Dear Vasudev,
if you want to include only Grey matter you have to load also the GM
segment c1*.nii:
hdr=spm_vol('filename'); % read header
img=spm_read_vols(hdr); % read image
GM_hdr=spm_vol('c1_file.nii');
GM_vol=spm_read_vols(GM_hdr);
img = img(GM_vol>0.5); % convert 3D image to vector
Regards,
Michael
Am 26.01.2017 um 21:33 schrieb Christian Gaser:
> Dear Vasudev,
>
> the first idea that came into my mind was to use the search function in
> the mail-list:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1206&L=spm&P=R70683&1=spm&9=A&I=-3&J=on&K=2&X=AF592E003ED73506A5&Y=christian.gaser%40uni-jena.de&d=No+Match%3BMatch%3BMatches&z=4
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1206&L=spm&P=R70841&1=spm&9=A&I=-3&J=on&K=2&X=AF592E003ED73506A5&Y=christian.gaser%40uni-jena.de&d=No+Match%3BMatch%3BMatches&z=4
> https://en.wikibooks.org/wiki/SPM/Programming_intro
>
> hdr=spm_vol('filename'); % read header
> img=spm_read_vols(hdr); % read image
> img = img(:); % convert 3D image to vector
>
> Best,
>
> Christian
>
> ------------------------------------------------------------------------
>
> Christian Gaser, Ph.D.
> Professor of Computational Neuroscience/Neuroimaging
> Biomagnetic Center
> Structural Brain Mapping Group
> Department of Neurology
> Jena University Hospital
> Am Klinikum 1, D-07747 Jena, Germany
> Tel: ++49-3641-9325778 Fax: ++49-3641-9325772
> e-mail: [log in to unmask] <mailto:[log in to unmask]>
> http://www.neuro.uni-jena.de
> On 26 Jan 2017, at 15:10, Dev vasu wrote:
>
> Dear Sir,
>
> Is there any way to convert Grey matter volume image into a row
> vector in matlab ?
>
> Thanks
> Vasudev
>
> On 26 January 2017 at 08:38, Dev vasu
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Sir,
>
> I want to pre process fMRI data and generate ALFF maps , there
> were some tools provided by Dr. Calhoun for multimodal fusion of
> sMRI,fMRI,DTI using mCCA+ jICA approach , following is the link
> to journal :
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666029/
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666029/>
>
>
> I would like to implement the same method in my scenario for
> which i would like to generate ALFF maps for resting state data
> of each subject.
>
>
> Thanks
> Vasudev
>
> On 25 January 2017 at 22:40, Christian Gaser
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Vasudev,
>
> in order to analyze 3D (voxel) measures on the surface it is
> necessary to map these measures from 3D space to the
> surface. This is not yet prepared for DTI data, but works
> well for fMRI data. Please use the function CAT12 -> Extract
> & Map Surface Data -> Map Volume (Native Space) to
> Individual Surface. The default values in newer versions
> (check that sample function is set to "Absolute Maximum")
> maps the absolute maximal values inside gray matter from the
> volume to the individual surface. These mapped values can
> then be resampled to template space for analysis using the
> function CAT12 -> Resample & Smooth Surfaces. Please note
> that it is recommend to rather map unsmoothed to the surface
> which are then resampled and smoothed on the surface.
> Smoothing on the surface is of some advantage. However, I
> have no experience with rfMRI data and don't know whether
> there any drawbacks to estimate rfMRI maps from unsmoothed data.
>
> The above described procedure allows to separately analyze
> 3D measures on the surface. However, I am not aware of a
> software that allows the analysis of multi-modal data to
> combine these measures.
>
> Best,
>
> Christian
>
> On Tue, 24 Jan 2017 15:33:26 +0100, Dev vasu
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> >Dear all,
> >
> >I have multi modal imaging data (T1w,DTI,rfMRI) and i would
> like to perform
> >surface based preprocessing through SPM 12 , is there any
> tool box which
> >does such task, I know CAT 12 generates .gii images for
> Structural Imaging
> >data, is there any approach for DTI and rfMRI to generate
> surface files ?.
> >
> >
> >Thanks
> >Vasudev
> >
>
>
>
>
--
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Dr. Michael Erb
Department of Biomedical Magnetic Resonance
University of Tübingen
Hoppe-Seyler-Str. 3
72076 Tübingen, Germany
Tel.: +49(0)7071/2987753 priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
e-mail: <[log in to unmask]>
www:
http://www.medizin.uni-tuebingen.de/Forschung/Kliniken/Radiologie/Biomedizinische+Magnetresonanz.html
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