Re: [Freesurfer] cortical parcellation question

[Daniel Ferreira]

Thanks Bruce,

When you say the atlas itself is included in the Freesurfer distribution,
do you mean there is a 3D version of it available in the download?

Also, I am not looking for the individual subjects' images, I just want a
copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the
same format as the Harvard-Oxford atlas that is downloaded with FSL).

Thanks a lot.

Daniel Ferreira



2012/10/3 Bruce Fischl 

> Hi Daniel,
>
> 1. Do you mean the atlas or the parcellation of your subjects? We cannot
> distribute the individual subjects in the atlas as the data was collected
> under an IRB long ago that didn't include this. The atlas itself (summary
> statistics derived from those subjects) is included in the FreeSurfer
> distribution.
>
> 2. The subcortical areas are the same, but not the cortical ones. That
> cortical parcellation is quite coarse, and while we did implement it we
> were never given permission to distribute the automated version, so it is
> not part of FreeSurfer. The boundaries that we define are thus different
> than that one (and since the  Harvard-Oxford one is based on volumetric
> labeling of folding patterns we found that it contained a bunch of errors
> in which e.g. the wrong side of a sulcus was labeled)
>
> cheers
> Bruce
>
>
>
> On Wed, 3 Oct 2012, Daniel Ferreira wrote:
>
>  Dear experts,
>> I have a couple of questions regarding the cortical parcellation atlas
>> that
>> is used in Freesurfer:
>>
>> 1) I would like to know if it is possible to obtain the Desikan-Killiany
>> atlas in 3D analyze/nifti format. With each region of the brain assigned a
>> discrete integer number (for example the all of the voxels of the left
>> inferior temporal lobe have an intensity  = 1, or the whole of the left
>> hippocampus = 2).
>>
>> 2) Are the Harvard-Oxford cortical and subcortical atlases that can be
>> downloaded with FSL the same as the cortical parcellation atlas that is
>> used
>> in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the
>> left inferior temporal cortex in the Freesurfer cortical parcellation =
>> the
>> left inferior temporal cortex in the Harvard-Oxford atlas downloaded with
>> FSL)
>>
>> Many thanks
>>
>> Daniel Ferreira
>>
>>
>>
>>
>>
>
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Re: [Freesurfer] fixing the talairach.xfm

[Douglas Greve]

Hi Eric,

the talairach.xfm will not be overwritten. When run recon-all the first 
time, it creates two files: talairach.auto.xfm and talairach.xfm, which 
have the same contents. When you edit the registration, it changes the 
talairach.xfm. When recon-all is run again, it sees that the 
talairach.auto.xfm is different than talairach.xfm and does not change 
the talairach.xfm. It will behave this way for all invokations of 
recon-all (unless you use the "clean" options). This same principle is 
applied to all other manual interventions (ie, it should detect that the 
automatic is different than the manual and not overwrite the manual).


doug



On 10/3/12 10:58 PM, Eric Cunningham wrote:

Hi,

I have a few very basic clarification questions regarding the 
recon-all processing pipeline.
I am currently following the instructions here: 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Near the end of the page, it instructs me to rerun the whole process 
using my new talairach, using the command: recon-all -all -subjid [subjid]


Questions:
(1) Since the talairach file is created during recon-all, wouldn't 
rerunning the whole process overwrite my freshly edited file with 
whatever it came up with the first time?
(2) Assuming the answer to question 1 is 'no', can i rerun the process 
in steps (-autorecon1, then -autorecons 2 and 3) without overwriting 
my freshly edited file?
(3) Are there any files that are unusual in their likelihood of being 
overwritten? (e.g. running recon-all -all will overwrite aseg.stats 
but not talairach.xfm)


Thank you for your help,
-Eric



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[Freesurfer] fixing the talairach.xfm

[Eric Cunningham]

Hi,

I have a few very basic clarification questions regarding the recon-all
processing pipeline.
I am currently following the instructions here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Near the end of the page, it instructs me to rerun the whole process using
my new talairach, using the command: recon-all -all -subjid [subjid]

Questions:
(1) Since the talairach file is created during recon-all, wouldn't
rerunning the whole process overwrite my freshly edited file with whatever
it came up with the first time?
(2) Assuming the answer to question 1 is 'no', can i rerun the process in
steps (-autorecon1, then -autorecons 2 and 3) without overwriting my
freshly edited file?
(3) Are there any files that are unusual in their likelihood of being
overwritten? (e.g. running recon-all -all will overwrite aseg.stats but not
talairach.xfm)

Thank you for your help,
-Eric
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Re: [Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi john,

thanks. that's the idea, but what i want is that sub-division is done
within regions that are either determined automatically through the
freesurfer classifier or through manual parcellations. not a fixed template
of parcels that's transferred via the spherical registration.

cheers,

satra


On Wed, Oct 3, 2012 at 7:13 PM, John Griffiths
wrote:

>
>
> Would the Lausanne2008 template from the connectome mapping toolkit not do
> the trick?
>
>
> http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html
>
>
>
> On 3 October 2012 23:18, Satrajit Ghosh  wrote:
>
>> hi bruce,
>>
>> is there a way to divide consistently (same number of regions and one to
>> one correspondence - obviously not the exact same areas) across subjects
>> within aparc regions?
>>
>> cheers,
>>
>> satra
>>
>>
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
>
> Mr. John Griffiths, MSc
>
> PhD Candidate
>
> Centre for Speech, Language, and the Brain
>
> Department of Experimental Psychology
>
> University of Cambridge, UK
>
>
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Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error?

[Nick Schmansky]

Liz,

a 64bit build is in the works.  in the meantime, you can get a version
of mri_robust_register built for lion (64b) here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-lion/

Nick


On Tue, 2012-10-02 at 12:12 -0400, Martin Reuter wrote:
> Hi Liz,
>  
> I have no idea about the progress of FS on 64 bit OSX. I think it
> should be possible to run Linux in a virtual box. Both these questions
> can probably be answered by Nick.
>  
> But I would recommend to first try to use a new version of
> mri_robust_template from our dev version (if it goes through, please
> double check 1 or two cases that the base norm.mgz looks good in the
> base and that all time points are aligned in the long directories). It
> may work as the new version needs less memory and I think 3.5 Gig
> should be enough for 3 time points.
>  
> Nick, can you point Liz to where to download a mac version of the
> mri_robust_template from dev?
>  
> Thanks, Martin
> - Original Message - 
> From: Liz Bowman 
> To: FreeSurfer List 
> Sent: Monday, October 01, 2012 10:04 PM
> Subject: Re: [Freesurfer] More than two time-points in
> longitudinal base = Memory allocation error?
> 
> 
> Hi Martin, 
> 
> 
> Thanks for your reply.
> 
> 
> My iMac has 14 GB of RAM.  However, the Mac OS version of
> FreeSurfer is only available as a 32-bit version, and thus any
> time FreeSurfer requires more than approximately 3.5 GB of
> memory it will exit with an error.  Are there any plans yet
> for a 64-bit Mac OS version?
> 
> 
> I have a number of clinical participants with between 3 and 8
> scans (timepoints) that I wish to analyse longitudinally.  I
> have already run the cross-sectional reconstructions,
> performed the necessary pial and white matter edits and
> inserted control points, and re-run all the cross sectional
> reconstructions again to take accounts of the edits.
> 
> 
> If I cannot now create the template reconstructions in Mac OS
> with all of my timepoints for all of my participants, what are
> my options?   
> 
> 
> Is it possible to run the 64-bit Linux version of FreeSurfer
> using VirtualBox on my iMac? 
> 
> 
> Could I then just create the template reconstructions for all
> my participants using virtualbox linux and return to Mac OS to
> run the final longitudinal stream on all the participants? I
> am aware that there are differences in how the 64-bit linux
> and the 32-bit Mac OS FreeSurfers will approach the analysis,
> but if I confine my use of the 64-bit Linux to just the
> creation of the templates for both (clinical and control)
> groups, then any differences between the systems should not
> affect the between-group comparisons?
> 
> 
> I do not have access to an actual Linux system.
> 
> 
> Best regards,
> 
> 
> EA Bowman
> 
> 
> > From: mreu...@nmr.mgh.harvard.edu
> > To: ea_bow...@hotmail.com
> > Date: Mon, 30 Jul 2012 18:00:29 -0400
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] More than two time-points in
> longitudinal base = Memory allocation error?
> > 
> > Hi Liz,
> > 
> > you need more memory (see the error message: cannot allocate
> memory).
> > 
> > Best, Martin
> > 
> > 
> > On Mon, 2012-07-23 at 10:21 +1000, Liz Bowman wrote:
> > > Hello,
> > > 
> > > 
> > > I have several patients scans taken over multiple time
> points (up to
> > > nine time points in some patients). I thought I might be
> able to use
> > > these to create a base template for longitudinal
> processing, however
> > > the process fails and exits with errors if I try to create
> a base with
> > > more than two time points from a patient. 
> > > 
> > > 
> > > This is a sample of the error log of the most recent
> attempt, with
> > > three timepoints:
> > > 
> > > 
> > > Resolution: 1 S( 128 128 128 ) T( 128 128 128 )
> > > Iteration(f): 1 -- diff. to prev. transform: 0.876663
> > > Iteration(f): 2 -- diff. to prev. transform: 0.0148738
> > > Iteration(f): 3 -- diff. to prev. transform: 0.00156813 <
> 0.01
> > > :-)
> > > 
> > > 
> > > Resolution: 0 S( 256 256 256 ) T( 256 256 256 )
> > > Iteration(f): 1 -- diff. to prev. transform: 0.263086
> > > Iteration(f): 2mri_robust_template(103

Re: [Freesurfer] subdividing consistently within aparc.annot

[John Griffiths]

Would the Lausanne2008 template from the connectome mapping toolkit not do
the trick?

http://nipy.sourceforge.net/nipype/users/examples/dmri_connectivity_advanced.html



On 3 October 2012 23:18, Satrajit Ghosh  wrote:

> hi bruce,
>
> is there a way to divide consistently (same number of regions and one to
> one correspondence - obviously not the exact same areas) across subjects
> within aparc regions?
>
> cheers,
>
> satra
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 

Mr. John Griffiths, MSc

PhD Candidate

Centre for Speech, Language, and the Brain

Department of Experimental Psychology

University of Cambridge, UK
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[Freesurfer] subdividing consistently within aparc.annot

[Satrajit Ghosh]

hi bruce,

is there a way to divide consistently (same number of regions and one to
one correspondence - obviously not the exact same areas) across subjects
within aparc regions?

cheers,

satra
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Re: [Freesurfer] is skull strip needed

[Bruce Fischl]

You are right, no need to
Bruce

On Oct 3, 2012, at 5:46 PM, Gregory Kirk  wrote:

> 
> if there is extra skull left after skull stripping but the pial surface is 
> fine ( i.e. the left skull did not get 
> included in the pial surface ) is it nessesary to adjust watershed parameters 
> or manually
> remove it and reprocess the data set ? I am thinking it is not needed if it 
> is not causing
> an error in the surface.
> 
> 
> thanks
> greg
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> 

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[Freesurfer] is skull strip needed

[Gregory Kirk]

if there is extra skull left after skull stripping but the pial surface is fine 
( i.e. the left skull did not get 
included in the pial surface ) is it nessesary to adjust watershed parameters 
or manually
remove it and reprocess the data set ? I am thinking it is not needed if it is 
not causing
an error in the surface.


thanks
greg
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[Freesurfer] mris_pmake options

[octavian lie]

Dear all,

I need to measure the distance between 2 points on the same hemisphere for
subject A, in the common surface space as I have to compare it with the
distance between other 2 points for subjects B, C...
I used

mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1
sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:1,endVertex:2
Questions:
1. Is the calculated path the geodesic, in this case
spherical, measure that can be directly compared with that from another
subject, or not?
2. How could I compare the distance on the pial surface  of subject 1
(vertex 1-vertex 2) to subject 2 (vertex 1 to2). Is changing
--surface0 argument to pial enough? (In the Recon-all Dev table, sphere.reg
is an imput to generating label/?h.aparc.annot, which in turn is used to
generate ?h.pial surfaces, does that mean that pial surfaces from 2
subjects are already registered?)
3. I do not understand the choice of defaults for  --surface0 (inflated) ,
--surface1 (smoothwm), curve 0 and 1. This is not surprising, since I do
not have the math expression for the cost function available; just
wondering, what is the reason to have inlated as the default for surface 0?
Do I need to change any of the auxilliary terms used above with sphere.reg
to accomplish what I want to accomplish?
4. Last, is there a way to mark the vertices for these geodesic path on the
main surface used in order to use then for label creation?

Your insight is very important,
thank you,
Octavian.
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Re: [Freesurfer] long_mris_slopes error

[Martin Reuter]

Not sure.
Maybe try the updated scripts
From
http://martinos.org/~mreuter/long/ 

Best Martin

Alexandru Hanganu  wrote:

>Dear Freesurfer Experts,
>
>While performing the long_mris_slopes cmd, we receive an error:
>
>---
>SUBJECT pls_pd_base00  Running Within-Subject GLM
>
>Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ...
>
>mri_glmfit --y 
>/Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh
>
>--X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof
>
>  --no-contrasts-ok --surf pls_pd_base00 lh --label 
>/Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label
>
>--glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm
>
>Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/long_mris_slopes", line 732, in 
>
> run_cmd(cmd,'mri_glmfit did not work?')
>   File "/Applications/freesurfer/bin/long_mris_slopes", line 422, in 
>run_cmd
> retcode = subprocess.call(args)
>   File 
>"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
>
>line 443, in call
> return Popen(*popenargs, **kwargs).wait()
>   File 
>"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
>
>line 593, in __init__
> errread, errwrite)
>   File 
>"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
>
>line 1079, in _execute_child
> raise child_exception
>OSError: [Errno 8] Exec format error
>---
>
>we changed the mris_calc and mri_glmfit files with the new ones (8.2MB
>/ 
>15.8MB).
>
>Can you please help with this ?
>
>Thank you in advance,
>
>Sincerely,
>Alex.
>
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[Freesurfer] A question about downsmapling mulitple surfaces (white, pial, sphere) for registration

[Longchuan Li]

Hi, FreeSurfer experts

Currently, I am planning to run tractography using wm surfaces as seed masks 
and pial surfaces as stop masks implemented in FSL. In order to make fibers go 
through one hemisphere to another, I need to remove the medial wall from both 
seed surfaces and the pial surfaces. However, as the original surfaces' 
resolution is too high, I will need to downsample the surfaces first, in order 
to manage the computational time to a reasonable time limit. My strategy is 
like this: 

(1) downasample the sphere, pial and white from original 700K to 10K using 
"mris_decimate" with a factor of 0.1
(2) register the subject's downsampled sphere to the template surface sphere
(3) transfer the label file with medial wall excluded from the template space 
to the subject's sphere space based on the warping file. 
(4) convert the label file to seed mask (based on white surface) and stop mask 
(based on pial surface). using a FSL tool  

My questions are: 
(1) Can surface-based registration be properly done when I used the downsampled 
version of the sphere to register to the template's sphere?
(2) As my pial, sphere and white surfaces are 
downsampled separately by repeatedly using the "mris_decimate", will they still 
have that point-to-point correspondence as the original ones?

I would appreciate if anyone could help on this and point out any potential 
problems and/or better strategies

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Re: [Freesurfer] Lesioned brain (surface) registration to fs average

[octavian lie]

Actually, the white matter is affected too within the resection bed.

Just to make sure, using mri_label2label with surface option to pass a
label from subject 1 to subject 2 is equivalent to registering that label
to fsaverage via sphere.reg for that subject, then transferring the label
from fs average to subject 2 via sphere.reg for subject 2. I assume I can
use it to transfer the label to fsaverage as well; is it better or
same/equivalent to use mri_surf2surf vs mri_label2label to transfer a label
from one subject to another

Thank you very much,

Octavian.
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Re: [Freesurfer] Configuring freesurfer developer's environment on Ubuntu

[Azeez Adebimpe]

I am running the freesufer on ubuntu and working fine without any other 
configuration. I followed the configuration and it is simple 
http://mirko.windhoff.net/how_to/install_freesurfer_on_ubuntu
azeez
> From: dkim...@cw.bc.ca
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Wed, 3 Oct 2012 13:03:49 -0700
> Subject: [Freesurfer] Configuring freesurfer developer's environment on   
> Ubuntu
> 
> Hello freesurfer users!
> 
> I've got a brand new PC with Ubuntu 12.04 64-bit running and following the 
> freesurfer developer's guide to set up a developer environment, I'm getting 
> numerous "undeclared function / undefined type" errors during make.
> Seeing that the undeclared functions or variable types are actually defined 
> in .h files that are being declared correctly, I'm suspecting there's 
> configuration problem and was wondering has anyone had success in building 
> freesurfer on Ubuntu 12.04 64-bit or building freesurfer on any previous 
> Ubuntu release?
> 
> The steps I took to get as far as getting undeclared function/undefined type 
> errors are:
> 
> - Pre-built 3rd party libraries were downloaded and put into 
> /usr/pubsw/packages/
> 
> During configuration, I've made modification to bypass errors:
> - changed configure script so that script will not end when libvtkfreetype, 
> libBLT is "not found" by the script, although, I have the .so files in the 
> correct library
> - disabled -Werror flag
> - copied /usr/bin/libtool into ~/dev/ in order to avoid libtool version 
> mismatch error
> - In Makefile for ~/utils/ commented out any rules for 
> unwarpGradientNonLinearity since this file is no where to be seen
> 
> Thank you for any advice and pointers!
> 
> Danny Kim
> BC Children's Hospital
> 
> 
> Danny Kim
> Children's Brain Mapping Centre
> BC Children's Hospital
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[Freesurfer] Configuring freesurfer developer's environment on Ubuntu

[Kim, Daniel]

Hello freesurfer users!

I've got a brand new PC with Ubuntu 12.04 64-bit running and following the 
freesurfer developer's guide to set up a developer environment, I'm getting 
numerous "undeclared function / undefined type" errors during make.
Seeing that the undeclared functions or variable types are actually defined in 
.h files that are being declared correctly, I'm suspecting there's 
configuration problem and was wondering has anyone had success in building 
freesurfer on Ubuntu 12.04 64-bit or building freesurfer on any previous Ubuntu 
release?

The steps I took to get as far as getting undeclared function/undefined type 
errors are:

- Pre-built 3rd party libraries were downloaded and put into 
/usr/pubsw/packages/

During configuration, I've made modification to bypass errors:
- changed configure script so that script will not end when libvtkfreetype, 
libBLT is "not found" by the script, although, I have the .so files in the 
correct library
- disabled -Werror flag
- copied /usr/bin/libtool into ~/dev/ in order to avoid libtool version 
mismatch error
- In Makefile for ~/utils/ commented out any rules for 
unwarpGradientNonLinearity since this file is no where to be seen

Thank you for any advice and pointers!

Danny Kim
BC Children's Hospital


Danny Kim
Children's Brain Mapping Centre
BC Children's Hospital
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[Freesurfer] long_mris_slopes error

[Alexandru Hanganu]

Dear Freesurfer Experts,

While performing the long_mris_slopes cmd, we receive an error:

---
SUBJECT pls_pd_base00  Running Within-Subject GLM

Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ...

mri_glmfit --y 
/Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh
 
--X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof 
  --no-contrasts-ok --surf pls_pd_base00 lh --label 
/Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label 
--glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm

Traceback (most recent call last):
   File "/Applications/freesurfer/bin/long_mris_slopes", line 732, in 

 run_cmd(cmd,'mri_glmfit did not work?')
   File "/Applications/freesurfer/bin/long_mris_slopes", line 422, in 
run_cmd
 retcode = subprocess.call(args)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
 
line 443, in call
 return Popen(*popenargs, **kwargs).wait()
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
 
line 593, in __init__
 errread, errwrite)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py",
 
line 1079, in _execute_child
 raise child_exception
OSError: [Errno 8] Exec format error
---

we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 
15.8MB).

Can you please help with this ?

Thank you in advance,

Sincerely,
Alex.

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Re: [Freesurfer] Freesurfer and FSL

[Ana Arruda]

Yes, you're right. But in that case, these changes would be quite similar
for right-hippocampus too.

Based on my analysis and literature, Freesurfer has more accurate measures
than FSL. The doctors are quite conservative about boundaries so that
measures are the smallest between Freesurfer and FSL. In other words, the
measures obtained by Freesurfer are in the middle, they are bigger than
manual and smaller than FSL.

However, for left-hippocampus the volumes measured by Freesurfer are always
bigger than FSL and Manual segmentation. The only reason I can find, once
the softwares use the same criteria for left and right-hippocampus, is
related with the doctor responsible for the manual segmentation.
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Re: [Freesurfer] Freesurfer and FSL

[Bruce Fischl]

Hi Ana

the point is that even if you aren't segmenting individual structures, if 
some are not in your manual protocol but are in ours, then lateralization 
in them will cause lateralization differences in the degree of overlap 
between the two


cheers
Bruce

On Wed, 3 
Oct 2012, Ana Arruda wrote:



I haven't gone so far. I've just done the simplest way. I've search the
proper commands just to do the hippocampus segmentation, but not its
subfields. All my analysis was made with the left and right-hippocampus
volumes from the aseg.stats file. 
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Re: [Freesurfer] Freesurfer and FSL

[Ana Arruda]

I haven't gone so far. I've just done the simplest way. I've search the
proper commands just to do the hippocampus segmentation, but not its
subfields. All my analysis was made with the left and right-hippocampus
volumes from the *aseg.stats *file.
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Re: [Freesurfer] Freesurfer and FSL

[Bruce Fischl]

kind of. There are natural lateralizations in the brain that are taken into 
account. Not sure what is known about lateralizations of hippocampal 
subfield and white matter components though
Bruce




On Wed, 3 Oct 2012, Ana Arruda wrote:

> Thank you very much!
> 
> About the previous question, do the softwares use the same criteria for each
> hippocampus?
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Freesurfer and FSL

[Ana Arruda]

Thank you very much!

About the previous question, do the softwares use the same criteria for
each hippocampus?
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Re: [Freesurfer] cortical parcellation question

[Bruce Fischl]

Hi Daniel,

1. Do you mean the atlas or the parcellation of your subjects? We cannot 
distribute the individual subjects in the atlas as the data was collected 
under an IRB long ago that didn't include this. The atlas itself (summary 
statistics derived from those subjects) is included in the FreeSurfer 
distribution.


2. The subcortical areas are the same, but not the cortical ones. That 
cortical parcellation is quite coarse, and while we did implement it we 
were never given permission to distribute the automated version, so it is 
not part of FreeSurfer. The boundaries that we define are thus different 
than that one (and since the  Harvard-Oxford one is based on volumetric 
labeling of folding patterns we found that it contained a bunch of errors 
in which e.g. the wrong side of a sulcus was labeled)


cheers
Bruce


On Wed, 3 Oct 
2012, Daniel Ferreira wrote:



Dear experts,
I have a couple of questions regarding the cortical parcellation atlas that
is used in Freesurfer:

1) I would like to know if it is possible to obtain the Desikan-Killiany
atlas in 3D analyze/nifti format. With each region of the brain assigned a
discrete integer number (for example the all of the voxels of the left
inferior temporal lobe have an intensity  = 1, or the whole of the left
hippocampus = 2).

2) Are the Harvard-Oxford cortical and subcortical atlases that can be
downloaded with FSL the same as the cortical parcellation atlas that is used
in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the
left inferior temporal cortex in the Freesurfer cortical parcellation = the
left inferior temporal cortex in the Harvard-Oxford atlas downloaded with
FSL)

Many thanks

Daniel Ferreira



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[Freesurfer] cortical parcellation question

[Daniel Ferreira]

Dear experts,

I have a couple of questions regarding the cortical parcellation atlas that
is used in Freesurfer:

1) I would like to know if it is possible to obtain the Desikan-Killiany
atlas in 3D analyze/nifti format. With each region of the brain assigned a
discrete integer number (for example the all of the voxels of the left
inferior temporal lobe have an intensity  = 1, or the whole of the left
hippocampus = 2).

2) Are the Harvard-Oxford cortical and subcortical atlases that can be
downloaded with FSL the same as the cortical parcellation atlas that is
used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does
the left inferior temporal cortex in the Freesurfer cortical parcellation =
the left inferior temporal cortex in the Harvard-Oxford atlas downloaded
with FSL)

Many thanks

Daniel Ferreira
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Re: [Freesurfer] Freesurfer and FSL

[Bruce Fischl]

Hi Ana

yes, our Neuron (2002) and NeuroImage (2004) papers describe the 
techniques.


cheers
Bruce
On Wed, 3 Oct 2012, Ana Arruda wrote:


I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares,  FSL and Freesurfer,
don't have a different away to operate in either hippocampus. Do you agree?
That way of operating confuses me on how to interpret the differences found
only for the left hippocampus.

Anyway, thank you for your help.

Another thing, in my thesis I'll have to describe what I've done in
Freesurfer to obtain the hippocampus segmentation. Is there any article that
describes in a general and brief way  all the steps to be followed towards
the final goal?

Thank you all, again.


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Re: [Freesurfer] Freesurfer and FSL

[Ana Arruda]

I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares,  FSL and Freesurfer,
don't have a different away to operate in either hippocampus. Do you agree?
That way of operating confuses me on how to interpret the differences found
only for the left hippocampus.

Anyway, thank you for your help.

Another thing, in my thesis I'll have to describe what I've done in
Freesurfer to obtain the hippocampus segmentation. Is there any article
that describes in a general and brief way  all the steps to be followed
towards the final goal?

Thank you all, again.
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Re: [Freesurfer] Skullstrip error issue

[Louis Nicholas Vinke]

Hi Rashmi,
I assume you've read the skullstrip wiki page, but I've included it below 
just in case.

Have you tried different watershed thresholds?  Also, you do not need to 
include the -clean-bm flag every time.  You can run the skullstrip step 
once with the -clean-bm to start from scratch, and the run skullstripping 
again without the -clean-bm flag so that you are performing additional 
skullstripping on the output from the last run.  So something like this:

first:
recon-all -skullstrip -clean-bm -s 
second run:
recon-all -skullstrip -s 

or maybe some variant of those commands where you are also specifying new 
watershed thresholds.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix

Hope that helps.
-Louis

On Tue, 2 Oct 2012, Rashmi Singh wrote:

> Thank you Bruce,
> I certainly understand your point. In my study I am trying to use whole
> brain volume to normalize my volumetrics data. Due to the inclusion of the
> dura into brain, I may get variation in the whole brain volume across
> subjects.
> In addition the current issue is affecting the graymatter/whitematter
> boundary that will also bring variation in the cortical thickness
> measurements.
> That is the reason I was trying to get good skull stripping.
>
> Your suggestions and guidance will help me.
> Thanks,
> Rashmi.
>
>
>
>
> On 10/2/12 2:05 PM, "Bruce Fischl"  wrote:
>
>> Hi Rashmi
>>
>> getting rid of all the dura without removing any problem is exceedingly
>> difficult (if not impossible). Usually we live with some remaining dura
>> as it doesn't affect the surface placement much.
>>
>> cheers
>> Bruce
>> On Tue, 2 Oct 2012, Rashmi
>> Singh wrote:
>>
>>> Hello experts,
>>>  I am getting skull strip issues with FreeSurfer recon-all runs in every
>>> data.
>>> I ran recon-all on my T1-data and noticed that the skullstrip is not so
>>> good. Almost in every subjects there were  dura included, so I tried the
>>> suggestion of using the flags -skullstrip and -Clean?bm and ?gcut in my
>>> recon-all command line for one subject. Forexmaple:
>>> I ran reconall using the following command lin:
>>> recon-all ?skullstrip first -clean?bm ?gcut ?sAA***.T* -all
>>> -use?mritotal
>>>
>>> The run was complete and I looked at the brainmask.mgz file of the
>>> output.
>>> But I didn't see any correction.
>>> I am attaching the jpg image of the sagittal view of brainmask.nii ( I
>>> converted the mgz file to nii to view tham in afni)
>>> SubjFS: is the image from recon-all run
>>> SubjFS: is the image  from recon-all that was run with
>>> Skullstrip/clean-bm/gcut options included.
>>>
>>> Did I do anything wrong?
>>> Your guidance and suggestion needed.
>>> Thanks,
>>> Rashmi.
>>>
>>>
>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
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>> properly
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>
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