>>
>> Is it possible to find out the the coordinate system of the T1.mgz file
>> and
>> the surface file created by FreeSurfer?
>>
>> Thanks!
>>
>> On Fri, Feb 26, 2016 at 3:36 PM, dgw  wrote:
>>   Maheen,
>>
>>   it sounds like a question that could be better answered by the
>>   Homer2 list.
>>
>>   hth
>>   d
>>
>>   On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
>>    wrote:
>>   > Dear FreeSurfer Users,
>>   >
>>   > I have a head surface mesh and a pial surface mesh obtained
>>   after
>>   > segmentation of a T1 MRI scan. I am going to importing these
>>   into Homer2
>>   > Atlas Viewer as subject anatomy.
>>   >
>>   > However before I can do this import successfully, I need to
>>   bring the two
>>   > meshes into the same coordinate system. At the moment they are
>>   in different
>>   > coordinate systems (as pictured) and I need to bring the pial
>>   surface mesh
>>   > into the head surface mesh. I am a little unsure how to do
>>   this.
>>   >
>>   > Does anybody have any experience with this? Or any advice on
>>   what I could do
>>   > possibly?
>>   >
>>   > Thanks,
>>   >
>>   > Maheen
>>   >
>> > ___
>> > 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.
>> >
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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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> dispose of the e-mail.
>
>
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Re: [Freesurfer] (no subject)

2016-02-26 Thread Bruce Fischl

yes, they are documented pretty extensively on our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On Fri, 26 Feb 
2016, 
Maheen Siddiqui wrote:

Hi, 
Thanks for your reply. I have sought advice from someone who is experienced
in Homer2 atlas viewer.

Is it possible to find out the the coordinate system of the T1.mgz file and
the surface file created by FreeSurfer?

Thanks!

On Fri, Feb 26, 2016 at 3:36 PM, dgw  wrote:
  Maheen,

  it sounds like a question that could be better answered by the
  Homer2 list.

  hth
  d

  On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
   wrote:
  > Dear FreeSurfer Users,
  >
  > I have a head surface mesh and a pial surface mesh obtained
  after
  > segmentation of a T1 MRI scan. I am going to importing these
  into Homer2
  > Atlas Viewer as subject anatomy.
  >
  > However before I can do this import successfully, I need to
  bring the two
  > meshes into the same coordinate system. At the moment they are
  in different
  > coordinate systems (as pictured) and I need to bring the pial
  surface mesh
  > into the head surface mesh. I am a little unsure how to do
  this.
  >
  > Does anybody have any experience with this? Or any advice on
  what I could do
  > possibly?
  >
  > Thanks,
  >
  > Maheen
  >
> ___
> 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.
>
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Re: [Freesurfer] (no subject)

2016-02-26 Thread Maheen Siddiqui

Hi,

Thanks for your reply. I have sought advice from someone who is experienced
in Homer2 atlas viewer.

Is it possible to find out the the coordinate system of the T1.mgz file and
the surface file created by FreeSurfer?

Thanks!

On Fri, Feb 26, 2016 at 3:36 PM, dgw  wrote:

> Maheen,
>
> it sounds like a question that could be better answered by the Homer2 list.
>
> hth
> d
>
> On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
>  wrote:
> > Dear FreeSurfer Users,
> >
> > I have a head surface mesh and a pial surface mesh obtained after
> > segmentation of a T1 MRI scan. I am going to importing these into Homer2
> > Atlas Viewer as subject anatomy.
> >
> > However before I can do this import successfully, I need to bring the two
> > meshes into the same coordinate system. At the moment they are in
> different
> > coordinate systems (as pictured) and I need to bring the pial surface
> mesh
> > into the head surface mesh. I am a little unsure how to do this.
> >
> > Does anybody have any experience with this? Or any advice on what I
> could do
> > possibly?
> >
> > Thanks,
> >
> > Maheen
> >
> > ___
> > 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.
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] (no subject)

2016-02-26 Thread dgw

Maheen,

it sounds like a question that could be better answered by the Homer2 list.

hth
d

On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
 wrote:
> Dear FreeSurfer Users,
>
> I have a head surface mesh and a pial surface mesh obtained after
> segmentation of a T1 MRI scan. I am going to importing these into Homer2
> Atlas Viewer as subject anatomy.
>
> However before I can do this import successfully, I need to bring the two
> meshes into the same coordinate system. At the moment they are in different
> coordinate systems (as pictured) and I need to bring the pial surface mesh
> into the head surface mesh. I am a little unsure how to do this.
>
> Does anybody have any experience with this? Or any advice on what I could do
> possibly?
>
> Thanks,
>
> Maheen
>
> ___
> 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.
>
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[Freesurfer] Recon-all error

2016-02-26 Thread m . bahri

Dear Experts,

I have the following error with recon-all (freesurfer v 5.3) in the orig_nu.log 
file. Could anyone help to solve the problem?

Many thanks,

Mohamed



Iteration 1 Fri Feb 26 14:13:20 CET 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc 
./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50
Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl 
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct 
line 37.
ERROR: nu_correct
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

2016-02-26 Thread Maheen Siddiqui

Just FYI, I could not get this issue resolved by altering the script. I
was, however, successfully able to get the head surface mesh using the
iso2mesh toolbox, with the vol2surf function.

On Tue, Feb 23, 2016 at 2:51 PM, Bruce Fischl 
wrote:

> the magic # 16777213 means it's a quad file, not a triangle file. I still
> would have thought we could read it fine. Do you want to email us the
> surface file and someone will take a look?
>
>
> On Tue, 23 Feb 2016, Douglas Greve wrote:
>
> Can you load it in tksurfer or freeview?
>>
>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>   Hi FreeSurfer users,
>> I have used the "mkheadsurf" command to create a head surface for my
>> subject. However when I try to use "read_surf" to
>> read the "lh.seghead" file that is created, the magic number is not one
>> that is recognised.
>>
>> Having read some previous posts/questions with similar problem/error, I
>> think the problem is probably within the
>> "lh.seghead" file. I think someone wrote that incompatibility of the
>> magic number means that the surface is corrupted. Is
>> there a way to check errors of mkheadsurf? Or whether something is wrong?
>> It looked fine in freeview.
>>
>> Does anybody have any advice?
>>
>> Thanks,
>>
>> Maheen
>>
>>
>> ___
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>>
>>
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
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> e-mail
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> HelpLine at
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>
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[Freesurfer] Freesurfer course in Tours, France, 26-27 May 2016

[Freesurfer] FS on Macaque

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

[Freesurfer] Recon-all error

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

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