Re: [Freesurfer] PetSurfer gtmpvc

[Greve, Douglas N.,Ph.D.]

Yes, look in the gtm.stats.dat file. See this page for whichi column you need 
to look at
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


On 5/17/2019 12:42 PM, Boris Rauchmann wrote:

External Email - Use Caution

Hi all,

is there a way to easily get the volume stats for all regions after pvc 
correction using mri_gtmpvc ? I think its not included in gtm.stats.dat.

Thanks,
Boris



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Postdoctoral position in object and face recognition at NYU Abu Dhabi

[Olivia Cheung]

External Email - Use Caution

*Postdoctoral position in object and face recognition at NYU Abu Dhabi*

A postdoctoral research position is open at the Objects and Knowledge
Laboratory, headed by Dr. Olivia Cheung, at New York University Abu Dhabi (
http://www.oliviacheunglab.org/). The postdoctoral researcher will carry
out behavioral and fMRI experiments on human object, face, letter, and/or
scene recognition. Potential research projects include, but are not limited
to, investigations of the influences of experience and conceptual knowledge
on recognition processes.

Applicants must have a Ph.D. in Psychology, Cognitive Neuroscience, or a
related field, and should possess strong programming skills (e.g., Matlab).
Prior experience with neuroimaging and psychophysical techniques is highly
preferred. Initial appointment is for up to two years. Starting date is
flexible, preferably between August/September 2019.

The Objects and Knowledge Laboratory is part of the rapidly growing
Psychology division at New York University Abu Dhabi. The lab is located in
the campus on Saadiyat Island (Abu Dhabi’s cultural hub), and has access to
the state-of-the-art neuroimaging and behavioral facilities (including MRI,
MEG, eyetracking).

Apart from a generous salary, the postdoctoral researcher will receive
housing and other benefits. More information about living in Abu Dhabi can
be found here:
http://nyuad.nyu.edu/en/campus-life/residential-education-and-housing/living-in-abu-dhabi.html

New York University has established itself as a Global Network University,
a multi-site, organically connected network encompassing key global cities
and idea capitals. The network has three foundational degree-granting
campuses: New York, Abu Dhabi, and Shanghai, complimented by a network of
eleven research and study-away sites across five continents. Faculty and
students circulate within this global network in pursuit of common research
interests and the promotion of cross-cultural and interdisciplinary
solutions for problems both local and global.

Informal inquiries regarding the position, university, or area, are
encouraged. To apply, individuals should email a curriculum vita, a brief
statement of research interests, the expected date of availability, and
contact information of two referees. All correspondence should be sent to
Olivia Cheung (olivia.che...@nyu.edu).

**Olivia Cheung is at the Vision Sciences Society (VSS) conference this
week and will be happy to meet with any individuals who are interested in
learning more about the position.**
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] PetSurfer gtmpvc

[Boris Rauchmann]

External Email - Use Caution

Hi all,

is there a way to easily get the volume stats for all regions after pvc
correction using mri_gtmpvc ? I think its not included in gtm.stats.dat.

Thanks,
Boris
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Alright, thanks I confused that. I already found a better way for my purposes. 
Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non 
PVC subcortical SUVs.

> Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz 
> --ctab-default ...
> when you use --annot, you are saying that the input is on the surface.
> 
> On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer community,
>> 
>> I am trying to extract SUV values from sub-cortical segmentation or gtmseg I 
>> don t want to use any PVC. 
>> 
>> I used the following commands:
>> 
>> gtmseg --s xyz
>> 
>> then 
>> mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta
>> 
>> following
>> mri_vol2vol --mov abetapet.nii
>>  --reg abetapet.reg.lta --targ orig.mgz --o abetapet.sm00.nii.gz
>> and
>> 
>> mri_segstats  --annot
>>  xyz lh gtmseg --i abetapet.sm00.nii.gz --sum xyz_abeta.stats
>> 
>> resulting in this dimension mismatch error:
>> input 256 256 256
>>   seg   416 450 476
>> 
>> Is that the correct way for doing this analysis? any suggestions how to 
>> solve the mismatch error?
>> 
>> Thanks,
>> Boris
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default 
...
when you use --annot, you are saying that the input is on the surface.

On 5/17/2019 9:07 AM, Boris Rauchmann wrote:

External Email - Use Caution

Dear Freesurfer community,

I am trying to extract SUV values from sub-cortical segmentation or gtmseg I 
don t want to use any PVC.

I used the following commands:

gtmseg --s xyz

then
mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta

following

mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o 
abetapet.sm00.nii.gz

and


mri_segstats  --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum 
xyz_abeta.stats

resulting in this dimension mismatch error:
input 256 256 256
  seg   416 450 476

Is that the correct way for doing this analysis? any suggestions how to solve 
the mismatch error?

Thanks,
Boris



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MP-RAGE protocol

[Bruce Fischl]

Hi Mustafa

1. Your mprage ran through recon-all fine and the results look good. The 
saggital field of view is tight, so make sure that they don't crop brain in 
that direction.


2. Your recon-all command line is incorrect. You should point the 
SUBJECTS_DIR environment variable to whereever you want to store all of 
your FreeSurfer-processed data, then use the -i switch to path to the input 
volume. You can also specify SUBJECTS_DIR on the command line. So in your 
case something like:



recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 -sd \
   /path/to/my/subjecs -all

should do the trick. There is also no need to convert to nifti first

cheers
Bruce


On Fri, 
17 May 2019, mustafa amin wrote:




External Email - Use Caution

Hi Bruce,

Herewith I attach within the email the command that didn't work when I wanted 
to reconall. Please
have a look. What about the previous dicom that I have sent to you? Please 
share some thoughts.Thank
you very much.

Yours faithfully,

Mustafa


Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl  
menulis:


Hi Mustafa

can you give us some detials? What didn't work? Can you send us the full
command line, screen output and recon-all.log?

cheers
Bruce


On Thu, 16 May 2019, mustafa amin wrote:

>
> External Email - Use Caution
>
> Hi Douglas,
>
> I tried to follow the instruction to recon-all the data however it didn't 
work. Please give
> some thoughts. Thank you in advance.
>
> Yours faithfully,
>
> Mustafa
>
> Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. 

> menulis:
>
>
> Hi Mustafa, why not just run recon-all on the data you have and see
> whether it looks ok?
>
> On 4/15/19 7:06 AM, mustafa amin wrote:
> >          External Email - Use Caution
> >
> > Hi Bruce,
> >
> > I’ve talked to the MRI operator and she told me that the best thing to do 
the MP-RAGE
> protocol is doing the T1 weighted 3D gradient echo with SENSE, she can’t set 
the TE, TR, TI
> just like the ADNI protocol asked, though. She can set the thickness to 1 mm. 
Is this set
> up okay?
> >
> > I have the DIACOM files of some subjects with the set up above. Can I send 
them to you to
> look at them?
> >
> >  I am terribly sorry for keep asking this basic question due to we never 
had experience
> doing it in Indonesia.
> >
> > Many thanks!
> >
> >
> > Mustafa M. Amin
> > Consultant Psychiatrist in Biological Psychiatry
> > Department of Psychiatry
> > Faculty of Medicine
> > Universitas Sumatera Utara
> >
> >> On 2 Apr 2019, at 20.49, Bruce Fischl  wrote:
> >>
> >> Hi Mustafa
> >>
> >> MRI is an amazingly versatile technology that can be messed up in an
> >> astonishing number of ways. By far the best thing to do would be to acquire
> >> a dataset and run it through recon-all and see if the results look
> >> accurate. If you have permission to do so, you are welcome to acquire one
> >> and send it to us to try out instead.
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 2 Apr 2019, mustafa amin
> >> wrote:
> >>
> >>>        External Email - Use Caution
> >>>
> >>> Dear Freesurfer experts,
> >>>
> >>> I need advice, the MRI operator need to confirm whether she had done the
> >>> right protocol of MP-RAGE. I have attached the picture that has been
> >>> taken by her. Please share some thoughts. Thank you in advance.
> >>>
> >>>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Generating cortical correspondence vectors

[Bruce Fischl]

Hi Konrad

sorry, I never really packaged this up nicely. Currently it is embedded in 
the mris_thickness binary, and you run it by using:


mris_thickness -variational -w 0   

this will write out two files:

?h.normals.init.mgz
?h.normals.mgz

the first is the initial vector field along the pial-white direction, and 
the second is the results of the minimization of the variational functional 
and should be the ones you want.

It is all pretty experimental and only lightly used so may have problems 
(but hopefully not).

Let me know how it goes. I'll be curious to hear if it helps

cheers
Bruce


  On Thu, 16 May 2019, K. 
Wagstyl wrote:

>External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm interested in regenerating cortical correspondence vectors between
> pial and white surfaces as described in "Microstructural parcellation of
> the human brain."
>
> Is this currently the default way that freesurfer extracts the
> vectors/surfaces?
> Or is there flag/separate code to generate these vectors?
>
> Thanks!
>
> Konrad
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Dear Freesurfer community,

I am trying to extract SUV values from sub-cortical segmentation or gtmseg
I don t want to use any PVC.

I used the following commands:

gtmseg --s xyz

then
mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta

following


mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o
abetapet.sm00.nii.gz


and

mri_segstats  --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum
xyz_abeta.stats

resulting in this dimension mismatch error:
input 256 256 256
  seg   416 450 476

Is that the correct way for doing this analysis? any suggestions how to
solve the mismatch error?

Thanks,
Boris
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer