[Freesurfer] volumetric version of fsaverage brain

[Ritobrato Datta]

Hello All,

Which is the volumetric version of the fsaverage brain in freesurfer ? Can you 
tell me what is it called ? 

Thanks

Ri



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Re: [Freesurfer] recon-all: Stages 6-11 only

[Bruce Fischl]

Hi Nasim,

I don't think there's a flag for that, but you can specify exactly which 
steps you want on the command line (it will just be rather long)..

cheers,
Bruce
On Mon, 
12 Apr 2010, Nasim Maleki wrote:

> Hi all,
>
> Is there a flag that you could run stages 6-11 ONLY of the autorecon process 
> stages (after running the stages 1-5) instead of doing the whole 6-23 with 
> -autorecon2 flag?
>
> Thank you,
> Nasim
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[Freesurfer] recon-all: Stages 6-11 only

[Nasim Maleki]

Hi all, 

Is there a flag that you could run stages 6-11 ONLY of the autorecon process 
stages (after running the stages 1-5) instead of doing the whole 6-23 with 
-autorecon2 flag?

Thank you,
Nasim
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Re: [Freesurfer] creating a binary mask volume

[Douglas N Greve]

you can also use mri_vol2vol with --regheader.

Bruce Fischl wrote:
> yes, that sounds right
> Bruce
> On Sun, 11 Apr 2010, Mehul Sampat wrote:
>
>   
>> Thanks Bruce. Following that, to convert the rth.mgz back to native space I
>> think I can use the following command:
>> mri_convert -rl orig/001.mgz -rt nearest rth.mgz rth.nii
>>
>> thanks
>> Mehul
>>
>> On Sun, Apr 11, 2010 at 1:38 PM, Bruce Fischl 
>> wrote:
>>
>> 
>>> Hi Mehul,
>>> try mri_binarize instead. It would be something like:
>>>
>>> mri_binarize --match 49 --i aseg.mgz --o rth.mgz
>>>
>>> where 49 is the index for right thalamus proper (from the
>>> FreeSurferColorLUT.txt file) and rth.mgz is the output volume
>>>
>>> cheers,
>>> Bruce
>>>
>>> On Sun, 11 Apr 2010, Mehul Sampat wrote:
>>>
>>>  Hi Folks,
>>>   
 I would like to create a binary mask volume for the Right-Thalamus (all
 voxels of right-thalamus as 1 and 0 otherwise).

 I looked at this help page
 http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi
 and i think I should use the following command described on this page:

 mri_vol2roi --label your.label --srcvol f --srcreg register.dat
 --finalmskvol labelbinmask --roiavg /tmp/not.wanted.dat

 is this correct ? also could someone give me an example? i am not sure
 what
 all of the parameters are.
 thanks
 Mehul


 
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Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

[Douglas N Greve]

The id is the value in the mask. So if it's a binary mask, use --id 1



John Gelburg wrote:
> I am sorry, but I still struggle to make it work :(
> Here is my syntax:
> mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label
> I am getting "ERROR: must supply a label id" error message.
> I do not have any label id, because it's my custom mask, which was 
> created in the SPM.
>
> On Fri, Apr 9, 2010 at 11:14 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> It will still work.
>
> from mri_cor2label --help :
>
> Note: the name of this program is a bit misleading as it will operate
> on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr,
> analyze, etc).
>
>
> John Gelburg wrote:
>
> thanks, but isn't COR volume and my ANALYZE image is not the
> same thing?
>
> On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>try mri_cor2label
>
>John Gelburg wrote:
>
>Hi,
>
>I have ANLYZE binary mask which I would like to convert to
>FreeSurfer labels. Is there any more automatic way to do it
>than loading it as an overlay and then selecting
> manually as a
>label?
>
>Thanks for help,
>John
>  
>  
> 
>
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>-- Douglas N. Greve, Ph.D.
>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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> 
>
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> 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
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>

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Douglas N. Greve, Ph.D.
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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Re: [Freesurfer] Extracting time series from aparc.a2009s+aseg.mgz

[Douglas N Greve]

Use mri_segstats with the --avgwf option.

liang wang wrote:
> Hi FSusers,
>  
> Is there a way to extract averaged BOLD signal from the 
> identified cortical regions in aparc.a2009s+aseg.mgz. Thanks
>  
> Liang
>
> -- 
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> Postdoctoral Fellow
> Woodward Lab
> Department of Psychiatry
> University of British Columbia
> BC Mental Health & Addiction Services
> 938 West 28th Avenue
> Vancouver BC V5Z 4H4
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[Freesurfer] Gabriel Castrillón wants to stay in t ouch on LinkedIn

[Gabriel Castrillón]

LinkedIn
Gabriel Castrillón souhaite se connecter à vous sur LinkedIn :
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Freesurfer,

I'd like to add you to my professional network on LinkedIn.

- Gabriel Castrillón

Accepter l'invitation de Gabriel Castrillón
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[Freesurfer] Postdoctoral Fellowship: Multimodal Imaging at MGH

[sheraz]

Postdoctoral Fellowship: Multimodal Imaging

Description:

A two year postdoctoral position pursuing multimodal imaging is available
with the TRANSCEND Research Program (www.transcendresearch.org) at the
Martinos Center for Biomedical Imaging in Charlestown, MA
(www.martinos.org) which is affiliated with the Massachusetts General
Hospital, Harvard and MIT.  There is a second location at a clinical site,
the MGH-affiliated Lurie Family Center for Autism, where we have a 128
lead EGI EEG in a shielded room as well as a photogrammetry machine.

The program’s emphasis is on pathophysiologically oriented brain research
and application of advanced imaging acquisition and analysis techniques to
neurological and sensory aspects of autism spectrum disorders.  Emphasis
will be on MRI (DTI, spectroscopy, morphometry, ASL) and on co-registering
EEG and MEG with MRI.  This position will involve analysis of existing
multimodal imaging data and collection of new data.  It will involve
working closely with a multidisciplinary team and with children, and will
also involve some research oriented analysis of data collected for
clinical purposes.  The age range of our subjects is primarily from early
infancy to mid-adolescence, with some additional studies including young
adults. An ample opportunity will also be provided to the candidate to
self-explore and lead research.

Requirements:

Candidates must have PhD in neuroscience, physics, electrical engineering,
computer science or other related fields. Prior experience in MRI analysis
and EEG signal processing is required. Salary will be consistent with
Massachusetts General Hospital, Harvard Medical School policies for
Postdoctoral trainees and will range between $45,000 to $55,000 depending
upon qualifications and experience. Compensation also includes full staff
benefits, including health insurance, and vacation time.

Contact:

Interested applicants may send a CV and statement of interest addressing
background and specific pertinence of the candidate’s interest to Dr.
Martha R. Herbert at mherbe...@partners.org and cc transc...@partners.org.
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[Freesurfer] problems on converting images from the GE scanner

[Chun-Hsien Hsu]

Hi FreeSurfer users,

I have the anatomical MR images from the GE scanner, and want to convert the
images into the mgz file.

These images's file name looks as follows:

IM1
IM2
.
.
IM176


I use the function "mri_convert" to converting the file:

% mri_convert -it dicom IM1 $SUBJECTS_DIR/15/mri/orig/001.mgz

The problem is that the image in the output file (001.mgz) looks like "white
noise". I have posted the logs regarding to this function at the end.

I have tried several ways, such as converting the files into *.ima files or
a nii file before running "mri_convert", and still have the same problem.

Would someone have ideas about what to do?

Thanks!

Chun-Hsien Hsu


mri_convert -it dicom IM1 /Users/kevin/Subjects/15/mri/orig/001.mgz
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from IM1...
Starting DICOMRead2()
dcmfile = /Users/kevin/Subjects/15/mri/IM1
dcmdir = /Users/kevin/Subjects/15/mri
Ref Series No = 3
Found 179 files, checking for dicoms
Found 176 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0.007 -0.168 0.9856
Vs: 0.00700112 -0.168027 0.985758
Second Sorting
Counting frames
nframes = 1
nslices = 176
ndcmfiles = 176
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
jpegUID:   --1.2.840.10008.1.2.4--
Loading pixel data
TR=3.06, TE=0.82, TI=1100.00, flip angle=7.00
i_ras = (-0.35, -0.00973536, -0.00592059)
j_ras = (0.00860625, -0.985602, 0.16886)
k_ras = (-0.00700112, 0.168027, 0.985758)
writing to /Users/kevin/Subjects/15/mri/orig/001.mgz...
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[Freesurfer] Miao Wen wants to stay in touch on LinkedIn

[Miao Wen]

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I'd like to add you to my professional network on LinkedIn.

- Miao Wen

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