Re: [Freesurfer] Resample to cropped FOV in anatomical space

[Michael Waskom]

OK I think a way around this is to use tkregister2 to generate a
registration between the conformed brain image and the cropped one:

tkregister2 --mov brain.nii --targ brain-crop.nii --regheader --reg
anat2crop.dat --noedit

I can then convert this to an FSL-style matrix and use convert_xfm to
concatenate the func2anat and anat2crop matrix so it can be applied with a
single interpolation.

By the way is it possible to combine two tkreg style matrices in that
format? I don't see an obvious option in tkregister2. That is I want to
combine a2b.dat and b2c.dat into a2c.dat.

Thanks,
Michael

On Fri, Aug 18, 2017 at 2:00 PM, Michael Waskom <mwas...@nyu.edu> wrote:

> Alternatively, is it possible to pass bbregister a different target volume
> that's in register with the surfaces?
>
> On Thu, Aug 17, 2017 at 6:10 PM, Michael Waskom <mwas...@nyu.edu> wrote:
>
>> Hi Doug,
>>
>> I'd like to use the registration matrix from bbregister to transform
>> functional data into a cropped FOV that corresponds with the anatomy.
>>
>> I thought that bbregister outputs a ras2ras transform, so if I could crop
>> the anatomical volume with a correct header vox2ras, things should be fine.
>> Is my thinking here wrong?
>>
>> Here is roughly what I have done:
>>
>> 1. Generate a registration matrix to the full anatomy
>>
>> bbregister --s subj --mov func.nii --reg reg.dat --t2
>>
>> 2. Crop the anatomy:
>>
>> mri_convert brain.mgz brain.nii
>> fslroi brain.nii brain_crop.nii 50 150 50 150 50 150
>>
>> (I know this is an fsl tool but I couldn't find an option to do exactly
>> this in mri_convert)
>>
>> 3. Check the output -- looks fine so far
>>
>> tkregister2 --mov brain-crop.nii --regheader --s subj --surfs --reg
>> /dev/null
>>
>> 4. Resample the functional volume
>>
>> mri_vol2vol --mov func.nii --targ brain_crop.nii --reg reg.dat --o
>> func_xfm.nii
>>
>> 5. Check the output
>>
>> tkregister2 --mov func_xfm.nii --regheader --s subj --surfs --reg
>> /dev/null
>>
>> The resulting functional image is shifted superior about ~20cm
>>
>> What am I missing in my understanding of the bbregister and header
>> transformation matrices?
>>
>> Thanks!
>> Michael
>>
>
>
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Re: [Freesurfer] Resample to cropped FOV in anatomical space

[Michael Waskom]

Alternatively, is it possible to pass bbregister a different target volume
that's in register with the surfaces?

On Thu, Aug 17, 2017 at 6:10 PM, Michael Waskom <mwas...@nyu.edu> wrote:

> Hi Doug,
>
> I'd like to use the registration matrix from bbregister to transform
> functional data into a cropped FOV that corresponds with the anatomy.
>
> I thought that bbregister outputs a ras2ras transform, so if I could crop
> the anatomical volume with a correct header vox2ras, things should be fine.
> Is my thinking here wrong?
>
> Here is roughly what I have done:
>
> 1. Generate a registration matrix to the full anatomy
>
> bbregister --s subj --mov func.nii --reg reg.dat --t2
>
> 2. Crop the anatomy:
>
> mri_convert brain.mgz brain.nii
> fslroi brain.nii brain_crop.nii 50 150 50 150 50 150
>
> (I know this is an fsl tool but I couldn't find an option to do exactly
> this in mri_convert)
>
> 3. Check the output -- looks fine so far
>
> tkregister2 --mov brain-crop.nii --regheader --s subj --surfs --reg
> /dev/null
>
> 4. Resample the functional volume
>
> mri_vol2vol --mov func.nii --targ brain_crop.nii --reg reg.dat --o
> func_xfm.nii
>
> 5. Check the output
>
> tkregister2 --mov func_xfm.nii --regheader --s subj --surfs --reg /dev/null
>
> The resulting functional image is shifted superior about ~20cm
>
> What am I missing in my understanding of the bbregister and header
> transformation matrices?
>
> Thanks!
> Michael
>
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[Freesurfer] Resample to cropped FOV in anatomical space

[Michael Waskom]

Hi Doug,

I'd like to use the registration matrix from bbregister to transform
functional data into a cropped FOV that corresponds with the anatomy.

I thought that bbregister outputs a ras2ras transform, so if I could crop
the anatomical volume with a correct header vox2ras, things should be fine.
Is my thinking here wrong?

Here is roughly what I have done:

1. Generate a registration matrix to the full anatomy

bbregister --s subj --mov func.nii --reg reg.dat --t2

2. Crop the anatomy:

mri_convert brain.mgz brain.nii
fslroi brain.nii brain_crop.nii 50 150 50 150 50 150

(I know this is an fsl tool but I couldn't find an option to do exactly
this in mri_convert)

3. Check the output -- looks fine so far

tkregister2 --mov brain-crop.nii --regheader --s subj --surfs --reg
/dev/null

4. Resample the functional volume

mri_vol2vol --mov func.nii --targ brain_crop.nii --reg reg.dat --o
func_xfm.nii

5. Check the output

tkregister2 --mov func_xfm.nii --regheader --s subj --surfs --reg /dev/null

The resulting functional image is shifted superior about ~20cm

What am I missing in my understanding of the bbregister and header
transformation matrices?

Thanks!
Michael
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Re: [Freesurfer] Speeding up mri_robust_register with --cost ROBENT

[Michael Waskom]

Hi Freesurfers,

(Sending again as I think the original may have been lost in the OHBM
shuffle)

I'm using mri_robust_register to obtain a registration between high
resolution (.7mm isotropic) whole-head T1w and T2w images from the same
subject. An example command line is:

mri_robust_register --mov T2w.nii.gz --dst T1w.nii.gz --lta T2w_to_T1w.lta
--warp T2w_reg.nii.gz --cost ROBENT --entradius 2 --entcorrection --satit
--iscale

This works extremely well -- much better than FLIRT. (I'm using this
registration to do some preprocessing before running recon-all, so
unfortunately bbregister is not an option).

But, it takes *forever*. (My runtimes are about 90 minutes using OMP
parallelization with 24 cores, or about 16 hours running in serial).

I'm interested in playing with the various options to see if I can get a
suitable registration with a faster runtime. But it's not obvious to me how
I should fiddle with the knobs to get started. For example, would
increasing or decreasing `entradius` be expected to make things go faster?
Also, I am acquiring the images in the same session, back to back, so I can
assume that the images start off with a pretty good (but not exact)
registration. Is there a way to use that assumption to speed things up?

Thanks,
Michael

On Tue, Jun 27, 2017 at 10:35 AM, Michael Waskom <mwas...@nyu.edu> wrote:

>
> I'm using mri_robust_register to obtain a registration between high
> resolution (.7mm isotropic) whole-head T1w and T2w images from the same
> subject. An example command line is:
>
> mri_robust_register --mov T2w.nii.gz --dst T1w.nii.gz --lta T2w_to_T1w.lta
> --warp T2w_reg.nii.gz --cost ROBENT --entradius 2 --entcorrection --satit
> --iscale
>
> This works extremely well -- much better than FLIRT. (I'm using this
> registration to do some preprocessing before running recon-all, so
> unfortunately bbregister is not an option).
>
> But, it takes *forever*. (My runtimes are about 90 minutes using OMP
> parallelization with 24 cores, or about 16 hours running in serial).
>
> I'm interested in playing with the various options to see if I can get a
> suitable registration with a faster runtime. But it's not obvious to me how
> I should fiddle with the knobs to get started. For example, would
> increasing or decreasing `entradius` be expected to make things go faster?
> Also, I am acquiring the images in the same session, back to back, so I can
> assume that the images start off with a pretty good (but not exact)
> registration. Is there a way to use that assumption to speed things up?
>
> Thanks,
> Michael
>
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[Freesurfer] Speeding up mri_robust_register with --cost ROBENT

[Michael Waskom]

Hi Freesurfers,

I'm using mri_robust_register to obtain a registration between high
resolution (.7mm isotropic) whole-head T1w and T2w images from the same
subject. An example command line is:

mri_robust_register --mov T2w.nii.gz --dst T1w.nii.gz --lta T2w_to_T1w.lta
--warp T2w_reg.nii.gz --cost ROBENT --entradius 2 --entcorrection --satit
--iscale

This works extremely well -- much better than FLIRT. (I'm using this
registration to do some preprocessing before running recon-all, so
unfortunately bbregister is not an option).

But, it takes *forever*. (My runtimes are about 90 minutes using OMP
parallelization with 24 cores, or about 16 hours running in serial).

I'm interested in playing with the various options to see if I can get a
suitable registration with a faster runtime. But it's not obvious to me how
I should fiddle with the knobs to get started. For example, would
increasing or decreasing `entradius` be expected to make things go faster?
Also, I am acquiring the images in the same session, back to back, so I can
assume that the images start off with a pretty good (but not exact)
registration. Is there a way to use that assumption to speed things up?

Thanks,
Michael
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[Freesurfer] Direction of bbregister transformation

[Michael Waskom]

Hi Freesurfers,

I have a question about the direction of the transformation written out to
the register.dat file by bbregister.

I have looked at the fscoordinates powerpoint presentation, which I think
is telling me that this matrix actually maps from the orig.mgz RAS
coordinates to the functional RAS coordinates. That agrees with the results
I get when I try to use the matrix outside of Freesurfer. However, this is
a little surprising, because I think of the bbregister process as aligning
the functional (moving) with the anatomy (target) so I would have expected
the transform matrix to represent that mapping.

Can you please confirm whether my understanding of the fscoordinates
presentation is correct, or help me out if I am off base?

Thanks!
Michael
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[Freesurfer] Correct/best way to find the midthickness surface

[Michael Waskom]

Hi Freesurfers,

I have seen at least three ways for identifying an intermediate surface
between the white and pial surfaces:

- Multiply the surface normal vector for each white surface vertex by half
of the cortical thickness and add it to each vertex coordinate
- Average the white and pial coordinates for each vertex
- Use mris_expand, e.g. `mris_expand -thickness lh.smoothwm 0.5 lh.graymid`

I have found that these approaches all give similar, but not identical
results.

Is there a consensus that one approach is best relative to the others?

Thanks,
Michael
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Re: [Freesurfer] Visualising regional values on the surface

[Michael Waskom]

Hi Kirstie,

Nibabel has a write_annot function that should work:
http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot

Best,
Michael

On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker <kw...@cam.ac.uk> wrote:

> Thank you Michael! I <3 Pysurfer.
>
> (and freesurfer of course!)
>
> The *real* goal is to integrate the code that I've written as a wrapper
> around pysurfer to show regional values (exactly as you suggest) with
> BrainNet <https://www.nitrc.org/projects/bnv/> which can show the network
> nicely on top of freesurfer files.
>
> Here's the wiki for my pysurfer wrapper:
> https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer
>
> And the code itself
> https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py
>
> Unfortunately I don't use BrainNet so I'm having difficulty helping my lab
> mate make his pretty plots of network nodes and edges overlayed on top of
> surface colors (eg: modular partition)!
>
> Is there a way of writing out an annot file from pysurfer into freesurfer
> format? Maybe that would bring the two packages closer together
>
> Kx
>
>
>
>
>
> On 29 March 2016 at 16:29, Michael Waskom <mwas...@stanford.edu> wrote:
>
>> Hi Kirstie,
>>
>> Here's an example of how to do this in PySurfer:
>> http://pysurfer.github.io/examples/plot_parc_values.html
>>
>> Hope that helps,
>> Michael
>>
>> On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwake...@gmail.com> wrote:
>>
>>> Hi Kirstie,
>>>
>>> You could write your own CLUT file with the color corresponding to the
>>> correlation you want to show?
>>> Just open up the file and play with the values in the color columns.
>>> Then simply load the color table in Freeview and use it to visualize
>>> the annotation.
>>>
>>> There are of course other ways, but this is probably the quickest.
>>>
>>> hth
>>> d
>>>
>>>
>>> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw...@cam.ac.uk>
>>> wrote:
>>> > Hi,
>>> >
>>> > I'd like to show correlation coefficients by region on the brain
>>> surface. So
>>> > for example, if I've calculated a modular decomposition in a network
>>> > analysis for each region of the D-K atlas I'd like to be able to color
>>> each
>>> > atlas region according to the module it has been assigned to.
>>> >
>>> > It seems like I have to do something with the ?h.aparc.annot files and
>>> a
>>> > colour lookup table but I'm not sure exactly what.
>>> >
>>> > Thank you!
>>> > Kx
>>> >
>>> > --
>>> > Kirstie Whitaker, PhD
>>> > Research Associate
>>> >
>>> > Department of Psychiatry
>>> > University of Cambridge
>>> >
>>> > Mailing Address
>>> > Brain Mapping Unit
>>> > Department of Psychiatry
>>> > Sir William Hardy Building
>>> > Downing Street
>>> > Cambridge CB2 3EB
>>> >
>>> > Phone: +44 7583 535 307
>>> > Website: www.kirstiewhitaker.com
>>> >
>>> > ___
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>>> >
>>> >
>>> > The information in this e-mail is intended only for the person to whom
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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
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>>> > 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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Re: [Freesurfer] Visualising regional values on the surface

[Michael Waskom]

Hi Kirstie,

Here's an example of how to do this in PySurfer:
http://pysurfer.github.io/examples/plot_parc_values.html

Hope that helps,
Michael

On Tue, Mar 29, 2016 at 8:08 AM, dgw  wrote:

> Hi Kirstie,
>
> You could write your own CLUT file with the color corresponding to the
> correlation you want to show?
> Just open up the file and play with the values in the color columns.
> Then simply load the color table in Freeview and use it to visualize
> the annotation.
>
> There are of course other ways, but this is probably the quickest.
>
> hth
> d
>
>
> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker 
> wrote:
> > Hi,
> >
> > I'd like to show correlation coefficients by region on the brain
> surface. So
> > for example, if I've calculated a modular decomposition in a network
> > analysis for each region of the D-K atlas I'd like to be able to color
> each
> > atlas region according to the module it has been assigned to.
> >
> > It seems like I have to do something with the ?h.aparc.annot files and a
> > colour lookup table but I'm not sure exactly what.
> >
> > Thank you!
> > Kx
> >
> > --
> > Kirstie Whitaker, PhD
> > Research Associate
> >
> > Department of Psychiatry
> > University of Cambridge
> >
> > Mailing Address
> > Brain Mapping Unit
> > Department of Psychiatry
> > Sir William Hardy Building
> > Downing Street
> > Cambridge CB2 3EB
> >
> > Phone: +44 7583 535 307
> > Website: www.kirstiewhitaker.com
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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> 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] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[Michael Waskom]

Hi,

Can you say a bit more about what you mean?

> If my memory serves, as you go to higher resolutions you end up with
multiple points being mapped to the same location,

Do you mean multiple icosahedron vertices being mapped to the same native
mesh vertex, or the other way around?

In any case, the issue here is a little bit different, in that it is just
raised when trying to generate a color table for the annotation:
https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540

Michael

On Fri, Mar 25, 2016 at 11:27 AM, dgw <dgwake...@gmail.com> wrote:

> Hi Michael,
>
> I think this is a problem that crops up periodically for us in the
> MEEG world, where we use these downsampling
> as calculated in MNE. If my memory serves, as you go to higher
> resolutions you end up with multiple points
> being mapped to the same location, which I don't believe we have ever
> found a solution to. Note, this can even happen
> at ico 5 (particularly on smaller brains).
>
>
> hth
> d
>
> On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom <mwas...@stanford.edu>
> wrote:
> > Hi Freesurfers,
> >
> > I'd like to use mris_make_face_parcellation to downsample an individual
> > subject's surface mesh to a resolution similar to fsaverage6.
> >
> > My understanding is that mris_make_face_parcellation should let me do
> this,
> > and it does what I expect with ic3-5. However when I run it with ic6 as
> the
> > target, it fails:
> >
> > [surf]$ mris_make_face_parcellation lh.sphere
> > $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
> > Reading lh.sphere
> > Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
> > parcellating hemisphere into 40962 units
> > INFO: CTABunique() could not find a unique set in 10 tries
> > INFO: CTABunique() could not find a unique set in 100 tries
> > ERROR: could not find a unique color table
> >
> > I don't really care if the colors themselves are distinct, and it should
> be
> > possible to just programmatically generate a valid color table (since
> 255 ^
> > 3 > 40962). I thought that providing a colortable with unique values
> through
> > the -ctab option might work, but looking at the source code it seems that
> > option will *write* a colortable, not read one.
> >
> > So, is there any way to accomplish the downsampling I want?
> >
> > Thanks in advance,
> > Michael
> >
> > ___
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> >
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[Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[Michael Waskom]

Hi Freesurfers,

I'd like to use mris_make_face_parcellation to downsample an individual
subject's surface mesh to a resolution similar to fsaverage6.

My understanding is that mris_make_face_parcellation should let me do this,
and it does what I expect with ic3-5. However when I run it with ic6 as the
target, it fails:

[surf]$ mris_make_face_parcellation lh.sphere
$FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
Reading lh.sphere
Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
parcellating hemisphere into 40962 units
INFO: CTABunique() could not find a unique set in 10 tries
INFO: CTABunique() could not find a unique set in 100 tries
ERROR: could not find a unique color table

I don't really care if the colors themselves are distinct, and it should be
possible to just programmatically generate a valid color table (since 255 ^
3 > 40962). I thought that providing a colortable with unique values
through the -ctab option might work, but looking at the source code it
seems that option will *write* a colortable, not read one.

So, is there any way to accomplish the downsampling I want?

Thanks in advance,
Michael
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[Freesurfer] Announcing PySurfer version 0.6

[Michael Waskom]

Hello everyone,

We are pleased to announce the 0.6 release of PySurfer
http://pysurfer.github.io/, a Python library for visualizing MRI and MEG
data.

Changes in this version include:

- Simplified the selection of parameters that customize the visualization
- Enhanced plotting of Freesurfer morphometry overlays (thickness,
curvature, etc.)
- Enhanced plotting of statistical overlays using contour maps
- Improved support for scripted animation of the brain visualization

See the release notes https://github.com/nipy/PySurfer/releases/tag/0.6
for more details about these changes.

For information on installation, documentation, and the example gallery,
you can visit our website (http://pysurfer.github.com/).

We hope you will find it useful in your research!

Michael Waskom, Eric Larson, Christian Brodbeck, and the rest of the Nipy
team
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Re: [Freesurfer] mri_label2label problem revisited

[Michael Waskom]

Hi Bruce,

Not the same Michael but I see this all the time with 5.3.

Interestingly, transforming annotations using mri_surf2surf does not run
into the issue — perhaps that is what you're thinking of?

Best,
Michael

On Tue, Jun 23, 2015 at 8:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Michael

 what version are you using? I thought this was fixed long ago

 cheers
 Bruce

 On Tue, 16 Jun 2015, Michael Kranz wrote:

  Hi guys,
 I have created a custom surface label in the fsaverage template. I then
 used
 mri_label2label to map onto an individual subject. Despite the fsaverage
 label looking ok, the label mapped onto the individual subject is not as
 the
 label is spotty and has holes. On the free surfer archive it seems
 that
 some people have had this problem and described it as eroded  or
 islands(see
 https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.h
 tml), but it wasn't clear to me that this issue has been solved.

 The above link recommended using one of the predefined labels to see if
 the
 problem persisted. I used rh.BA45.label and there was were no problems.

 I also used mri_surfcluster (as was done in the above link) to make my
 label. Below is the 1.) command 2.) the fsaverage label in tksurfer 3.) a
 pic of the same label mapped onto a subject in tksurfer

 Do you have an idea of what the issue is? Let me know if you need more
 info!

 mri_label2label \
--srcsubject fsaverage \
--srclabel ${srclabelpwd}/${rhROI} \
--trgsubject $subbase \
--trglabel ${SUBJECTS_DIR}/${subbase}/label/${rhROI} \
--hemi rh \
--regmethod surface


 Inline image 1

 Inline image 2








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Re: [Freesurfer] Taking a measure of cluster width and length on flat surface

[Michael Waskom]

Hi Bruce,

Is there some way to know when cuts have been made correctly so that
distortion can be minimized? (Or conversely, some way to know when a given
patch has or will undergo too much distortion during flattening?

Thanks!
Michael

On Mon, May 11, 2015 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Sarah

 the unfolding tries very hard to preserve exactly this - the metric
 properties. If you cut off the occipital third of cortex and flatten it
 (after introducing some cut along the axis of the cone) you should be
 able to get to around 10% distortion or below, which I assume is good
 enough.

 cheers
 Bruce



 On Mon, 11 May 2015, Sarah Finnegan wrote:

  Dear all,
 I am looking to take two measures within the visual cortex.
 1) A measure of width and length for each activation cluster overlaid onto
 the flattened cortical surface.
 2) A measure of spacing between each cluster

 I can find how to take measures of area but I specifically want to know
 the
 width and length separately to correlate this to potential stripe
 systems.
 My plan was to fit an oval to each of these clusters and measure length
 through the cardinal axis and width through the minor, spacing would be
 calculated from a line fit to the minor axis of each cluster.
 Unfortunately
 I think the unfolding process will have changed the spacing relationships
 between clusters to make this inappropriate.

 I wonder if there is a command or established pipeline to take such
 measures?

 Thanks for your help!
 Sarah


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Re: [Freesurfer] Generate patch files outside of tksurfer

[Michael Waskom]

Perfect. Thanks Bruce!

On Thu, Apr 23, 2015 at 6:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Michael

 you can use label2patch for this.

 cheers
 Bruce
 On Wed, 22 Apr 2015, Michael Waskom wrote:

  Hi Freesurfers,
  Is there a way to generate patch files from surfaces outside of
 tksurfer? I'm specifically
  hoping that there is some tool that will allow me to use a label file to
 define the part of
  the surface I want to keep as a patch.
 
  Thanks!
  Michael
 
 
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[Freesurfer] Generate patch files outside of tksurfer

[Michael Waskom]

Hi Freesurfers,

Is there a way to generate patch files from surfaces outside of tksurfer?
I'm specifically hoping that there is some tool that will allow me to use a
label file to define the part of the surface I want to keep as a patch.

Thanks!
Michael
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[Freesurfer] Announcing PySurfer version 0.5

[Michael Waskom]

Hello everyone,

We are pleased to announce the release of PySurfer
http://pysurfer.github.io/ version 0.5.

PySurfer is a Python library for making beautiful and reproducible
visualizations of Freesurfer data.

Changes in this version include

- The statistical overlay functions can now use a wider variety of
colormaps, with any matplotlib colormap
http://matplotlib.org/examples/color/colormaps_reference.html (including
the _r reversed versions) accepted.
- Surface normals are used when rendering the cortex for a smoother
visualization.
- Changed the default colormap for some functions to more perceptually
appropriate options.
- Added control over the width of label and annotation borders.
- Added 2D grids of images when saving a montage.

Additionally, we have substantially improved the docs with a new example
gallery http://pysurfer.github.io/examples/index.html and an updated
installation
guide http://pysurfer.github.io/install.html describing how to get over
some hurdles that can be encountered on OSX.

To install or upgrade, just run:

pip install -U pysurfer

We hope you find it useful. As always, contributions, suggestions, and bug
reports are welcome on our github page https://github.com/nipy/PySurfer/.

- PySurfer Devs
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[Freesurfer] mri_cvs_register failure from missing shared lib

[Michael Waskom]

Hi, I had mri_cvs_register die on me when it couldn't find a shared
library. Relevant bit is (full log is attached):

mris_resample: error while loading shared libraries:
libboost_program_options.so.5: cannot open shared object file: No such file
or directory

Freesurfer bugr info:



FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago)

Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64

--

Any thoughts on how to proceed? Thanks!

Michael


cvs_register.log
Description: Binary data
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[Freesurfer] Easy automated workflow for separating non-contiguous labels

[Michael Waskom]

Hi Freesurfers,

Some of the Freesurfer annotations (specifically the Yeo atlases) have
multiple disconnected regions with the same label.

What's the best way to separate these annotations (or the labels produced
by mri_annotation2label) so that I can get multiple label files where each
label has all contiguous vertices? In other words, I want to do something
like a clustering procedure, and I'd like to stay on the surface.

Can this be done (easily)?

Thanks
Michael
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[Freesurfer] Seg fault with mri_segstats?

[Michael Waskom]

Hi Doug,

I'm running into a strange seg fault when trying to use mri_segstats (it's
actually ocurring within mri_glmfit-sim, but I can reproduce it manually)

This is the line that fails (stripping the leading paths for readability):

mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0  --i
concat_output.nii.gz  --sum mri_glmfit-sim.junk.84357  --avgwf
cache.th20.pos.y.ocn.dat

With the log:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg
/Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh
--exclude 0 --i
/Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz
--sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat
sysname  Darwin
hostname ben-octocore.stanford.edu
machine  i386
user mwaskom
UseRobust  0
Loading
/Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh
Loading
/Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   5 segmentations
Computing statistics for each segmentation
  1 1  10934   10934.000
  2 2   24092409.000
  3 3   16201620.000
  4 4   20442044.000

Reporting on   4 segmentations
Computing spatial average of each frame
  0  1  2  3Segmentation fault


Intriguingly, it does not segfault if I remove the --avgwf parameter OR the
--exclude 0 parameter. It does segfault if I use --avgwfvol instead of
--avgwf

I'm not too sure what's going on, I can otherwise read the segmentation
file and --y file and do statistical operations on them, and I can write
other files to the directory I'm testing this in.

Here's my system info:

FREESURFER_HOME: /usr/local/freesurfer/5.3.0

Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0

Kernel info: Darwin 10.8.0 i386

Any thoughts?

Michael
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Re: [Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

Hi, quick question

I'm just going to rerun these without the -T2 stuff for now so I can get
going on analysis.

What stages of recon-all do I have to run to fix everything the -T2pial
mishap broke? The process flow tables on the website seem a bit out of date.

mw


On Sat, Sep 28, 2013 at 3:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 hmmm, maybe Nick or Doug can investigate, although we are crazy busy at
 the moment

 On Sat, 28 Sep 2013, Michael Waskom wrote:


 On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 
 wrote:
   hmmm. That would be strange and would result in complete failure


 I agree, but

 $ grep bbregister recon_log_withT2.txt
 $ grep fslregister recon_log_withT2.txt

 both turn up empty





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Re: [Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 hmmm. That would be strange and would result in complete failure


I agree, but

$ grep bbregister recon_log_withT2.txt
$ grep fslregister recon_log_withT2.txt

both turn up empty
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[Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

Hi,

I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the
pial mesh.

However, I've found that using the T2 is causing rather dramatic problems
with the pial surface.

I processed the same subject's data with and without the -T2pial option.
Here are links to a) pial surface image b) slices through the volume and c)
the recon-all.log:

With -T2pial

https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt

Without -T2pial

https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt

The release notes for 5.3 claim that the T2 is registered to the T1 before
refining the surface, but I actually can't find any evidence of that
sequence in the log file. For this subject, the T1 and T2 came from
different scan sessions, although I have other data where they were
acquired in the same session that have similar, if less dramatic, problems
with the pial surface.

Any ideas?

Michael
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Re: [Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the pial surface from the -T2pial run in red
and the pial surface from the normal run in cyan:
https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png


On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.eduwrote:

 Hi,

 I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the
 pial mesh.

 However, I've found that using the T2 is causing rather dramatic problems
 with the pial surface.

 I processed the same subject's data with and without the -T2pial option.
 Here are links to a) pial surface image b) slices through the volume and c)
 the recon-all.log:

 With -T2pial
 
 https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
 https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
 https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt

 Without -T2pial
 
 https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
 https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
 https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt

 The release notes for 5.3 claim that the T2 is registered to the T1 before
 refining the surface, but I actually can't find any evidence of that
 sequence in the log file. For this subject, the T1 and T2 came from
 different scan sessions, although I have other data where they were
 acquired in the same session that have similar, if less dramatic, problems
 with the pial surface.

 Any ideas?

 Michael

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Re: [Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

Hi Matt,

It's this sequence:
http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)

You can click the console screenshots for a closer view of the parameters
-- let me know if you need me to track down more info.

mw


On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote:

 Someone sent me a different kind of T2w image and it didn't work so well,
 so we need to know what kind of image this is.

 Peace,

 Matt.

 On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 nope, pretty much only with T2-space with and without a flair pulse
 On Fri,
 27 Sep 2013, Matt Glasser wrote:
 
  Also, what kind of T2w sequence is this?  I think we've mostly tested it
  with the T2-SPACE (unless Bruce has tested with other things).
 
  Peace,
 
  Matt.
 
  On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
  Hi Michael
 
  that looks pretty bad! What is the resolution of the T2? The T1 that
 you
  overlay on also looks somewhat blurry - what was it?
 
  Bruce
 
 
  On Fri, 27 Sep
  2013, Michael Waskom wrote:
 
  Hi, just to make the problem a bit more transparent, I took a second
  screenshot of the slices with the pial surface from the -T2pial run in
  red
  and the pial surface from the normal run in
  cyan:
 https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
 
  On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
 mwas...@stanford.edu
  wrote:
Hi,
  I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
  the pial mesh.
 
  However, I've found that using the T2 is causing rather dramatic
  problems with the pial surface.
 
  I processed the same subject's data with and without the -T2pial
  option. Here are links to a) pial surface image b) slices through the
  volume and c) the recon-all.log:
 
  With -T2pial
  
  https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
  https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
  https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
 
  Without -T2pial
  
  https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
  https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
  https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
 
  The release notes for 5.3 claim that the T2 is registered to the T1
  before refining the surface, but I actually can't find any evidence of
  that sequence in the log file. For this subject, the T1 and T2 came
  from different scan sessions, although I have other data where they
  were acquired in the same session that have similar, if less dramatic,
  problems with the pial surface.
 
  Any ideas?
 
  Michael
 
 
 
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Re: [Freesurfer] Major problems with T2-based pial removal

[Michael Waskom]

Hmm, Ok. Thanks Matt.

I still think it's weird that the T2 didn't seem to ever get registered to
the FS volume, but it's not a huge loss if we can't use them. With that
said, it might help to clarify the docs on this point a bit, as it sort of
sounded like any reasonably-sized T2-weighted image would be useful, and I
would have tried to collect a different image if I had known!


On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote:

 So the T2-SPACE is a variable flip angle sequence that actually has a fair
 amount of T1 and MT contrast in it and relatively less T2 contrast.  As a
 result, you can clearly see the difference between grey and white matter,
 and CSF is not massively brighter than grey and white matter.  If you are
 using a different kind of T2w sequence where the distance between CSF
 intensity and grey matter intensity is much greater, some of the internal
 settings to the -T2pial flag will likely not be optimal.  I don't know if
 recon-all allows you to modify those with expert options or not.  Bruce, is
 it possible for the user to modify the –nsigma_above and -nsigma_below
 flags for mris_make_surfaces when using -T2pial?

 Peace,

 Matt.

 From: Michael Waskom mwas...@stanford.edu
 Date: Friday, September 27, 2013 2:20 PM
 To: Matt Glasser m...@ma-tea.com
 Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, 
 Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Major problems with T2-based pial removal

 Hi Matt,

 It's this sequence:
 http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2)

 You can click the console screenshots for a closer view of the parameters
 -- let me know if you need me to track down more info.

 mw


 On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote:

 Someone sent me a different kind of T2w image and it didn't work so well,
 so we need to know what kind of image this is.

 Peace,

 Matt.

 On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 nope, pretty much only with T2-space with and without a flair pulse
 On Fri,
 27 Sep 2013, Matt Glasser wrote:
 
  Also, what kind of T2w sequence is this?  I think we've mostly tested
 it
  with the T2-SPACE (unless Bruce has tested with other things).
 
  Peace,
 
  Matt.
 
  On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
  Hi Michael
 
  that looks pretty bad! What is the resolution of the T2? The T1 that
 you
  overlay on also looks somewhat blurry - what was it?
 
  Bruce
 
 
  On Fri, 27 Sep
  2013, Michael Waskom wrote:
 
  Hi, just to make the problem a bit more transparent, I took a second
  screenshot of the slices with the pial surface from the -T2pial run
 in
  red
  and the pial surface from the normal run in
  cyan:
 https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png
 
  On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom
 mwas...@stanford.edu
  wrote:
Hi,
  I'm using FS 5.3 and trying to use hires T2-weighted scans to refine
  the pial mesh.
 
  However, I've found that using the T2 is causing rather dramatic
  problems with the pial surface.
 
  I processed the same subject's data with and without the -T2pial
  option. Here are links to a) pial surface image b) slices through the
  volume and c) the recon-all.log:
 
  With -T2pial
  
  https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png
  https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png
  https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt
 
  Without -T2pial
  
  https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png
  https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png
  https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt
 
  The release notes for 5.3 claim that the T2 is registered to the T1
  before refining the surface, but I actually can't find any evidence
 of
  that sequence in the log file. For this subject, the T1 and T2 came
  from different scan sessions, although I have other data where they
  were acquired in the same session that have similar, if less
 dramatic,
  problems with the pial surface.
 
  Any ideas?
 
  Michael
 
 
 
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[Freesurfer] Morphological operations on surface labels

[Michael Waskom]

Hi,

Are there any utilities for performing basic morphological operations on
surface-based label files buried somewhere within Freesurfer? Specifically
I am hoping to perform a closing.

Thanks!
mw
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Re: [Freesurfer] Morphological operations on surface labels

[Michael Waskom]

Thanks Jürgen. From the help it looks like this operates in the volume, and
-l just constrains the operations to a label. Does it work on surface
meshes too?


On Sat, Jun 8, 2013 at 11:58 PM, Jürgen Hänggi j.haen...@psychologie.uzh.ch
 wrote:

  Hi Michael

 Try mri_morphology with the –l option. It can do closing.

 Cheers
 Jürgen



 On [DATE], Michael Waskom [ADDRESS] wrote:

 Hi,

 Are there any utilities for performing basic morphological operations on
 surface-based label files buried somewhere within Freesurfer? Specifically
 I am hoping to perform a closing.

 Thanks!
 mw

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Re: [Freesurfer] Morphological operations on surface labels

[Michael Waskom]

Hi Bruce

Dev version as in post 5.3?  I'd prefer to avoid tksurfer as I'd like to do
this programmatically for a large number of subjects and labels.

mw


On Sun, Jun 9, 2013 at 5:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Michael

 you can do this in the tksurfer gui (label-open/close/dilate/**erode) or
 in a tcl script (labl_open, )

 I think I also put it in the newest version of mri_label2label but it's
 probably only in dev (which we could give you if you want).

 cheers
 Bruce



 On Sun, 9 Jun 2013, Michael Waskom wrote:

  Thanks Jürgen. From the help it looks like this operates in the volume,
 and
 -l just constrains the operations to a label. Does it work on surface
 meshes
 too?


 On Sat, Jun 8, 2013 at 11:58 PM, Jürgen Hänggi
 j.haen...@psychologie.uzh.ch wrote:
   Hi Michael

   Try mri_morphology with the –l option. It can do closing.

   Cheers
   Jürgen


   On [DATE], Michael Waskom [ADDRESS] wrote:

   Hi,

   Are there any utilities for performing basic morphological
   operations on surface-based label files buried somewhere
   within Freesurfer? Specifically I am hoping to perform a
   closing.

   Thanks!
   mw

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Re: [Freesurfer] FDR Correction of NHP Surface Data

[Michael Waskom]

Hi Clark,

If you're loading the data into Python anyway to use with PySurfer, Nipy
seems to have some utilities to do an FDR correction
(docshttp://nipy.sourceforge.net/nipy/stable/api/generated/nipy.algorithms.statistics.empirical_pvalue.html
/sourcehttps://github.com/nipy/nipy/blob/master/nipy/algorithms/statistics/empirical_pvalue.py).
I've never used these, but they look pretty straightforward.

Also it looks like FDR is built into mri_surfcluster.

Best,
Michael

On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher
cfis...@mail.rockefeller.eduwrote:

 Hi Sebastian,

 I think you are right, both about tksurfer thresholding and the correct
 interpretation of FDR. As you point out though, there is some value in
 having maps that show how relatively well different points on the surface
 fit your model.

 At the very least, is there any way to automate the retrieving of the
 threshold that tksurfer provides? I'd still also be interested in some
 adjustment to the whole map, if there's a way to do that as well.

 I could probably find a way to do this in Matlab, but I trust the
 bug-squishing abilities of the freesurfer community more than I trust my
 own.

 -Clark


 On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:

  Hi Clark,
 
 
  On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
 
  Hi Bruce,
 
  Thanks.  I actually have used this function of tksurfer, but am looking
 for a way to save the corrected maps, so that they could be manipulated by
 other tools (for instance, viewed by PySurfer).
 
Does it really correct the map? I thought all it does is figure
 out the corrected threshold. By the way, if I understand correctly, FDR
 maps should be considered to be binary, that is you really do not know
 which voxels might be false positives, so you should not interpret all
 voxels to be equally significant. Having said that, almost everybody I know
 still looks at the p-value spatial distribution when looking at those FDR
 thresholded maps… (then again, I do not know any statistician...)
 
 
  best
Sebastian
 
  I recognize that this may not be an officially supported functionality,
 but is there some way to save the adjusted overlays from tksurfer, or
 create them in some other way?
 
  Best,
  Clark
 
 
  On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
 
  Hi Clark
 
  you shouldn't need either. Load your overlays then click the button to
 compute the FDR threshold in the tksurfer configure overlay interface.
 
  cheers
  Bruce
  On Tue, 28 Aug 2012, Clark Fisher wrote:
 
  Ok, maybe I'm making this question too intricate. Here's the short
 version:
  How can I FDR correct painted surface significance maps when I have
 no talraich .xfm file and no cortical segmentation?
  Thanks again,
  Clark
  Hi Freesurfers,
  I have another monkey-specific question.  I'd like to output
 FDR-corrected signficance surface maps for my monkey data, or at least
 FDR-threshold the maps.  It seems like mri_surfcluster might be one way to
 go about this however:
   1) I don't have any .xfm files for my monkeys, as I'm working in
 native space, and
   2) Without segmentation, I don't have a good mask to use for the
 cortex only. My first attempts at work-arounds would be:
   1)Try to create an identity .xfm file
   2)Use the cortical ribbons from mris_volmask as a cortex mask
  Should these work?  If so, how should I make an identity .xfm file?
  If not, is there another way to FDR correct my surface data?
  Thanks,
  Clark
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Re: [Freesurfer] Splotchy labels after transformation from fsaverage to native

[Michael Waskom]

Hi, just wanted to bump this up since it looks like Doug is back.

On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom mwas...@stanford.eduwrote:

 Hi,

 I'm using mri_label2label to reverse normalize labels from fsaverage
 space to the native surface.

 I'm ending up with some splotchy-looking labels, for lack of a better
 word.  See what I mean here:
 http://web.mit.edu/mwaskom/www/splotchy.png

 I'm doing this normalization in a script with the following relevant
 line, which seems to be what happens inthe BAlabes step of recon-all

 mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
 --srcsubject fsaverage --trgsubject ${subj} \
 --trglabel label/$hemi.${roi}.label \
 --regmethod surface --hemi $hemi

 Any idea how I can avoid this splotchiness or, failing that, do a
 closing on the label to clean up some of the noise?

 Cheers,
 Michael

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Re: [Freesurfer] Splotchy labels after transformation from fsaverage to native

[Michael Waskom]

Hmm, ok.  Are there no functions for doing a dilation/erosion on a surface
label?

On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 There is not an easy/good way to handle this situation. The way it works
 is that it goes through each point in the source and finds the closest
 vertex in the target. If the target is more densely sampled, then there
 are some points in the target in the middle of the label that are not
 the closest vertex to any label vertex in the source. It is hard to
 figure out computationally whether an unlabeled point is in the middle
 of the label or halfway around the brain. One thing that might work ok
 is to save the output as a binary mask (--outmask), then smooth it a
 little (mris_fwhm  or mri_surf2surf), then re-binarize the mask
 (mri_binarize), then convert it to a label  (mri_cor2label --i
 smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white --o
 lh.label.yoursubject).

 doug

 On 07/16/2012 03:30 PM, Michael Waskom wrote:
  Hi, just wanted to bump this up since it looks like Doug is back.
 
  On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom mwas...@stanford.edu
  mailto:mwas...@stanford.edu wrote:
 
  Hi,
 
  I'm using mri_label2label to reverse normalize labels from fsaverage
  space to the native surface.
 
  I'm ending up with some splotchy-looking labels, for lack of a better
  word.  See what I mean here:
  http://web.mit.edu/mwaskom/www/splotchy.png
 
  I'm doing this normalization in a script with the following relevant
  line, which seems to be what happens inthe BAlabes step of recon-all
 
  mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
  --srcsubject fsaverage --trgsubject ${subj} \
  --trglabel label/$hemi.${roi}.label \
  --regmethod surface --hemi $hemi
 
  Any idea how I can avoid this splotchiness or, failing that, do a
  closing on the label to clean up some of the noise?
 
  Cheers,
  Michael
 
 
 
 
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[Freesurfer] Splotchy labels after transformation from fsaverage to native

[Michael Waskom]

Hi,

I'm using mri_label2label to reverse normalize labels from fsaverage
space to the native surface.

I'm ending up with some splotchy-looking labels, for lack of a better
word.  See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png

I'm doing this normalization in a script with the following relevant
line, which seems to be what happens inthe BAlabes step of recon-all

mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
--srcsubject fsaverage --trgsubject ${subj} \
--trglabel label/$hemi.${roi}.label \
--regmethod surface --hemi $hemi

Any idea how I can avoid this splotchiness or, failing that, do a
closing on the label to clean up some of the noise?

Cheers,
Michael
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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Michael Waskom]

Oops i just realized I only sent this to Bruce:

Thanks!  It looks like this involves some manual intervention.  Matt., I
assume you're not manually making control points on 1000s of subjects (I
imagine this is for the human connectcome project).  Is your code public
somewhere?

Cheers,
Michael

On Tue, May 15, 2012 at 7:36 PM, Michael Waskom mwas...@stanford.eduwrote:

 Thanks!  It looks like this involves some manual intervention.  Matt., I
 assume you're not manually making control points on 1000s of subjects (I
 imagine this is for the human connectcome project).  Is your code public
 somewhere?

 Cheers,
 Michael


 On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl 
 fis...@nmr.mgh.harvard.eduwrote:

 sure, here's mine. Matt's is probably a lot more polished as they intend
 to run it on hundreds or thousands of subjects

 On Tue, 15 May 2012, Michael Waskom wrote:

  Hi Bruce,
 Sounds cool, I'd be very interested in checking out the script.

 Cheers,
 Michael

 On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edu
 wrote:
  you need to call mris_make_surfaces directly. It's a bit
  complicated as you need to intensity normalize and register the
  hires volume to the surfaces first. I have an example script if
  anyone is interested, but no one has used it yet but me I don't
  think (unless Matt Glasser has gotten his version working, which
  on second thought he probably has)

  On Mon, 14 May 2012, Michael Waskom wrote:

Hi Bruce,
Is there a flag for this on recon-all?  Or do you
need to use
mri_make_surfaces directly?

Best,
Michael

On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
wrote:
 Hi Joshua

 yes, we already have upgraded
mris_make_surfaces to take higher
 res data
 and refine the surfaces with it. Haven't tried
it on the aseg
 yet, but if
 you upload a sample dataset I could see how
hard it is.

 cheers
 Bruce
 On Mon, 14 May 2012,
 Joshua Lee wrote:

  Dear Freesurfers,
 
  Over the last years, MR imaging technology
hasimproved such
 that sub 1-mm
  isotropic scans can be obtained with good
signal to noise
 characteristics.
  For example, our lab uses 0.7mm isotropic
structural MR
 images. I understand
  that the Freesurfer pipeline will up-sample
these to 1mm
 isotropic, but it
  seems a shame that so much information is
left unused which
 could be used to
  improve the accuracy of sub-cortical and
cortical
 segmentation. My question
  is whether there are any plans at Freesurfer
to change the
 reference
  standard resolution from 1mm isotropic, or
provide another
 solution that can
  help researchers make the most of your
technology.
 
  Sincerely,
 
 
  Joshua
  -
  Joshua
 
 
 
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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Michael Waskom]

Hi Bruce,

Is there a flag for this on recon-all?  Or do you need to use
mri_make_surfaces directly?

Best,
Michael

On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Joshua

 yes, we already have upgraded mris_make_surfaces to take higher res data
 and refine the surfaces with it. Haven't tried it on the aseg yet, but if
 you upload a sample dataset I could see how hard it is.

 cheers
 Bruce
 On Mon, 14 May 2012,
 Joshua Lee wrote:

  Dear Freesurfers,
 
  Over the last years, MR imaging technology hasimproved such that sub 1-mm
  isotropic scans can be obtained with good signal to noise
 characteristics.
  For example, our lab uses 0.7mm isotropic structural MR images. I
 understand
  that the Freesurfer pipeline will up-sample these to 1mm isotropic, but
 it
  seems a shame that so much information is left unused which could be
 used to
  improve the accuracy of sub-cortical and cortical segmentation. My
 question
  is whether there are any plans at Freesurfer to change the reference
  standard resolution from 1mm isotropic, or provide another solution that
 can
  help researchers make the most of your technology.
 
  Sincerely,
 
 
  Joshua
  -
  Joshua
 
 
 
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Re: [Freesurfer] load multiple overlays with different colors

[Michael Waskom]

Hi,

If you're somewhat handy with Python, you can use PySurfer for this.
See this example:
http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html

Best,
Michael

On Wed, May 2, 2012 at 7:51 AM, keepmoon keepmoon1...@googlemail.com wrote:
 Dear all,

 I search my question before I post it. I did find similar questions, but
 didn't find answer. I want to overlay two files with different colors. For
 example, one is sig1.mgh from cortical thickness, the other is sig2.mgh from
 area. I want to use tksurfer overlaying them with three colors: red is
 significant regions of thickness; blue is significant regions of area; green
 is overlap significant regions of thickness and area.

 I tried to use the following command:

 tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay
 sig1.mgh  -overlay sig2.mgh

 It just can display sig1.mgh or sig2.mgh, but can't display two together. In
 addition, I don't know how to control overlap and other regions color.

 Anyone knows how to do this?

 Any help will be appreciated!

 Thanks in advance!

 Kathy

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[Freesurfer] Announcing Release of PySurfer 0.3

[Michael Waskom]

Dear All,

We are pleased to announce the 0.3 release of PySurfer, a Python-based
package for visualizing Freesurfer data. This release includes bugfixes and
quite a few enhancements, including:

- Tools for reading and manipulating MEG data from MNE (thanks to work from
Martin Luessi and Alex Gramfort)
- The ability to visualize 4D (containing a dimension for time, etc.) data,
with a lightweight GUI interface
- A convenience function to project volume data in one step (currently a
wrapper around mri_vol2surf)
- Increased flexibility in controlling the appearance of overlay data,
labels, foci, and the scene itself
 - Five new example scripts, with additions to existing scripts,
demonstrating these enhancements
- A variety of minor improvements here and there

Please see our website (http://pysurfer.github.com/) for information on
installation, documentation, and the example gallery.

We hope you find it useful in your research!

Michael Waskom and the Nipy team
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Re: [Freesurfer] mri_segstats output

[Michael Waskom]

Hi Marco,

The columns correspond to the integer IDs in the --seg image, so assuming
you passed in a binary mask the first column is mean over everything that
isn't your ROI and the second column is the mean in your ROI.

Cheers,
Michael

On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia ma...@nmr.mgh.harvard.eduwrote:

 Dear all,

 Given a series of fsaverage-registered rCBF maps, I am trying to extract
 the average rCBF value from one specific region. This region, which was a
 significant cluster from a volumetric (fsl) analysis, was binarized and
 then converted to surface.

 When I run mri_segstats with the --avgwf I obtain two columns. Can you
 please remind me which one is the average extracted from that ROI, and
 what is the other column?

 Thanks!
 Marco




 mri_vol2surf --mov

 DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz
 --mni152reg --hemi rh --o

 /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz



 cd

 /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF

 for f in `ls *.mgz` ; do

 mri_segstats --seg $f --in

 /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh
 --avgwf $f_RH_nopaired_diff.txt
 done


 nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt 

 38.2811 47.6476
 40.3997 36.0856
 42.6304 46.2465
 44.4789 36.7066
 69.2376 51.4098
 66.0043 47.2098
 34.5957 40.3854
 36.8976 42.2028
 38.2475 35.875
 39.9503 37.0186
 35.1582 36.6949
 35.1924 38.874
 43.4415 36.2505
 43.3516 34.5041
 58.3073 50.3295
 61.8703 60.8415
 61.1754 51.3476
 47.9508 51.594
 51.5809 48.2985
 49.6545 50.974
 62.9431 72.1211
 54.0272 55.7234
 35.0701 34.5995
 37.9241 35.3844
 37.2277 42.3105
 38.2136 46.7896
 45.0951 51.9831
 45.4391 51.6242
 46.2971 47.5424
 44.3713 41.1725
 37.4132 36.1166
 36.7285 39.2947
 44.0285 46.501
 45.4698 50.5906
 51.0392 48.2324
 55.0885 50.9392
 66.7224 67.7807
 64.8932 68.5847
 45.5101 45.6065
 46.7002 45.232
 40.6324 48.9768
 44.3654 45.9017
 39.4908 32.8936
 39.5983 36.4909
 55.9295 59.1527
 55.6738 55.7016
 44.7433 50.9412
 42.6953 50.0857
 42.4522 48.7366
 43.5595 42.3424
 43.9283 36.5026
 41.9838 36.8662
 39.9873 44.505
 43.442 49.2243
 57.6304 55.5628
 53.3496 49.4215
 43.2505 42.5797
 43.5452 42.0694
 50.4555 47.993
 49.8977 49.6568
 41.5077 42.8473
 40.2357 42.3246
 40.3846 39.1473
 38.7073 41.502



 __

 Marco L. Loggia, PhD
 Postdoctoral Fellow, Mass General Hospital  Brigham and Women's Hospital
 Harvard Medical School

 Psychiatric Neuroimaging Research Program
 CNY Building 120, suite 100
 Charlestown, Massachusetts 02129
 Phone:  (617) 643-7267
 Fax:  (617) 643-7340
 ma...@nmr.mgh.harvard.edu
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Re: [Freesurfer] autmatic image with panel of hemisphere made by script

[Michael Waskom]

Hi,

On the off chance that you are comfortable with Python, you may find that
PySurfer http://pysurfer.github.com/ provides a more pleasant scripting
environment than the tcl-based TkSurfer interface :)

Best,
Michael

On Tue, Feb 7, 2012 at 12:46 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Hi Knut, you can check out my script called tksnap (uses accopanying
 mytks.tcl). It will take pics in different orientations. Note: this is
 not a supported script, so it's up to you to figure out what it does and
 how it does it. I provide it as a way to help you figure this stuff out.
 If you don't know csh and tcl, then it's not going to be much use to
 you. Good luck!
 doug

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksnap
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mytks.tcl


 Knut J Bjuland wrote:
  Hi Bruce
 
 
  Is it possible to use ascript to create a similar figure to the jpg
  file I am  attaching?
 
  Knut J
 
 
 
  On 07. feb. 2012 15:09, Bruce Fischl wrote:
  Hi Knut
 
  you can use  a tcl script in tksurfer if you want. You are probably
  better off doing the 10^-log(p) on your own and saving it as a
  separate overlay. There are plenty of tcl scripts in the distribution
  as examples. A simple one would be:
 
  set val $home/$subject/label/$hemi.your_overlay.mgz
  puts loading overlay $val
  sclv_read_binary_values sclv_current_field
  redraw
  save_tiff $odir/$hemi.your_overlay.lateral.tif
  rotate_brain_y 180
  redraw
  save_tiff $odir/$hemi.your_overlay.medial.tif
 
 
  put that in a file named something.tcl then load tksurfer with -tcl
  something.tcl
 
  I don't know about the 500dpi though, sorry.
 
  cheers
  Bruce
 
 
 
  On Tue, 7 Feb 2012, Knut J Bjuland wrote:
 
  I have used Tksurfer to make image from cross subject statistics
  maps in
  mgh files. Is it possible to use a script to make image with both
  hemisphere in lateral and medial view.  I would also like to display p
  values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How
  can
  I produce image with 500 dpi in tksurfer?
 
  Knut J
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 --
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 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] error when using mri_sur2vol: has many more faces than vertices!

[Michael Waskom]

Hi Minjie,

You'll want to give tksurfer the name of one of the regular surfaces
(e.g., inflated, pial, etc.) as the third positional argument and then view
your FA file as an overlay ( -overlay rh.fa.vol2surf2.w ).  The former
gives the surface geometry information (where the vertices are and which
are connected in the mesh) while the latter gives an arbitrary scalar value
associated with each vertex (in your case, FA).

Best,
Michael

On Wed, Dec 21, 2011 at 11:39 AM, Minjie Wu minji...@gmail.com wrote:

 Dear Surfer,

 I was trying to project a DTI FA image onto the T1 WM surface (for
 now), and eventually into the fsaverage as in a recent paper: Phillips
 OR, Nuechterlein KH, Asarnow RF, Clark KA, Cabeen R, Yang Y, et al.
 Mapping corticocortical structural integrity in schizophrenia and
 effects of genetic liability. Biological psychiatry. 2011;70(7):680-9.

 1. align the lowb.nii.gz from DTI data to T1.mgz image using
 bbregister to create the register.dat file.
 bbregister --s 20808 --mov lowb.nii.gz --reg lowb2orig.dat --dti --init-fsl

 2. project FA into surface space
 mri_vol2surf --mov dtifit_FA.nii.gz --reg lowb2orig.dat --hemi rh --o
 rh.fa.vol2surf2.w --projfrac 0 --interp nearest --surf white
 --out_type paint

 Here is the error message when I tried to check the surface in subject T1
 space

 [Minjie-Wus-Mac-Pro:subjects/20808/dmri] minjiewu% tksurfer 20808 rh
 fa.vol2surf2.w
 subject is 20808
 hemiis rh
 surface is fa.vol2surf2.w
 surfer: current subjects dir: /Volumes/Lion/projects/surface/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /Volumes/Lion/projects/surface/subjects/20808/dmri
 checking for nofix files in 'fa.vol2surf2.w'
 Reading image info (/Volumes/Lion/projects/surface/subjects/20808)
 Reading /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz
 surfer: Reading header info from
 /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz
 nquads=14348288,  nvertices=1
 ERROR: MRISread: file
 '/Volumes/Lion/projects/surface/subjects/20808/surf/rh.fa.vol2surf2.w'
 has many more faces than vertices!
 Probably trying to use a scalar data file as a surfa


 Thank you very much for your help.

 Minjie
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Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

[Michael Waskom]

Hi Satra and Doug,

That script is good to know about.  But, from what I can tell, it looks
like it will output a timeseries in the same space as the original template
(each frame gets transformed with a combination of the matrix specifying
its registration to the anatomical and the inverse of the matrix specifying
the registration from the template to the anatomical). So this might give
me somewhat better motion correction, but it won't give me a common space
across runs.

Best,
Michael

On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 That may or may not do what you want. I think that version keeps the
 functional data in the functional space. It would be better to register
 each TR to the anat, then simply sample each TR to the anatomical space
 (volume or surface) rather than going back into functional space.
 doug


 Satrajit Ghosh wrote:
  hey mike,
 
  take a look at:
 
  ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
 
  cheers,
 
  satra
 
 
 
  On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom mwas...@stanford.edu
  mailto:mwas...@stanford.edu wrote:
 
  Hi Doug,
 
  Is it possible to use the bbregister parameters to resample a
  functional image such that it is in register with the anatomical
  image but retains the epi geometry? I actually don't care so much
  about the epi-anat registration, but what I would like to be able
  to do is motion correct and otherwise preprocess my timeserieses
  within session* and then move different sessions into a common
  volumetric space for analysis. As I have great faith in
  bbregister, ideally the transformation would be determined with
  this method (I suspect it is superior to picking a slice from one
  of the sessions to use as a motion correction target across all
  sessions). Additionally, I would prefer not to upsample the source
  voxels either into 1x1x1 anatomical geometry or to surface
  vertices. Unfortunately, my affine understanding isn't deep enough
  for me to figure this out myself.
 
  Does that make sense, and (if so) do you have any ideas?
 
  Thanks!
  Michael
 
  * Here i use session in the sense of run, which is different I
  think from FSFast terminology so apologies for any confusion.
 
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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] Use bbregister parameters to transform to EPI geometry

[Michael Waskom]

Sorry, I guess it's not clear what I'm hoping to do.

Because I'm going to use this data for mvpa, I don't want to resample into
1x1x1 voxels or go onto the surface. But I have multiple runs that I want
to use, so I need there to be a voxel-to-brain correspondence across the
different runs.

Michael

On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
 wrote:

 It will output a register.dat for each frame. You can extract the frame
 from the time series (mri_convert --frame ), apply the reg with mri_vol2vol
 or mri_vol2surf, then concatenate the results back into a time series
 (mri_concat)
 doug

 Michael Waskom wrote:

 Hi Satra and Doug,

 That script is good to know about.  But, from what I can tell, it looks
 like it will output a timeseries in the same space as the original template
 (each frame gets transformed with a combination of the matrix specifying
 its registration to the anatomical and the inverse of the matrix specifying
 the registration from the template to the anatomical). So this might give
 me somewhat better motion correction, but it won't give me a common space
 across runs.

 Best,
 Michael

 On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

That may or may not do what you want. I think that version keeps the
functional data in the functional space. It would be better to
register
each TR to the anat, then simply sample each TR to the anatomical
space
(volume or surface) rather than going back into functional space.
doug


Satrajit Ghosh wrote:
 hey mike,

 take a look at:

 ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr

 cheers,

 satra



 On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
mwas...@stanford.edu mailto:mwas...@stanford.edu
 mailto:mwas...@stanford.edu mailto:mwas...@stanford.edu**
 wrote:

 Hi Doug,

 Is it possible to use the bbregister parameters to resample a
 functional image such that it is in register with the anatomical
 image but retains the epi geometry? I actually don't care so
much
 about the epi-anat registration, but what I would like to be
able
 to do is motion correct and otherwise preprocess my timeserieses
 within session* and then move different sessions into a common
 volumetric space for analysis. As I have great faith in
 bbregister, ideally the transformation would be determined with
 this method (I suspect it is superior to picking a slice
from one
 of the sessions to use as a motion correction target across all
 sessions). Additionally, I would prefer not to upsample the
source
 voxels either into 1x1x1 anatomical geometry or to surface
 vertices. Unfortunately, my affine understanding isn't deep
enough
 for me to figure this out myself.

 Does that make sense, and (if so) do you have any ideas?

 Thanks!
 Michael

 * Here i use session in the sense of run, which is
different I
 think from FSFast terminology so apologies for any confusion.

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 mailto:gr...@nmr.mgh.harvard

Re: [Freesurfer] Use bbregister parameters to transform to EPI geometry

[Michael Waskom]

OK, cool, I'll look into this for the future.

But back to my original question. If I already have data preprocessed with
several runs, each run motion-corrected within-session, and an affine
registration from each run's space to the anatomical determined by
bbregister, is there any way to use those transformation parameters to take
the function scans into a common space that retains the original voxel size?

Michael

On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh sa...@mit.edu wrote:

 hi michael,

 so for each frame of every session you get a bbreg file and the script
 ends up aligning the volumes to some reference. all you need to do is
 propagate that reference across your sessions. you might for example want
 this to be the middle volume of your entire experiment.

 cheers,

 satra


 On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom mwas...@stanford.eduwrote:

 Sorry, I guess it's not clear what I'm hoping to do.

 Because I'm going to use this data for mvpa, I don't want to resample
 into 1x1x1 voxels or go onto the surface. But I have multiple runs that I
 want to use, so I need there to be a voxel-to-brain correspondence across
 the different runs.

 Michael


 On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu wrote:

 It will output a register.dat for each frame. You can extract the frame
 from the time series (mri_convert --frame ), apply the reg with mri_vol2vol
 or mri_vol2surf, then concatenate the results back into a time series
 (mri_concat)
 doug

 Michael Waskom wrote:

 Hi Satra and Doug,

 That script is good to know about.  But, from what I can tell, it looks
 like it will output a timeseries in the same space as the original template
 (each frame gets transformed with a combination of the matrix specifying
 its registration to the anatomical and the inverse of the matrix specifying
 the registration from the template to the anatomical). So this might give
 me somewhat better motion correction, but it won't give me a common space
 across runs.

 Best,
 Michael

 On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

That may or may not do what you want. I think that version keeps the
functional data in the functional space. It would be better to
register
each TR to the anat, then simply sample each TR to the anatomical
space
(volume or surface) rather than going back into functional space.
doug


Satrajit Ghosh wrote:
 hey mike,

 take a look at:

 ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
 greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr

 cheers,

 satra



 On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
mwas...@stanford.edu mailto:mwas...@stanford.edu
 mailto:mwas...@stanford.edu mailto:mwas...@stanford.edu**
 wrote:

 Hi Doug,

 Is it possible to use the bbregister parameters to resample a
 functional image such that it is in register with the
 anatomical
 image but retains the epi geometry? I actually don't care so
much
 about the epi-anat registration, but what I would like to be
able
 to do is motion correct and otherwise preprocess my
 timeserieses
 within session* and then move different sessions into a common
 volumetric space for analysis. As I have great faith in
 bbregister, ideally the transformation would be determined with
 this method (I suspect it is superior to picking a slice
from one
 of the sessions to use as a motion correction target across all
 sessions). Additionally, I would prefer not to upsample the
source
 voxels either into 1x1x1 anatomical geometry or to surface
 vertices. Unfortunately, my affine understanding isn't deep
enough
 for me to figure this out myself.

 Does that make sense, and (if so) do you have any ideas?

 Thanks!
 Michael

 * Here i use session in the sense of run, which is
different I
 think from FSFast terminology so apologies for any confusion.

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[Freesurfer] Use bbregister parameters to transform to EPI geometry

[Michael Waskom]

Hi Doug,

Is it possible to use the bbregister parameters to resample a functional
image such that it is in register with the anatomical image but retains the
epi geometry? I actually don't care so much about the epi-anat
registration, but what I would like to be able to do is motion correct and
otherwise preprocess my timeserieses within session* and then move
different sessions into a common volumetric space for analysis. As I have
great faith in bbregister, ideally the transformation would be determined
with this method (I suspect it is superior to picking a slice from one of
the sessions to use as a motion correction target across all sessions).
Additionally, I would prefer not to upsample the source voxels either into
1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine
understanding isn't deep enough for me to figure this out myself.

Does that make sense, and (if so) do you have any ideas?

Thanks!
Michael

* Here i use session in the sense of run, which is different I think
from FSFast terminology so apologies for any confusion.
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Re: [Freesurfer] Freesurfer projecting vector results for segmented cortical regions

[Michael Waskom]

If you've got any Python users in the lab, this shouldn't be to hard to
accomplish with pysurfer: pysurfer.github.com

I'm happy to walk you through the steps if you're interested.

Michael

On Mon, Nov 28, 2011 at 8:52 AM, Weisinger, Brian (NIH/NIMH) [F] 
brian.weisin...@nih.gov wrote:

 Thanks for the help. We don't have matlab here in our lab, but we do have
 R. Is there a way to use R and get the same desired result?


 On 11/28/11 11:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Brian,

 I guess you can use read_annotation.m in matlab and set every vertex within
 the given parcellation to the value you specify below, then write it out as
 either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m

 cheers
 Bruce


 On Mon, 28 Nov 2011, Weisinger, Brian
 (NIH/NIMH) [F] wrote:

  hello
 
  we are trying to project a vector of results for  segmented cortical
 regions
  (i.e.,...
  lh_middletemporal_thickness 0.000757119
  rh_middletemporal_thickness 8.06E-05
  lh_parahippocampal_thickness -0.000510407
  rh_parahippocampal_thickness 0.000625997
  lh_pericalcarine_thickness 0.000499749
  rh_pericalcarine_thickness 0.000903678
  lh_superiortemporal_thickness 0.001732855
  rh_superiortemporal_thickness 0.000184256
  lh_temporalpole_thickness 0.001075362
  rh_temporalpole_thickness -0.000381165
  lh_transversetemporal_thickness 0.000558122
  rh_transversetemporal_thickness 6.65E-05
  ...)
 
  however, we are unsure of how to do this.
  so, our question is? what is the sequence of steps we need to take to
 visualize our results on the segmented 3D template in tksurfer.
 
 
  Thanks for your help,
 
  Brian Weisinger
 
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Re: [Freesurfer] Recon-all step estimate

[Michael Waskom]

Hi Pedro,

Here's a script that (I think) will do what you're looking for:

http://web.mit.edu/mwaskom/stuff/recon_status

I hope it's useful

Michael

2011/11/8 Bruce Fischl fis...@nmr.mgh.harvard.edu

 the recon-all.cmd file I think gets written to the scripts dir with every
 command that is run

 Bruce

 On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

  Is there any script that I can use to estimate which step recon-all are
 in?
 My idea is to have a progress indicator for recon-all and this script
 would be very useful.

 thanks

 Pedro Paulo Jr



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Re: [Freesurfer] Error During Talairach Transform

[Michael Waskom]

Hi,

What was the reason for this switch?  Intuitively it seems that a
bias-corrected image is likely to get a better registration (since I assume
the target has essentially uniform intensities).

Michael

On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote:

 no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1
 uses orig.mgz.

 its hard to say why it would fail for some subjects but not others,
 other than head positioning and to some degree ventricle size makes a
 difference.

 n.

 On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
  Thanks Nick,
 
  Is use-mritotal equivalent to what version 5.0 does by default?
 
  Also,  any suggestions on why this talairach error would occur only on
  a portion of my data, despite all being collected with the same
  imaging protocol, same conversions from dicom, etc?
  -
 
  Joshua Lee
 
  Graduate Student
  Center for Mind and Brain 
 
  Department of Psychology
 
  University of California, Davis
  530.747.3805
 
 
  On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky
  ni...@nmr.mgh.harvard.edu wrote:
  joshua,
 
  try adding -use-mritotal to the end of your recon-all
  command.  it will
  use an alternate way to compute the talairach.xfm which works
  better on
  some data.
 
  the change from v5.0 to v5.1 in the talairach stage was that
  in v5.1,
  the talairach.xfm is needed to compute nu.mgz, so the
  talairach stage
  needs to precede the nu_correct stage.  this means the
  talairach stage
  can no longer use nu.mgz as input, which seems to work better
  than
  orig.mgz for some data (and is the case for your data).
 
  in the next release of freesurfer, recon-all will
  automatically try the
  alternate method (mritotal) if the default talairach_avi
  method fails
  the tal-check.
 
  n.
 
 
 
  On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
   can you send us an example that works in 5.0 and fails in
  5.1?
  
   thanks
   Bruce
   On Wed, 2 Nov
   2011, Joshua Lee wrote:
  
Small Update: Error Disappears if Using Freesurfer version
  5.0 instead of
5.1. However, since I am keenly interested in the
  hippocampal-subfield
segmentation capabilities of the most recent version, I am
  loathe to regress
to an earlier version of FreeSurfer
-
Joshua Lee
Graduate Student
Center for Mind and Brain 
Department of Psychology
University of California, Davis
530.747.3805
   
   
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee
  jki...@ucdavis.edu wrote:
  #@# Talairach Failure Detection Wed Nov  2 02:03:32
  EDT 2011
  /home/virtualuser/freesurfer/subjects/test005/mri
   
   talairach_afd -T 0.005 -xfm
  transforms/talairach.xfm
   
  I am receiving the error (pasted below) on about
  half of my
  scans, despite all cans using same protocol. I
  detect no obvious
  issue with the quality of the images. I have
  original dicoms,
  and am using mri_convert to save into a single .mgz
  (or .nii,
  doesn't neem to make a difference), and the
  unpredictability of
  the error makes diagnosis problematic. TKMedit2
  reveals
  absolutely wacky registrations. I am processing on
  Freesurfer
  5.1, and have replicated issue on two different
  installations. I
  am designing a new longitudinal study inheriting the
  same
  imaging protocol and I do not want to get in a
  situation
  demanding manual editing of the talairach. Can
  anyone help me
  out? Thanks, Joshua
   
  ERROR: talairach_afd: Talairach Transform:
  transforms/talairach.xfm ***FAILED*** (p=0.0030,
  pval=0. 
  threshold=0.0050)
  Manual Talairach alignment may be necessary, or
  include the -notal-check flag to skip this test,
  making sure the -notal-check flag follows -all
  or -autorecon1 in the command string.
  See
   
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
  Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP
  Fri Apr 17
  01:57:59 UTC 2009 i686 GNU/Linux
   
  recon-all -s test005 exited with ERRORS at Wed Nov
   2 02:03:32
 

Re: [Freesurfer] mris_convert exporting parcellation per vertex

[Michael Waskom]

If you know Python, you can likely do this pretty easily with tools from the
PySurfer package:  http://pysurfer.github.com/

(Check out surfer.io.read_annotation).

If you're just using the io routines, you won't need the somewhat heavy
Mayavi visualization dependencies.  You should be able to read in and
manipulate surfaces/annotations just with numpy.

Best,
Michael

2011/10/8 Bruce Fischl fis...@nmr.mgh.harvard.edu

 it wouldn't be that hard to put something together if you want to avoid
 matlab. Spec out what you need and send me a sample, maybe on Bert

 Bruce

 On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

  Thanks.

 I suppose I can't do this without matlab. Right?

 -- iOS 5.0

 Em 08/10/2011, às 19:29, Bruce Fischl fis...@nmr.mgh.harvard.edu
 escreveu:

  there is a write_annotation.m file you can use
 On Sat, 8 Oct 2011, Anderson Winkler wrote:

  ops, it seems the comments inside the dpxwrite.m no longer reflect what
 it does. You probably don't need this, but anyway, the version attached is
 more up-to-date.
 Anderson
 On 08/10/11 17:28, Anderson Winkler wrote:
 Hi Pedro,

 There is probably a way to do that using FS tools from the command
 line, but the attached script should do the same. The result is a
 data-per-vertex file, which
 is the same as the .asc files from mris_convert. There is no
 geometry input, hence the vertex coordinates are all set to (0,0,0).

 Hope it helps!

 All the best,

 Anderson

 On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote:
   I need to create a file where I have the parcellation value
 (structure name) per vertex.
 I've tried�mris_convert --annot /Applications/freesurfer/**
 subjects/bert/label/lh.aparc.**annot 
 /Applications/freesurfer/**subjects/bert/surf/lh.pial
 parc.asc
 But I get the error:�ERROR: unknown file annot file type specified for
 output: saida.asc
 Has someone done this before?
 Thanks
 --**--**
 -
 Pedro Paulo de Magalh�es Oliveira Junior
 Netfilter  SpeedComm Telecom -- www.netfilter.com.br
 -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
 id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441
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[Freesurfer] Patch file to ascii issues

[Michael Waskom]

Hi,

Two issues related to patch files.

Issue number 1:

If I generate an ascii flat patch file like so:

$ bin_patch=fsaverage/surf/lh.cortex.patch.flat
$ mris_convert -p $bin_patch lh.cortex.patch.flat.asc

And then inspect the file that gets created:

$ head lh.cortex.patch.flat.asc
#!ascii version of patch fsaverage/surf/lh.orig. The 1st index is not a
vertex number
149297 296943
1 vno=0
-60.013611  4.446770  0.00
2 vno=1
-56.163204  88.759064  0.00
3 vno=2
-112.137077  -18.977211  0.00
4 vno=3
-34.436668  -72.297958  0.00

This is sort of annoying if I want to read it into Matlab, etc. (actually
Python) using routines that expect an array of numbers.  Is there any way to
suppress the intercoordinate output?

Issue number 2:

Even if I get around the text file formatting issues, I run into some
problems when I try and generate meshes with the resulting data.  It seems
like the triangles component of the surface makes references to vertex ids
that don't exist anymore.  In other words, the triangles array contains
values that are larger than the number of rows in the vertices array.

Obviously I'm doing things that aren't officially supported by Freesurfer
there, but does that jive with your knowledge of how the patch files are
written?

Thanks!

Michael
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[Freesurfer] PySurfer - A package for visualizing surfaces

[Michael Waskom]

Dear Freesurfers,

We are pleased to announce the 0.1 release of PySurfer, a Python-based
package for the visualization of surface data from Freesurfer.  Please
see our website at http://pysurfer.github.com/ for information on how
to install the package and a gallery of examples.  We hope you'll find
it useful in your research!

Best,
Michael Waskom
Alexandre Gramfort
Scott Burns
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Re: [Freesurfer] PySurfer - A package for visualizing surfaces

[Michael Waskom]

Hi Matt,

In theory it could, as we use Nibabel for i/o and they support Gifti.
However, I have no data in Gifti format at the moment to work with, so
at the moment I would say we are Freesurfer specific.

Best,
Michael

On Fri, Jul 22, 2011 at 2:09 PM, Matt Glasser m...@ma-tea.com wrote:
 Hi Michael,

 Out of curiosity, does this also support the GIFTI format?  If so, one could
 use it to view surface data from a wide variety of software packages.

 Thanks,

 Matt.

 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Waskom
 Sent: Friday, July 22, 2011 1:07 PM
 To: Freesurfer@nmr.mgh.harvard.edu
 Cc: Alexandre Gramfort; Scott Burns
 Subject: [Freesurfer] PySurfer - A package for visualizing surfaces

 Dear Freesurfers,

 We are pleased to announce the 0.1 release of PySurfer, a Python-based
 package for the visualization of surface data from Freesurfer.  Please
 see our website at http://pysurfer.github.com/ for information on how
 to install the package and a gallery of examples.  We hope you'll find
 it useful in your research!

 Best,
 Michael Waskom
 Alexandre Gramfort
 Scott Burns
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[Freesurfer] Choice of input surface for mris_make_face_parcellation

[Michael Waskom]

Hi Bruce,

I'm playing around with mris_make_face_parcellation, and I'm looking
for guidance on choosing the input surface.

In the usage message, the example that is given says:

example: mris_make_face_parcellation lh.inflated
$FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot

The choice of the inflated surface seems weird to me, as isn't it
really just used for visualization?  Seems like you'd either want to
use a surface that's representative of the actual brain geometry (e.g.
white, or graymid) or the sphere.  But I'm a little confused in
general about what's going on behind the scenes here so I don't trust
my intuition.

Cheers,
Michael
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Re: [Freesurfer] stats on masked functional data

[Michael Waskom]

Hi,

I believe the mri_segstats program is exactly what you're looking for here.

Best,
Michael

On Tue, Jun 28, 2011 at 5:12 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
 Hi Ri

 Doug may have something to do this, but if not it would be easy enough
 in matlab
 Bruce


 On Tue, 28 Jun 2011, Ritobrato Datta wrote:

 Hello All,

 Looks like this question slipped through.
 I have a functional beta value overlay as a .mgh file and a V1 label file 
 and I want to compute the average beta value within that mask for each 
 subject.

 How do I do this ?

 Thanks a lot

 Ri
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[Freesurfer] Surface Normals in Freesurfer

[Michael Waskom]

Hi Bruce et al.

I have a quick question about the interpretation of surface normal
files and the various ways you can create them with Freesurfer.

As far as I know, there are two ways to get the normals information:

mris_convert -n lh.inflated lh.inflated.normals2

and

mri_surf2surf --s fsaverage --hemi lh --sval-nxyz inflated --tval
lh.inflated.normals2.mgz

The first writes an ascii file with 491522 rows and 4 columns (the
last of which is all 0's), while the second writes a surface scalar
image with dimensions 163842 x 1 x 1 x 3.

Am I right to assume that the coordinates in the mgz image and the
first n_vtx rows of coordinates in the ascii file correspond to the
surface normals at the vertices of the mesh?  And, furthermore, do the
remaining coordinates in the ascii file correspond to the surface
normals of the triangle faces on the mesh?

Thanks!

Michael
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Re: [Freesurfer] display results on fsaverage / calculate area

[Michael Waskom]

Hi Bruce,

I've seen this brought up on the list a few times, and, I have to admit,
I've never really been able to wrap my head around it.  The naive part of my
brain feel like, if fsaverage is an average subject, it should be smaller
than about half of subjects but also larger than about half of them. I'm
sure I'm just not thinking about it quite the right way, but would you mind
unpacking this a little bit? I suspect I'm not the only one for whom this is
somewhat unintuitive.

Thanks!

Michael

On Wed, May 11, 2011 at 6:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:


 2. The surface area of fsaverage is less than any individual, so you
 *definitely* don't want to use it.


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[Freesurfer] Run mri_ms_fitparms without motion correction

[Michael Waskom]

Hi Bruce, et all,

Is it possible to run mri_ms_fitparms without motion correction, if
your input images are already in register?  It seems like it would
save quite a bit of processing time, but the usage help isn't all that
useful (looks like there are a lot of hidden options buried in the
source code).  Thanks!

Michael
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Re: [Freesurfer] Fwd: bbregister bug? with init-spm option--flips left and right

[Michael Waskom]

Hi Tyler,

Doug can correct me if I'm wrong, but I believe if you use the --spm-nii
option it will fix this.

Cheers,
Michael

On Mon, Mar 28, 2011 at 1:47 PM, Tyler Seibert tseib...@ucsd.edu wrote:

 Screenshot2 attached


 -- Forwarded message --
 From: Tyler Seibert tseib...@ucsd.edu
 Date: Thu, Mar 17, 2011 at 4:02 PM
 Subject: bbregister bug? with init-spm option--flips left and right
 To: freesurfer@nmr.mgh.harvard.edu


 Hello,

 I hope this is the correct email list--this is my first time posting (just
 subscribed).

 I have been using bbregister to calculate a tranformation matrix between a
 T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with
 mri_vol2surf. I have found that the init-fsl option frequently gives very
 poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The
 init-spm option seemed to be working great. However, upon close inspection,
 I became suspicious this option was actually flipping the T2 so that the
 left hemisphere became right and vice versa. I am using FreeSurfer version
 4.5 and have spm8 referenced in my matlab path.

 I used a directory ~/bbreg_test in my home directory for the test (linux),
 which consisted simply of running bbregister with init-fsl and init-spm
 options. The attached log file (log.txt) contains the commands I used. The
 terminal output from each test was saved in text files as well, also
 attached.

 I have also attached two screenshots of the tkregister2 output for these
 tests. In each screenshot the far left image is the registered T2 using
 init-spm, and the far right image is the registered T2 using init-fsl. As
 the init-fsl version is clearly wrong, the middle image in each screenshot
 is the init-fsl output again, but manually rotated several degrees to the
 left to better emphasize the mirror-image relationship between the init-spm
 (far left) and init-fsl (middle and far right) output images.

 Please let me know if there is anything further you need from me to
 investigate this or if there is any insight you can give me as far as how to
 avoid this error. I noticed at line 209 of the spm_test.txt log file there
 is a message stating that RAS coordinate system is assumed (see below, where
 I have copied lines 208-213 for convenience). This may very well be the
 problem, as the T2brain.nii.gz volume is in LAS, according to mri_info
 output. However, I do not see where I can override this RAS assumption.

  /home/tylers/apps/spm8/spm_coreg.m
  INFO: Assuming RAS coordinate system
using
 /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img
 as the target image
  using
 /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img
 as the source image
  


 Thank you,

 --
 Tyler Seibert

 Dept. of Bioengineering
 Medical Scientist Training Program
 University of California, San Diego



 --
 Tyler Seibert

 Dept. of Bioengineering
 Medical Scientist Training Program
 University of California, San Diego


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[Freesurfer] BBRegister mincost and B0 Masking

[Michael Waskom]

Hey Doug,

When using the bbregister feature to mask areas with b0 distortion, I
find noticeably lower registration cost values (as revealed by the
first number in the .mincost file that gets generated).  When this
number is calculated, does it take into account the registration in
the areas affected by the mask?  In other words, are the lower numbers
evidence that masking distorted regions is significantly improving the
registration accuracy, or just an artifact of masking out regions
where the is bad registration from the cost calculation?

Thanks!
Mike
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Re: [Freesurfer] clusterwise correction ocn.annot missing and ICV in aseg.stats

[Michael Waskom]

Hi Pieter,

I think I may have run into this problem before by using mri_glmfit on
a surface dataset and forgetting to to include --surf subject
hemi.  The model fitting runs fine, but you end up with confusing
problems at the corrections stage because the residual smoothness
estimation doesn't work properly.  Do you happen to know whether you
included --surf in your mri_glmfit call?

Cheers,
Mike

On Sun, Feb 27, 2011 at 6:37 PM, Pieter van de Vijver pvij...@gmail.com wrote:
 Dear Freesurfer experts,

  I’m doing a longitudinal study on cortical thickness and subcortical
 volumes and got some questions. I used the longitudinal stream for the
 preprocessing



 1.   On cortical thickness, I’m doing a paired analysis as described in
 https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, and then a
 cluster-wise correction as described in
 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, with
 5000 simulations instead of 5, and a vertex-wise threshold of 3 .
 But I don’t get the ocn.annot map, instead I get a ocn.mgh and ocn.lut.
  The CSD file also looks weird (constantly about 150 clusters with max size
 one or 2) and the resulting cluster.summary also gives a huge list of very
 small but significant clusters. Am I doing something wrong? How should I go
 about this? I’m using FS 4.5. Files are included (jpg for sig.mgh and
 cluster.mgh for negative simulation,  and csd (zipped), summary and
 simulation log)

 2.   For the subcortical volumetric analysis I use the aseg.stats. Is
 the ICV a reliable measure to correct for overall brain size? I heard ICV
 measurements are not very reliable on T1’s (I get a mean of 2,4% decrease
 over 16 months...). Are other methods preferable to this one.

 3.   Is there a logic or rule of thumb for choosing the vertex-wise
 threshold?



 Thanks for your help!



 Pieter

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Re: [Freesurfer] FS 5.1

[Michael Waskom]

Hi,

For what it's worth, I have seen a very similar skull-strip failure on
at least one of my brains processed with Freesurfer 5.0 but not using
the -nuintensitycor-3T flag.  Happy to send data, if helpful.

Best.
Michael

On Wed, Feb 16, 2011 at 2:03 PM, Mehul Sampat mpsam...@gmail.com wrote:
 Hi Bruce,

 Okay. I will try it out 5.1 in the future and compare it to 4.5.

 I also have a question about comparisons between version 4.5 and 5.0

 In some cases, I saw that FS 4.5 does a slightly better job at skull
 stripping than FS 5.0.
 Esentially, FS 5.0 seems to make errors in the back of the brain and cuts
 out some tissue.
 (Please see attached images).

 The images are the same slice from the same subject processed with FS 4.5
 and 5.0 (This happens across 5-10 slices)
 In 5.0, I used the following command: recon-all -s subj--id -i
 nifti-file -all -nuintensitycor-3T
 (I have seen this issue in atleast 5 subjects in our data)

 Since 5.0 uses the graph cuts, could the error be due the combination of
 (graph cuts + -nuintensitycor-3T) ?
 Also, I guess I could run 5.0  and use only graph cuts or -nuintensitycor-3T
 to isolate the error ?

 Thanks
 Mehul



 On Tue, Feb 15, 2011 at 12:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

 Hi Mehul,

 I think 5.1 will work better for large ventricles than 4.5, but I'll be
 interested to hear your experience.

 cheers
 Bruce
 On Tue, 15 Feb 2011, Mehul Sampat wrote:

 Hi Bruce,
 We have two studies being conducted (one cross-sectional and one
 longitudinal)
 Some of the subjects in have a lot of atrophy and have large ventircles.

 For the cross-sectional analysis stream are there many differences
 between
 4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5 for
 cross-sectional analysis ?

 (I understand that for the longitudinal study, I should wait for 5.1 and
 process all the timepoints with 5.1)


 Thanks
 Mehul



 On Thu, Jan 20, 2011 at 10:36 AM, Bruce Fischl
 fis...@nmr.mgh.harvard.eduwrote:

 Hi Derin

 we are tracking down some issues with it and hope to have it out within
 a
 month

 cheers
 Bruce
 On Thu, 20 Jan 2011, Derin Cobia wrote:

 All,

 Just curious about the current estimated timeline for version 5.1,
 trying

 to schedule some projects around it.  Thanks!

 -Derin



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Re: [Freesurfer] Bbregister for fsl tractography

[Michael Waskom]

Hi Doug,

This reminds me: in the dt_recon script, when bbregister is used, the
gradient descent tolerance is changed (the command line includes --tol1d
1e-3 ).

I was just wondering why this happens.

Thanks!
Mike

On Tue, Jan 25, 2011 at 1:31 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 I get a file-not-found to that link, so I can't check it out. But, yes,
 you should just be able to use bbregister passing it the low-b as the
 template (or whatever you used at the target for motion correction). and
 specifying --bold or --t2.

 doug

 Lena Palaniyappan wrote:
  Dear Doug  others
 
 
  The FSL page on fa to freesurfer registration (
  http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html)
  http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html%29  contain info
  that uses tkregister2.
 
 
 
  To determine freesurfer_to_fa space registration file, do we need to
  go through the freesurfer_to_struc and then struc_to_fa rooutine given
  in fsl pages.?
 
  I wonder if the registration can be done using the  bbregister currently.
 
  If that is the case how to get the fsl-type registration file?
  tkregister2 had an option for this but it is not working with bbregister
 
  Cheers
  Lena
  ___
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  *Clinical Lecturer  Honorary StR | Division of Psychiatry (
  University of Nottingham)
  South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
 
 
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[Freesurfer] mri_vol2surf --cortex and --mask flags appear ineffective

[Michael Waskom]

Hey  developers,

It seems as if the --cortex and --mask flags for mri_vol2surf are not
doing anything.  E.g., if I use the exact same command line:

mri_vol2surf --hemi rh --o rh.w-cortex.nii.gz --out_type niigz --reg
register.dat --reshape --projfrac-avg 0 1 .1 --mov cope2.nii.gz
--cortex

With and without --cortex and then diff the output, they are
identical.  When you load the overlay in tksurfer, the medial wall has
values that are not 0.

Here's my bugr data:

FREESURFER_HOME: /software/Freesurfer/5.0.0

Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-22-generic x86_64


Best,
Mike
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[Freesurfer] Best way to detect file type

[Michael Waskom]

Hi there,

Are there any Freesurfer utilities that I can use to query the file type of
an image directly?  i.e., more directly than mri(s)_info.  The problem is
that mris_info barfs when it gets an image that isn't a proper surface
file, and I'd like something that is maximally flexible.  Ideally, there
would be a program I could run that will just return the file type for
surface, volume, or curv files.  Thanks!

Best,
Mike
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[Freesurfer] Graphics Segfaults

[Michael Waskom]

Hey Nick/Krish,

Is there a way to exit tksurfer/tkmedit from a tcl script that doesn't
trigger a segfault?  Thanks!

Cheers,
Mike
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Re: [Freesurfer] mri_label2volume issues

[Michael Waskom]

Hi Prapti,

Basically, you just need to have a label file that you can turn into a
lh.your_annot_name.annot (assuming your actual ROI is in the right
hemisphere), so that mri_label2annot runs properly.

The easiest thing to do would be to rename any old label you have in
your subject's label directory to lh.dummy.label, and then create an
annotation from that label with mri_label2annot.  Then run
mris_aparc2aseg as you tried to do before, which will create a volume
that has 0's everywhere except in the area where your actual and dummy
labels were projected.  Figure out the voxel values for the ROI you
want (using Freeview or tkmedit), and then run:

mri_binarize --i your_annot_name+aseg.mgz --match that voxel value
--o you_roi_name.mgz

Which will have 1s where your ROI is and 0s everywhere else.

Best,
Mike

---Original Message---

Hi Doug,
Thanks for the reply. I am sorry, I am a bit confused about what you
mean by creating a dummy label. I am also not sure at which step I need
to do this.

As I understand it, I use mri_label2annot to transform my label into a
annotation file and this will be separate for the two hemispheres. Do I
then edit these files ? where exactly do I use mri_binarize?

Thanks,

Prapti

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Friday, 17 September 2010 12:44 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_label2volume issues

Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The

easiest thing is to make a dummy label for the other hemisphere. In the
final segmentation, left hemisphere will have an index of
1000+something, the right will have 2000+something. You can then use
mri_binarize with --match create a new binary volume with just your
hemisphere.

doug

Prapti Gautam wrote:
 Hi Doug,

 Thanks for the reply. I have tried using the method you've suggested,
 however, I'm stuck because mri_label2annot which I use to turn my
label
 into a annot file only works in one hemisphere while mri_aparc2aseg
 works for the whole brain. Do you know a work around for this?

 Can I merge the annot files created from each hemisphere so that I can
 pass it to mri_aparc2aseg?


 Thanks,

 Prapti



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Re: [Freesurfer] medialorbitofrontal_area

[Michael Waskom]

Hi Jose,

If you're using Freesurfer 4.5, the aparcstats2table program has a known bug
that causes the columns to be written in a random order.  Depending on how
you create a database from these files, it could lead to what looks like a
large asymmetry, when really you're just comparing columns from different
regions.

Best,
Mike

-- Forwarded message --
From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
To: Jose Soares zmsoa...@yahoo.com.br
Date: Fri, 13 Aug 2010 10:01:39 -0300
Subject: Re: [Freesurfer] medialorbitofrontal_area
It's not unusual to have asymmetries in some patients. I have seen some
myself in AD. Have you checked the segmentation in those areas?

-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter  SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Fri, Aug 13, 2010 at 07:12, Jose Soares zmsoa...@yahoo.com.br wrote:

 Hi all,

 I am doing a study about the medialorbitofrontal, and I am having some
 strange area  results in a lot of subjects.

 The rh areas are much higher than the lh areas of medialorbitofrontal: Some
 examples:

 lh rh
  1714.0 2822.0 1720.02632.0 1728.0 2675.0 1877.02733.0 1498.0 2719.0
 2067.02542.0 1870.0 2666.0 1554.02263.0 1535.0 2566.0 1794.02392.0 1487.0
 2547.0
 Why is this happening, any idea? Should I do any correction?

 Thanks for the help,

 Miguel.


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 e-mail
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2010/8/13 freesurfer-requ...@nmr.mgh.harvard.edu

 -- Forwarded message --
 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
 To: Jose Soares zmsoa...@yahoo.com.br
 Date: Fri, 13 Aug 2010 10:01:39 -0300
 Subject: Re: [Freesurfer] medialorbitofrontal_area
 It's not unusual to have asymmetries in some patients. I have seen some
 myself in AD. Have you checked the segmentation in those areas?

 -
 Pedro Paulo de Magalhães Oliveira Junior
 Diretor de Operações
 Netfilter  SpeedComm Telecom
 -- www.netfilter.com.br
 -- For mobile: http://www.netfilter.com.br/mobile




 On Fri, Aug 13, 2010 at 07:12, Jose Soares zmsoa...@yahoo.com.br wrote:

 Hi all,

 I am doing a study about the medialorbitofrontal, and I am having some
 strange area  results in a lot of subjects.

 The rh areas are much higher than the lh areas of medialorbitofrontal:
 Some examples:

 lh rh
   1714.0 2822.0  1720.0 2632.0  1728.0 2675.0  1877.0 2733.0  1498.0
 2719.0  2067.0 2542.0  1870.0 2666.0  1554.0 2263.0  1535.0 2566.0
 1794.0 2392.0  1487.0 2547.0
 Why is this happening, any idea? Should I do any correction?

 Thanks for the help,

 Miguel.


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[Freesurfer] 2009 Destrieux Parcellation on pre 4.5 recons

[Michael Waskom]

Hi Experts,

Is there any reason one should not generate the 2009 Destriuex parcellation
for brains that were recon-ned with earlier versions of Freesurfer?  (ie
using recon-all with -cortparc2 and -parcstats2 while in the 4.5
environment)  Thanks!

Cheers,
Mike
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Re: [Freesurfer] R: R: How means all the output file from a segmentation?

[Michael Waskom]

Hi Leonardo,

You might want to check out 3D slicer: http://www.slicer.org/  It sounds
like it might be able to do what you're looking for.

Best,
Mike

On Sun, 13 Jun 2010, Leonardo Chesi wrote:

Hi bruce,
my goal is to obtain a 3D surface of the hippocampal region for a visual
comparison with a manual segmentation made by a neuroradiologist. Today I
managed to extract the volume with mri_binarize but I can't transform it in
a surface that tkurfer can visualize. For that I try to use mri_vol2surf but
I obtain a surface with 0 vertices. Can you help me??
Cheers
Leonardo
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[Freesurfer] fsaverage aseg

[Michael Waskom]

Hi all,

How was the fsaverage aseg.mgz (in the 4.5 distribution, if it differs)
created?  I can't seem to find this information anywhere on the Freesurfer
website.

Thanks!
Mike
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Re: [Freesurfer] question about clustering simulation

[Michael Waskom]

Hi Doug,

This looks very helpful!  Should we use the fwhm size corresponding to the
argument of the --fwhm flag when recon-all runs mri_surf2surf (for
anatomical stats), or round the measure found in the fwhm.dat of the glmfit
dir?

Thanks,
Mike

-- Forwarded message --
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: port...@umn.edu
Date: Tue, 27 Apr 2010 11:17:24 -0400
Subject: Re: [Freesurfer] question about clustering simulation
Yea, that was a bug in the simulation program I used. I did confirm that the
simulations were done on the correct hemisphere. Feel free to edit the
files. I'll fix the master when I get a chance.

doug

James Porter wrote:

 Doug-

 Let me be the first to say thank you for saving me massive amounts of
 simulation time. One bug though: the right hemisphere files say they were
 created using the left hemisphere, and mri_surfcluster rejects them. Would
 it be verboten to just alter the csd files, or do you have versions that
 were created off of fsaverage's right hemisphere?

 matacao:mult-comp-cor porterj$ head
 fsaverage/rh/cortex/fwhm19/abs/th33/mc-z.csd
 # simtype null-z
 # anattype surface  fsaverage lh
 # FixGroupSubjectArea 1
 # merged  0
 # contrastNA
 # seed1271355821
 # thresh  3.30
 # threshsign  0.00
 # searchspace 74490.928733
 # nullfwhm19.00

 Jim Porter, M.A.
 Graduate Student
 Clinical Science  Psychopathology Research
 University of Minnesota


 On 7/22/64 1:59 PM, Douglas N Greve wrote:

 1. Correct on both counts. When I wrote the simulation, I was only trying
 to replicate the random fields analysis. But with a simulation, you have
 more freedom that I am not yet exploiting.
 2. This is what we are already doing with mc-z
 3. I'm working on this as well. It turns out that the random fields
 approximation works a lot better when using the number of vertices.

 Also, I've run mc-z simulations under a bunch of thresholding and FWHM
 conditions for whole-hemisphere cortex labels. These will be integrated in
 new version of  FS, but I've put them here
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gzas
  well. There's a README file in there. This will make running your own
 time-consuming simulations unnecessary (when using the cortex mask at
 least).

 doug

 Anthony Dick wrote:

 Hello all,

 I am interested in using the mri_glmfit simulation to control for
 multiple comparisons in data I have run on the surface in AFNI. Before doing
 this, I have a few questions:

 1. What does the simulation with the mc-z flag do, exactly? It claims to
 be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for
 each iteration, which is not exactly what AlphaSim does. Here is my guess:

 Given a surface, a given smoothness of the data, and a given per-vertex
 threshold, for each iteration the simulation populates that surface with
 random data taken from a normal distribution, thresholds the data, and
 applies the smoothness of the actual data (supplied as an input parameter).
 It then computes the maximum cluster size in area for that image. Doing
 this n iterations gives a distribution of maximum cluster sizes that occur
 for random data of a given smoothness, and taking cluster sizes above a
 certain percentile rank controls for the FWE at a level equal to that
 percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does
 something similar, although instead of taking maximum cluster sizes at each
 iteration it computes all given cluster sizes. AlphaSim also allows for
 different cluster connectivity radius, but it seems Freesurfer computes only
 for neighboring vertices. All in all, if this is correct, it seems like a
 good implementation.

 2. It is my understanding that one could bypass running the glm in
 Freesurfer and only compute the simulation, as the simulation only needs
 information about the surface, and the smoothness of the data (which are
 supplied by the user). To do so, you have to fake out Freesurfer to bypass
 glm, but that turns out to be pretty painless.

 3. In a future distribution, is it possible to modify this procedure to
 also output maximum cluster sizes in terms of number of nodes, rather than
 area?

 Can you please let me know if I am mistaken in any of these assumptions?
 Thanks in advance.

 Anthony





-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Scale factor for spherical distance

[Michael Waskom]

Hi Bruce,

I found some comments from your deep in the archive on converting
distance measured on the sphere to distance on the folded surface:
http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/msg00251.html

Is this still the case?  And, will loading the ?h.area file in matlab
and summing the .vol vector give you total surface area, or is there a
better way?

Thanks!
Mike
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Re: [Freesurfer] Missing usage for mris_distance_map

[Michael Waskom]

Thanks Bruce. My end goal here is to get a surface map where each
vertex has the value of the distance (along the surface) to a
reference vertex. So it sounds like this program can do what I'm
looking for. Thomas, if that sounds possible could you let me know how
to implement that?  In the meantime, Bruce, I'd probably find the
source code useful, so if you could send that my way I'd greatly
appreciate it.

Best,
Mike

On Saturday, April 10, 2010, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 Hi Mike,

 there are no options to that binary. There's also mris_distance_to_label that 
 might be more useful for you, or mris_distance_transform. Thomas Yeo (ccd) 
 wrote the algorithm and can give you more details if you want about how it is 
 implemented, or you are welcome to the source code if you want.

 cheers,
 Bruce

 On Sat, 10 Apr 2010, Michael Waskom wrote:


 Hi All,

 I'd like to use mris_distance_map, but it looks like the usage/help info is
 missing or broken (At least in 4.4.0/4.5.0).  When I try it with just the
 command or -help, it looks like this:

 mwas...@ba2:~$ mris_distance_map --help
 usage: mris_distance_map [options] input surface file output scalar field
 (.mgz)

 This program will compute a distance map of each point on the surface to a
 reference point (vertex 0 by default)

 valid options are:
 mwas...@ba2:~$

 Can someone help me out with these mysterious options?  Also, how is it
 calculating distance?  Thanks!

 Mike




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Re: [Freesurfer] Missing usage for mris_distance_map

[Michael Waskom]

Oh sure.  Here's the what I'm using:

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

Debian version: squeeze/sid

Kernel info: Linux 2.6.31-20-generic x86_64

Mike

On Sun, Apr 11, 2010 at 4:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Mike,
 Nick can get you the source code if you tell him your hardware/software
 platform.

 cheers,
 Bruce

 On Sun, 11 Apr 2010, Michael Waskom wrote:

  Thanks Bruce. My end goal here is to get a surface map where each
 vertex has the value of the distance (along the surface) to a
 reference vertex. So it sounds like this program can do what I'm
 looking for. Thomas, if that sounds possible could you let me know how
 to implement that?  In the meantime, Bruce, I'd probably find the
 source code useful, so if you could send that my way I'd greatly
 appreciate it.

 Best,
 Mike

 On Saturday, April 10, 2010, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:

 Hi Mike,

 there are no options to that binary. There's also mris_distance_to_label
 that might be more useful for you, or mris_distance_transform. Thomas Yeo
 (ccd) wrote the algorithm and can give you more details if you want about
 how it is implemented, or you are welcome to the source code if you want.

 cheers,
 Bruce

 On Sat, 10 Apr 2010, Michael Waskom wrote:


 Hi All,

 I'd like to use mris_distance_map, but it looks like the usage/help info
 is
 missing or broken (At least in 4.4.0/4.5.0).  When I try it with just the
 command or -help, it looks like this:

 mwas...@ba2:~$ mris_distance_map --help
 usage: mris_distance_map [options] input surface file output scalar
 field
 (.mgz)

 This program will compute a distance map of each point on the surface to
 a
 reference point (vertex 0 by default)

 valid options are:
 mwas...@ba2:~$

 Can someone help me out with these mysterious options?  Also, how is it
 calculating distance?  Thanks!

 Mike




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 e-mail
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[Freesurfer] Missing usage for mris_distance_map

[Michael Waskom]

Hi All,

I'd like to use mris_distance_map, but it looks like the usage/help info is
missing or broken (At least in 4.4.0/4.5.0).  When I try it with just the
command or -help, it looks like this:

mwas...@ba2:~$ mris_distance_map --help
usage: mris_distance_map [options] input surface file output scalar field
(.mgz)

This program will compute a distance map of each point on the surface to a
reference point (vertex 0 by default)

valid options are:
mwas...@ba2:~$

Can someone help me out with these mysterious options?  Also, how is it
calculating distance?  Thanks!

Mike
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Re: [Freesurfer] Segmentation fault during skull-stripping

[Michael Waskom]

Hi Sita,

Running it with the -no-wsgcaatlas seems to do the trick as far as avoiding
a segmentation fault.  The T1 looks like it has a some motion
artifact--might that be causing problems?  I checked the Talairach transform
and it looks generally alright, although I think it could be improved with
some tweaking.  It passed the automatic failure detection each time I ran
recon-all, though.  Would you recommend trying to improve the transform so
that things down the line run more smoothly?

Best,
Mike



On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori s...@nmr.mgh.harvard.eduwrote:


 Hi Mike,

 Did you check the talairach. And how do nu.mgz and T1.mgz look.
 Also you could probably try running the following command to see if the
 skull strip step finishes without errors.

 recon-all -skullstrip -no-wsgcaatlas -s subjid

 Sita.




 On Thu, 18 Mar 2010, Michael Waskom wrote:

  Hi Bruce, Nick,

 I'm getting a segmentation fault that's crashing recon-all at the start of
 the watershed during skull-stripping.  I've tried this three times, once
 starting the unpacking stream fresh from the raw dicoms, and it keeps
 happening at exactly the same place.  I've been reconstructing brains of
 other subjects in the same directory all the while, so I don't think it's
 a
 permissions issue of any sort.

 Full recon-all log is atatched, but here's the section where it crashes:

 *WATERSHED**
 Sorting...
 first estimation of the COG coord: x=116 y=166 z=95 r=51
 first estimation of the main basin volume: 585576 voxelsSegmentation
 fault
 Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010
 x86_64 GNU/Linux

 recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010


 And here's the OS data from the bugr script:

 FREESURFER_HOME: /software/Freesurfer/4.4.0

 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0

 Debian version: squeeze/sid

 Kernel info: Linux 2.6.31-20-generic x86_64


 Do you have any idea what might be going wrong?

 Thanks!
 Mike



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 is
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 e-mail
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[Freesurfer] BrainSegVol in asegstats table

[Michael Waskom]

Hi all,

What is the definition of the BrainSegVol field when you print the
segmentation stats to a table?  It's smaller than just adding up all of the
other fields in the table.  Thanks!

Best,
Mike
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[Freesurfer] 2009 Destrieux Parcellation for FSAverage?

[Michael Waskom]

Hi all,

Is there a way to get aparc.a2009s.annot files (the updated Destrieux
parcellation) for fsaverage?  Doesn't seem to be in the labels directory for
fsaverage for 4.5.0.  Thanks!

Best,
Mike
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