Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Inati, Souheil (NIH/NIMH) [E]]

Hi Matt,

Thanks for the link.

Reading on pages 29-31, I am struck by the complexity of the procedure.  Not to 
say that it doesn't work, or that the single T1w image free-surfer stuff is 
simple :-), on the contrary, it's just that I was expecting to see something 
about an optimization that used both images, rather than something based on the 
T1w image followed by an exclusion criterion based on the T2w image.  Anyway, 
works better than without.

Minor question on the acquisition of the anatomicals:
- Why are you using partial fourier in the read direction?  You're throwing 
away a lot of SNR at the high spatial frequencies, seems a shame to go to 0.7mm 
and then do that.

Cheers,
Souheil

On May 12, 2013, at 10:54 PM, Matt Glasser  wrote:

> This is available online now:
> 
> http://authors.elsevier.com/sd/article/S1053811913005053
> 
> 
> On 5/7/13 3:10 PM, "Bruce Fischl"  wrote:
> 
>> actually Matt Glasser points out that a brief description is in his paper
>> that is coming out soon, and there is also some description in Andre's
>> multi-echo mprage paper
>> Bruce
>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>> wrote:
>> 
>>> thanks :-)
>>> 
>>> On May 7, 2013, at 3:28 PM, Bruce Fischl 
>>> wrote:
>>> 
>>>> no, of course not :)
>>>> 
>>>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E]
>>>> wrote:
>>>> 
>>>>> Hi Bruce,
>>>>> 
>>>>> Out of curiosity and for reference for my users, do you have a paper
>>>>> on the T2 or FLAIR assisted segmentation?
>>>>> 
>>>>> Cheers,
>>>>> Souheil
>>>>> 
>>>>> -
>>>>> 
>>>>> Souheil Inati, PhD
>>>>> Staff Scientist
>>>>> FMRI Facility
>>>>> NIMH/NIH/DHHS
>>>>> souheil.in...@nih.gov<mailto:souheil.in...@nih.gov>
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On May 7, 2013, at 2:24 PM, Bruce Fischl
>>>>> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>>>> 
>>>>> Hi Katie
>>>>> 
>>>>> I'm really not sure. These days I would recommend a highres (e.g. 1mm
>>>>> isotropic) FLAIR if you can get one, or T2 if not. The T2* can help,
>>>>> but
>>>>> it's pretty noisy in brain.
>>>>> 
>>>>> cheers
>>>>> Bruce
>>>>> 
>>>>> On Tue, 7 May 2013, Katie Surrence wrote:
>>>>> 
>>>>> Dear Freesurfer gurus,
>>>>> 
>>>>> At the course, André van der Kouwe mentioned in his morphometry
>>>>> methods talk that T2* weighted contrast from
>>>>> MEMPRAGE could be used to further seperate dura from cortex, as also
>>>>> discussed in this paper:
>>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE
>>>>> scanner in our lab.  The internet suggests
>>>>> that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?
>>>>> Would it work the same way?  Could you also
>>>>> use these images with the mris_make_surfaces command?
>>>>> 
>>>>> Thanks very much for your insight -- and I enjoyed the course!
>>>>> 
>>>>> /Katie Surrence
>>>>> 
>>>>> --
>>>>> Research Coordinator
>>>>> Social Cognition Laboratory
>>>>> New York State Psychiatric Institute
>>>>> 
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>> 
>>>>> 
>>>>> The information in this e-mail is intended only for the person to
>>>>> whom it is
>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>> the e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>> 
>>>>> 
>>>>> 
>>> 
>>> 
>>> 
>>> ___
>> Freesurfer mailing list
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>> 
>> 
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> dispose of the e-mail.
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Re: [Freesurfer] MRI artifacts detection

[Inati, Souheil (NIH/NIMH) [E]]

Question from the MR Physics peanut gallery:
How are you defining/measuring SNR for the anatomical sequences?

(Sticking to Siemens.)  The way I think about this, if what you have are the 
dicoms from an mprage which was collected with a receiver array, acceleration 
and pre-scan normalization, then estimating anything about the electrical noise 
is impossible because (…. insert inappropriate vendor trashing here ….).  
Basically, the vendors have not designed their recon chains to produce images 
in SNR units.  Or even images with a body coil intensity reference (i.e. 
pre-scan normalize) with a proper accounting of the noise so that you could 
make an image of the noise variance at each pixel to then feed into a smart 
segmentation.

Thoughts?

-Souheil

-

Souheil Inati, PhD
Staff Scientist
FMRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov




On May 13, 2013, at 9:13 AM, Jordi Delgado 
mailto:jordi...@pic.es>> wrote:

Hi Bruce,

Thank you for your fast answer. I'm focusing on SNR, Motion Correction and 
Intensity Inhomogeneities.

Regards,


2013/5/13 Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>
Hi Jordi

this is definitely vendor specific. In Siemens you can for example turn on 
"prescan normalization" which will correct for intensity bias. You can have it 
generate two series - one with and one withour the correction. What other 
artifacts do you mean? There are lots of possibilities

cheers
Bruce




On Mon, 13 May 2013, Jordi Delgado wrote:

Dear FS experts,

I'm studying the most common artifacts on MRI scanning. I started with the SNR 
calculation (which is included
in recent FS versions), but I'm afraid that these artifact is 
filtered/processed with the scanner control
program, and I'm wasting time trying to calculate this ratio.

My qüestion is, any one of you know if the scanners control programs are 
correcting SNR, Inhomogeneties,
motion, etc? Have any sense to detect these artifacts, as a quality assurance 
method before to accept/decline
the adquired image with an external method of the scanner control program?

Thank you in advance,

--
Jordi Delgado Mengual
PIC (Port d'Informació Científica)
Campus UAB, Edifici D
E-08193 Bellaterra, Barcelona
Tel: +34 93 586 82 32 Fax: +34 93 581 41 
10
http://www.pic.es
Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html




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--
Jordi Delgado Mengual
PIC (Port d'Informació Científica)
Campus UAB, Edifici D
E-08193 Bellaterra, Barcelona
Tel: +34 93 586 82 32 Fax: +34 93 581 41 10
http://www.pic.es
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Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Inati, Souheil (NIH/NIMH) [E]]

thanks :-)

On May 7, 2013, at 3:28 PM, Bruce Fischl  wrote:

> no, of course not :)
> 
> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] 
> wrote:
> 
>> Hi Bruce,
>> 
>> Out of curiosity and for reference for my users, do you have a paper on the 
>> T2 or FLAIR assisted segmentation?
>> 
>> Cheers,
>> Souheil
>> 
>> -
>> 
>> Souheil Inati, PhD
>> Staff Scientist
>> FMRI Facility
>> NIMH/NIH/DHHS
>> souheil.in...@nih.gov<mailto:souheil.in...@nih.gov>
>> 
>> 
>> 
>> 
>> On May 7, 2013, at 2:24 PM, Bruce Fischl 
>> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> 
>> Hi Katie
>> 
>> I'm really not sure. These days I would recommend a highres (e.g. 1mm
>> isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
>> it's pretty noisy in brain.
>> 
>> cheers
>> Bruce
>> 
>> On Tue, 7 May 2013, Katie Surrence wrote:
>> 
>> Dear Freesurfer gurus,
>> 
>> At the course, André van der Kouwe mentioned in his morphometry methods talk 
>> that T2* weighted contrast from
>> MEMPRAGE could be used to further seperate dura from cortex, as also 
>> discussed in this paper:
>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner 
>> in our lab.  The internet suggests
>> that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it 
>> work the same way?  Could you also
>> use these images with the mris_make_surfaces command?
>> 
>> Thanks very much for your insight -- and I enjoyed the course!
>> 
>> /Katie Surrence
>> 
>> --
>> Research Coordinator
>> Social Cognition Laboratory
>> New York State Psychiatric Institute
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> 
>> 
>> 


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Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

[Inati, Souheil (NIH/NIMH) [E]]

Hi Bruce,

Out of curiosity and for reference for my users, do you have a paper on the T2 
or FLAIR assisted segmentation?

Cheers,
Souheil

-

Souheil Inati, PhD
Staff Scientist
FMRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov




On May 7, 2013, at 2:24 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Katie

I'm really not sure. These days I would recommend a highres (e.g. 1mm
isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but
it's pretty noisy in brain.

cheers
Bruce

On Tue, 7 May 2013, Katie Surrence wrote:

Dear Freesurfer gurus,

At the course, André van der Kouwe mentioned in his morphometry methods talk 
that T2* weighted contrast from
MEMPRAGE could be used to further seperate dura from cortex, as also discussed 
in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/.  We have a GE scanner in 
our lab.  The internet suggests
that a Multi-echo FSPGR/FGRE exists.  Would this be the analog?  Would it work 
the same way?  Could you also
use these images with the mris_make_surfaces command?

Thanks very much for your insight -- and I enjoyed the course!

/Katie Surrence

--
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute

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[Freesurfer] multi-echo mprage

[Inati, Souheil (NIH/NIMH) [E]]

Hi All,

I have some multi-echo mprage images from a sequence and protocol set up to 
emulate Andre's 2008 paper.  What's are the "best-practices" for using data 
from this type of sequence in Freesurfer?

Related side questions: 
I have used the suggested morphometry protocols on the FS wiki (1mm iso 
resolution, same FOV, bandwidth matched, etc)
1) are people who are using this method using 4 echoes of alternating polarity, 
or 4 echoes of the same polarity?
2) for some subjects I have also acquired a 3D T2.  Any recommendations on 
using these data together?

Thanks,
Souheil



Souheil Inati, PhD
Staff Scientist
Functional MRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov
301-402-9409




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Re: [Freesurfer] mprage resolution for surfaces/thicknes?

[Inati, Souheil (NIH/NIMH) [E]]

Thanks Bruce.  FYI, I got a couple of other emails off list.  One of them 
reminded me that the original ADNI protocol had this resolution.
Cheers,
Souheil


On Mar 5, 2013, at 9:50 AM, Bruce Fischl wrote:

> Hi Souheil
> 
> our standard acquisition used to be 1.33x1x1 so I don't think there 
> should be any problem (although it has been a long time since we used to 
> get those - 1.5T and single channel)
> 
> cheers
> Bruce
> On Tue, 5 Mar 2013, Inati, Souheil 
> (NIH/NIMH) [E] wrote:
> 
>> A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in 
>> plane, 1.3mm thick.  The SNR and CNR are pretty good.  I figured I'd ping 
>> the list to see if anyone have any experience running scans with the 
>> slightly thickish voxels through the recon-all pipeline.  Anything I ought 
>> to look out for in particular?
>> 
>> Thanks,
>> Souheil
>> 
>> 
>> Souheil Inati, PhD
>> Staff Scientist, Functional MRI Facility
>> NIMH/NIH/DHHS
>> souheil.in...@nih.gov
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
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> 
> 
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> at
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[Freesurfer] mprage resolution for surfaces/thicknes?

[Inati, Souheil (NIH/NIMH) [E]]

A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in 
plane, 1.3mm thick.  The SNR and CNR are pretty good.  I figured I'd ping the 
list to see if anyone have any experience running scans with the slightly 
thickish voxels through the recon-all pipeline.  Anything I ought to look out 
for in particular?

Thanks,
Souheil


Souheil Inati, PhD
Staff Scientist, Functional MRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov
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[Freesurfer] Import/export out of curry

[Inati, Souheil (NIH/NIMH) [E]]

Has anyone used freesurfer segmentations/labels in Curry?

--

Souheil Inati, PhD
Staff Scientist
Functional MRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov





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Re: [Freesurfer] mri_convert feature request?

[Inati, Souheil (NIH/NIMH) [E]]

You have to be clear when you say support.  I don't know what you're trying to 
do, but you can put anything you like in the extension part of the nifti 
header.  If you want to store TR, TE, flip angle, mother's date of birth, you 
can.  You just have to write the code to handle it.  Other programs that 
support nifti properly but don't know about your fields will silently ignore 
them.  AFNI stores a lot of information in the extension fields.  They are very 
useful for certain applications.

-SI


On Aug 28, 2012, at 1:50 PM, dgw wrote:

> Ok, so I guess my problem is that the formats don't support it. Sorry
> for the run around.
> 
> D
> 
> On Tue, Aug 28, 2012 at 1:46 PM, Inati, Souheil (NIH/NIMH) [E]
>  wrote:
>> Hi Bruce and Freesurfers,
>> 
>> The standard part of the nifti_1 header specifies that the first three 
>> dimensions are space and the fourth dimension is time and you can store 
>> dX,dY,dZ,dT and units.  This page has a nice description of that part of the 
>> standard:
>> http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/xyzt_units.html
>> "Time" can be TR, TE, frequency, whatever.
>> 
>> Whether or not these fields are set correctly is dicom converter dependent.  
>> I have no idea what most converters out there do.  If memory serves (which 
>> it does less and less in my middle-age), the converter that I was involved 
>> in at NYU (written by Valerio Luccio, 
>> http://cbi.nyu.edu/software/dinifti.php) assumes that you are doing fMRI and 
>> puts the TR in the fourth dimension.  Note also that what the label 'TR' 
>> means is another pulse sequence/vendor specific story.  For evenly sampled 
>> fmri experiments we know what we're talking about.  For other things, not so 
>> clear.
>> 
>> If you want to use the extension fields in the nifti header, then you could 
>> put more information there, but there's no real convention on how to do this.
>> 
>> This is all a mess.  NIFTI is not a real data format.  It's just a hack to 
>> get us past the misery that was fmri analysis software interoperability in 
>> the 1990s.  Unfortunately, DICOM is worse.  I'll back off of that 
>> inflammatory comment and say that for a restricted set of imaging, NIFTI is 
>> great and very useful, but it's not a good all purpose MRI image storage 
>> format.   Someday the MNI guys will win and we'll end up with a real HDF5 
>> based format.
>> 
>> If any of you are still reading this, there is an interesting project being 
>> put forward by the ISMRM and the MRM journal for a standardized format for 
>> MRI raw data storage.  The idea is that you can have reproducible research 
>> in image reconstruction unless you agree on a file format.  It's just 
>> getting off the ground, and it's not that useful for post processing, but 
>> the idea is to store all the scan parameters and the raw k-space data and 
>> sampling pattern, including things like diffusion encoding, physiological 
>> signals, etc.  Here's a link:
>> http://ismrmrd.sourceforge.net
>> 
>> Cheers,
>> Souheil
>> 
>> On Aug 28, 2012, at 12:39 PM, Bruce Fischl wrote:
>> 
>>> Hi Souheil,
>>> 
>>> does NIFTI store the MR parameters?
>>> 
>>> thanks
>>> Bruce
>>> 
>>> On Tue, 28 Aug 2012, Inati, Souheil (NIH/NIMH) [E] wrote:
>>> 
>>>> On most (all?) scanners TR is stored as an integer.  For example, on
>>> siemens it's in microseconds and then stored as a long.  (this is the value
>>> in the protocol, not the actual execution TR, but when/if there are no
>>> bugs, then this is correct).  When you convert a long to float (single or
>>> double precision) you will get some junk in the low bits because of type
>>> conversion.  In the dicom it's all string representations.
>>>> 
>>>> Does the dicom say 50.000 or 50?
>>>> How does the conversion from int
>>>> 
>>>> --
>>>> 
>>>> Souheil Inati, PhD
>>>> Staff Scientist
>>>> Functional MRI Facility
>>>> NIMH/NIH/DHHS
>>>> souheil.in...@nih.gov
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Aug 28, 2012, at 12:06 PM, Bruce Fischl wrote:
>>>> 
>>>>> does NIFTI support the MR parameters? I'm not sure it does. I suspect
>>>>> that 50 is correct and not 50.00745058060 (can you imagine setting
>>>>> that on the console)?
>&

Re: [Freesurfer] mri_convert feature request?

[Inati, Souheil (NIH/NIMH) [E]]

Hi Bruce and Freesurfers,

The standard part of the nifti_1 header specifies that the first three 
dimensions are space and the fourth dimension is time and you can store 
dX,dY,dZ,dT and units.  This page has a nice description of that part of the 
standard:
http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/xyzt_units.html
"Time" can be TR, TE, frequency, whatever.

Whether or not these fields are set correctly is dicom converter dependent.  I 
have no idea what most converters out there do.  If memory serves (which it 
does less and less in my middle-age), the converter that I was involved in at 
NYU (written by Valerio Luccio, http://cbi.nyu.edu/software/dinifti.php) 
assumes that you are doing fMRI and puts the TR in the fourth dimension.  Note 
also that what the label 'TR' means is another pulse sequence/vendor specific 
story.  For evenly sampled fmri experiments we know what we're talking about.  
For other things, not so clear.

If you want to use the extension fields in the nifti header, then you could put 
more information there, but there's no real convention on how to do this.

This is all a mess.  NIFTI is not a real data format.  It's just a hack to get 
us past the misery that was fmri analysis software interoperability in the 
1990s.  Unfortunately, DICOM is worse.  I'll back off of that inflammatory 
comment and say that for a restricted set of imaging, NIFTI is great and very 
useful, but it's not a good all purpose MRI image storage format.   Someday the 
MNI guys will win and we'll end up with a real HDF5 based format.

If any of you are still reading this, there is an interesting project being put 
forward by the ISMRM and the MRM journal for a standardized format for MRI raw 
data storage.  The idea is that you can have reproducible research in image 
reconstruction unless you agree on a file format.  It's just getting off the 
ground, and it's not that useful for post processing, but the idea is to store 
all the scan parameters and the raw k-space data and sampling pattern, 
including things like diffusion encoding, physiological signals, etc.  Here's a 
link:
http://ismrmrd.sourceforge.net

Cheers,
Souheil

On Aug 28, 2012, at 12:39 PM, Bruce Fischl wrote:

> Hi Souheil,
> 
> does NIFTI store the MR parameters?
> 
> thanks
> Bruce
> 
> On Tue, 28 Aug 2012, Inati, Souheil (NIH/NIMH) [E] wrote:
> 
>> On most (all?) scanners TR is stored as an integer.  For example, on 
> siemens it's in microseconds and then stored as a long.  (this is the value 
> in the protocol, not the actual execution TR, but when/if there are no 
> bugs, then this is correct).  When you convert a long to float (single or 
> double precision) you will get some junk in the low bits because of type 
> conversion.  In the dicom it's all string representations.
>> 
>> Does the dicom say 50.000 or 50?
>> How does the conversion from int
>> 
>> --
>> 
>> Souheil Inati, PhD
>> Staff Scientist
>> Functional MRI Facility
>> NIMH/NIH/DHHS
>> souheil.in...@nih.gov
>> 
>> 
>> 
>> 
>> On Aug 28, 2012, at 12:06 PM, Bruce Fischl wrote:
>> 
>>> does NIFTI support the MR parameters? I'm not sure it does. I suspect
>>> that 50 is correct and not 50.00745058060 (can you imagine setting
>>> that on the console)?
>>> On Tue, 28 Aug 2012, dgw wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I'm not sure if this is a bug report or a feature request. I have been
>>>> using mri_convert to convert dicoms to nii.gz and mgz files, and I
>>>> have noticed some discrepancies when reading the volumes in with
>>>> MRIread in either matlab or octave. The volumes differ in their
>>>> support of the flip angle, tr, te, and ti fields (I realize some of
>>>> this may be due to file type differences). Thought the standard output
>>>> of mri_convert shows the expected values.
>>>> 
>>>> In the mgz file the TR seems to be rounded i.e.
>>>> 50 instead of 50.00745058060 in the nii.gz
>>>> 
>>>> In the mgz file the flip angle and te are recorded
>>>> FA 0.52 while in the nii.gz it is 0
>>>> te 10.39... while in the nii.gz it is 0
>>>> 
>>>> The ti value appears strange to me in the mgz
>>>> ti = -1 while in the nii.gz it is 0
>>>> 
>>>> I have generated two files using mri convert off of the same MR volume
>>>> as a test case:
>>>> /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/877000-20-03.dcm
>>>> 
>>>> /cluster/hbot/agario_p2_2

Re: [Freesurfer] mri_convert feature request?

[Inati, Souheil (NIH/NIMH) [E]]

On most (all?) scanners TR is stored as an integer.  For example, on siemens 
it's in microseconds and then stored as a long.  (this is the value in the 
protocol, not the actual execution TR, but when/if there are no bugs, then this 
is correct).  When you convert a long to float (single or double precision) you 
will get some junk in the low bits because of type conversion.  In the dicom 
it's all string representations.  

Does the dicom say 50.000 or 50?
How does the conversion from int 

--

Souheil Inati, PhD
Staff Scientist
Functional MRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov




On Aug 28, 2012, at 12:06 PM, Bruce Fischl wrote:

> does NIFTI support the MR parameters? I'm not sure it does. I suspect 
> that 50 is correct and not 50.00745058060 (can you imagine setting 
> that on the console)?
> On Tue, 28 Aug 2012, dgw wrote:
> 
>> Hi,
>> 
>> I'm not sure if this is a bug report or a feature request. I have been
>> using mri_convert to convert dicoms to nii.gz and mgz files, and I
>> have noticed some discrepancies when reading the volumes in with
>> MRIread in either matlab or octave. The volumes differ in their
>> support of the flip angle, tr, te, and ti fields (I realize some of
>> this may be due to file type differences). Thought the standard output
>> of mri_convert shows the expected values.
>> 
>> In the mgz file the TR seems to be rounded i.e.
>> 50 instead of 50.00745058060 in the nii.gz
>> 
>> In the mgz file the flip angle and te are recorded
>> FA 0.52 while in the nii.gz it is 0
>> te 10.39... while in the nii.gz it is 0
>> 
>> The ti value appears strange to me in the mgz
>> ti = -1 while in the nii.gz it is 0
>> 
>> I have generated two files using mri convert off of the same MR volume
>> as a test case:
>> /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/877000-20-03.dcm
>> 
>> /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/volume.nii.gz
>> 
>> /cluster/hbot/agario_p2_2/dcm/test.mgz
>> 
>> These files were generated using /usr/local/freesurfer/stable5_1_0/
>> 
>> Thanks,
>> D
>> ___
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>> 
>> 
>> 
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Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

[Inati, Souheil (NIH/NIMH) [E]]

Hi Bruce,

I had a feeling you were going to say that I needed to be careful about 
scanners and sequence parameters :-)

The Oasis dataset looks like just what I would need to get a sense of things, 
as you said.  What should I do to get the segmentations?

Cheers,
Souheil

On Jan 17, 2012, at 8:49 AM, Bruce Fischl wrote:

> Hi Souheil,
> 
> the problem is that you'll really want to match acquisition parameters as 
> well as several demographics (e.g. age, gender, etc, SES, ...). If you just 
> want to get some feeling you could try looking at the Oasis dataset, for 
> which we have segmentations, or you could post your sequence parameters so 
> we could at least try to see if there are any datasets around that match it 
> more or less.
> 
> cheers
> Bruce
> 
> 
> On Mon, 16 Jan 2012, Inati, Souheil (NIH/NIMH) [E] wrote:
> 
>> Hi All,
>> 
>> I have a very small set of patients and I would like to compare the volumes 
>> of subcortical structures and thickness across the cortex to those of a 
>> large normative set.  I don't need all the underlying data, just means and 
>> standard deviations.  Is such a set of measures available?
>> 
>> Thanks,
>> Souheil
>> ___
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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
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[Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

[Inati, Souheil (NIH/NIMH) [E]]

Hi All,

I have a very small set of patients and I would like to compare the volumes of 
subcortical structures and thickness across the cortex to those of a large 
normative set.  I don't need all the underlying data, just means and standard 
deviations.  Is such a set of measures available?

Thanks,
Souheil
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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.