One tip: Use the nifti() function in SPM... it isn't in the 'spm_vol'
ecosystem, but is generally faster...
tic
A=nifti('Test4D.nii');
mean(A.dat(:,:,:,:),4);
toc
% Elapsed time is 0.269251 seconds.
tic
A=zeros([64,64,40,180]);
for t=1:40
V=spm_vol_nifti('Test4D.nii',t);
A(:,:,:,t)=spm_read_vols(V);
end
mean(A,4);
toc
% Elapsed time is 0.501510 seconds.
Also, note there is undocumented support for Gzipped NIFTI through
spm_vol.. e.g.
t = 2
V=spm_vol(sprintf('Resting.nii.gz,%d',t));
% Compressed NIfTI files are not supported.
A = spm_read_vols(V): ...
-Tom
On Mon, Jul 11, 2016 at 6:42 PM, Arnold, Thomas <[email protected]> wrote:
> Hello David,
>
> What SPM functions are you using to read in the data? What does your
> script look like? The following loop below works, but is painfully slow.
>
> data = zeros(91,109,91,1200); % preallocate space for data (~4GB)
> for img = 1:1200 % loop through all images
> hdr = spm_vol_nifti('rfMRI_REST1_RL_hp2000_clean.nii',img); % get hdr
> information for current iter
> data(:,:,:,img) = spm_read_vols(hdr); % store values in 4D data matrix
> end
>
> Notice if you attempt to go beyond the actual dimensions, matlab throws an
> error:
> hdr = spm_vol_nifti('rfMRI_REST1_RL_hp2000_clean.nii',1201); % index
> beyond bounds
> data(:,:,:,img) = spm_read_vols(hdr); % reference nonexistent indices
>
> Best,
> Thomas Campbell Arnold
>
> ------------------------------
> *From:* [email protected] <
> [email protected]> on behalf of
> [email protected] <
> [email protected]>
> *Sent:* Monday, July 11, 2016 1:00:01 PM
> *To:* [email protected]
> *Subject:* HCP-Users Digest, Vol 44, Issue 9
>
> Send HCP-Users mailing list submissions to
> [email protected]
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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> Today's Topics:
>
> 1. Re: Extracting ROI data from HCP resting state data - 2400
> data points instead of 1200 ? (David Hofmann)
> 2. Re: create cortical thickness maps for multiple subjects in
> the same template space (Dev vasu)
> 3. Re: create cortical thickness maps for multiple subjects in
> the same template space (Dierker, Donna)
> 4. Re: create cortical thickness maps for multiple subjects in
> the same template space (Dev vasu)
> 5. Re: create cortical thickness maps for multiple subjects in
> the same template space (Dierker, Donna)
> 6. Re: create cortical thickness maps for multiple subjects in
> the same template space (Dev vasu)
> 7. demographic information on 95 hcp MEG dataset (Marcus Siems)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Jul 2016 10:15:00 +0200
> From: David Hofmann <[email protected]>
> Subject: Re: [HCP-Users] Extracting ROI data from HCP resting state
> data - 2400 data points instead of 1200 ?
> To: "Dierker, Donna" <[email protected]>
> Cc: hcp-users <[email protected]>
> Message-ID:
> <
> caetivj0c+y_sjzix44ygaqwf5aqwv0lstt_005fbahazvk2...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Donna and others,
>
> thanks for your answer. I'm facing a difficulty with extracting data from
> the preprocessed files, that is they seems to each contain 2400 data points
> rather than 1200 like described in the documentation.
>
> I downloaded the 10 subjects data set and used the following files:
> *subjectcode_3T_rfMRI_REST1_preproc.zip,
> *from which I assume that these are the preprocessed files.
>
> It contains two datasets LR and RL:
>
> \MNINonLinear\Results\rfMRI_REST1_LR
> \MNINonLinear\Results\rfMRI_REST1_RL
>
> I unpacked these files:
>
> rfMRI_REST1_LR.nii.gz
> rfMRI_REST1_RL.nii.gz
>
> and read them as 4D NIFTI with Matlab and an SPM function. Afterwards they
> each contain 2400 data points (dimension: 91 109 91 2400), but in the
> documention it says they each should contain only 1200 data points. So I'm
> not sure if I did something wrong.
>
> greetings
>
> David
>
>
> 2016-06-30 18:30 GMT+02:00 Dierker, Donna <[email protected]>:
>
> > Hi David,
> >
> > I hope this publication answers your questions about HCP rfMRI
> > preprocessing:
> >
> > Resting-state fMRI in the Human Connectome Project.
> > Smith SM1, Beckmann CF, Andersson J, Auerbach EJ, Bijsterbosch J, Douaud
> > G, Duff E, Feinberg DA, Griffanti L, Harms MP, Kelly M, Laumann T, Miller
> > KL, Moeller S, Petersen S, Power J, Salimi-Khorshidi G, Snyder AZ, Vu AT,
> > Woolrich MW, Xu J, Yacoub E, U?urbil K, Van Essen DC, Glasser MF; WU-Minn
> > HCP Consortium.
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720828/
> >
> > I am only used to seeing what it is in the fix extended packages, so I'm
> > not sure all these volumes are in the basic fix packages, but here are
> > NIFTI volumes in a sample subject's rfMRI subdirectories:
> >
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
> > 177645/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
> > 177645/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/mask.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
> > 177645/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/mask.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_IC.nii.gz
> >
> >
> 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000.ica/filtered_func_data.ica/melodic_oIC.nii.gz
> > 177645/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL.nii.gz
> >
> > Maybe this page will help explain those:
> >
> >
> http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/rfMRIconnectivity/
> >
> > But keep in mind that for neocortex, you can take advantage of the
> surface
> > data the HCP provides (e.g., fsaverage_32k/*surf.gii, *dscalar.nii and
> > *dtseries.nii). You can get better inter-subject registration/alignment
> on
> > the surface, if that will be a factor in your study.
> >
> > Donna
> >
> >
> > On Jun 28, 2016, at 6:30 PM, David Hofmann <[email protected]>
> > wrote:
> >
> > > Hi all,
> > >
> > > I would like to extract ROI data (only neocortex) 'manually' e.g. using
> > a ROI from Harvard-Oxford atlas from HCP resting state data, but I'm not
> > sure which (nifti) files to use and where to find them. I'm also looking
> > for some information about the preprocessing steps applied to the resting
> > state data that is, if some additional steps (e.g. filtering) have to be
> > carried out before ROI extraction or if this has already been done.
> > >
> > > Any help on this appreciated!
> > >
> > > Thanks
> > >
> > > David
> > > _______________________________________________
> > > HCP-Users mailing list
> > > [email protected]
> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > >
> >
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Jul 2016 12:20:30 +0200
> From: Dev vasu <[email protected]>
> Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> To: "Harms, Michael" <[email protected]>,
> "<[email protected]>" <[email protected]>
> Message-ID:
> <
> cakwynu-m8uex647ntcntq0+_hwyofub7f8onwcelmvhj+cs...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Sir,
>
>
> can we used myelin style as a mapping method for Volume to surface mapping
> in wb_command to produce cortical thickness files,Unfortunately i only have
> T1w images and we have not acquired T2w images, i would like to use T1w
> images to generate Cortical thickness , could you please let me know if its
> appropriate way generate them using
>
> wb_command -volume-to-surface-mapping command and Myelin style mapping
> method ?.
>
>
>
> Thanks
>
> Vasudev
>
>
> On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote:
>
> >
> > Hi,
> > For statistical inference, I would recommend that you look into the PALM
> > tool.
> >
> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> >
> >
> > --
> > Michael Harms, Ph.D.
> > -----------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > 660 South Euclid Ave. Tel: 314-747-6173
> > St. Louis, MO 63110 Email: [email protected]
> >
> > From: Dev vasu <[email protected]>
> > Date: Friday, July 8, 2016 at 9:56 AM
> > To: "Harms, Michael" <[email protected]>
> > Cc: "<[email protected]>" <[email protected]>
> > Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> > subjects in the same template space
> >
> > Dear Sir,
> >
> > Is there any way to quantify the changes in cortical thickness between
> > healthy controls and non healthy controls ?.
> >
> >
> > Thanks
> > Vasudev
> >
> > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote:
> >
> >>
> >> HI,
> >> Cortical thickness maps on the surface mesh are already created for you.
> >> You should analyze/view the thickness on the surface; not try to project
> >> the thickness back onto the volume.
> >>
> >> cheers,
> >> -MH
> >>
> >> --
> >> Michael Harms, Ph.D.
> >> -----------------------------------------------------------
> >> Conte Center for the Neuroscience of Mental Disorders
> >> Washington University School of Medicine
> >> Department of Psychiatry, Box 8134
> >> 660 South Euclid Ave. Tel: 314-747-6173
> >> St. Louis, MO 63110 Email: [email protected]
> >>
> >> From: <[email protected]> on behalf of Dev vasu <
> >> [email protected]>
> >> Date: Friday, July 8, 2016 at 9:35 AM
> >> To: "<[email protected]>" <[email protected]>
> >> Subject: [HCP-Users] create cortical thickness maps for multiple
> >> subjects in the same template space
> >>
> >> Dear Sir /madam,
> >>
> >> I am able to successfully run Structural preprocessing pipeline on a
> >> group of 24 subjects, I would like to know how i can create cortical
> >> thickness maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> >>
> >>
> >>
> >> Thanks
> >> Vasudev
> >>
> >>
> >> _______________________________________________
> >> HCP-Users mailing list
> >> [email protected]
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >>
> >> ------------------------------
> >>
> >> The materials in this message are private and may contain Protected
> >> Healthcare Information or other information of a sensitive nature. If
> you
> >> are not the intended recipient, be advised that any unauthorized use,
> >> disclosure, copying or the taking of any action in reliance on the
> contents
> >> of this information is strictly prohibited. If you have received this
> email
> >> in error, please immediately notify the sender via telephone or return
> mail.
> >>
> >
> >
> > ------------------------------
> >
> > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature. If you
> > are not the intended recipient, be advised that any unauthorized use,
> > disclosure, copying or the taking of any action in reliance on the
> contents
> > of this information is strictly prohibited. If you have received this
> email
> > in error, please immediately notify the sender via telephone or return
> mail.
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Jul 2016 15:25:58 +0000
> From: "Dierker, Donna" <[email protected]>
> Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> To: Dev vasu <[email protected]>
> Cc: "[email protected] Listserv"
> <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Vasudev,
>
> This question confuses me a bit, I confess, but I would use Freesurfer to
> generate cortical thickness measurements from T1w volumes:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki
>
> Donna
>
>
> On Jul 11, 2016, at 5:20 AM, Dev vasu <
> [email protected]> wrote:
>
> > Dear Sir,
> >
> >
> > can we used myelin style as a mapping method for Volume to surface
> mapping in wb_command to produce cortical thickness files,Unfortunately i
> only have T1w images and we have not acquired T2w images, i would like to
> use T1w images to generate Cortical thickness , could you please let me
> know if its appropriate way generate them using
> > wb_command -volume-to-surface-mapping command and Myelin style mapping
> method ?.
> >
> >
> >
> > Thanks
> > Vasudev
> >
> >
> >
> > On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote:
> >
> > Hi,
> > For statistical inference, I would recommend that you look into the PALM
> tool.
> >
> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> >
> >
> > --
> > Michael Harms, Ph.D.
> > -----------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > 660 South Euclid Ave. Tel: 314-747-6173
> > St. Louis, MO 63110 Email: [email protected]
> >
> > From: Dev vasu <[email protected]>
> > Date: Friday, July 8, 2016 at 9:56 AM
> > To: "Harms, Michael" <[email protected]>
> > Cc: "<[email protected]>" <[email protected]>
> > Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> >
> > Dear Sir,
> >
> > Is there any way to quantify the changes in cortical thickness between
> healthy controls and non healthy controls ?.
> >
> >
> > Thanks
> > Vasudev
> >
> > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote:
> >
> > HI,
> > Cortical thickness maps on the surface mesh are already created for
> you. You should analyze/view the thickness on the surface; not try to
> project the thickness back onto the volume.
> >
> > cheers,
> > -MH
> >
> > --
> > Michael Harms, Ph.D.
> > -----------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > 660 South Euclid Ave. Tel: 314-747-6173
> > St. Louis, MO 63110 Email: [email protected]
> >
> > From: <[email protected]> on behalf of Dev vasu <
> [email protected]>
> > Date: Friday, July 8, 2016 at 9:35 AM
> > To: "<[email protected]>" <[email protected]>
> > Subject: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> >
> > Dear Sir /madam,
> >
> > I am able to successfully run Structural preprocessing pipeline on a
> group of 24 subjects, I would like to know how i can create cortical
> thickness maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> >
> >
> >
> > Thanks
> > Vasudev
> >
> >
> > _______________________________________________
> > HCP-Users mailing list
> > [email protected]
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> >
> >
> >
> > The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> >
> >
> >
> >
> >
> > The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> >
> >
> > _______________________________________________
> > HCP-Users mailing list
> > [email protected]
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 11 Jul 2016 17:36:54 +0200
> From: Dev vasu <[email protected]>
> Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> To: "Dierker, Donna" <[email protected]>
> Cc: "[email protected] Listserv"
> <[email protected]>
> Message-ID:
> <
> cakwynu8f91fhervt5spemusn9yngjbrseaure5mqexgbw9s...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear madam,
>
> Is there any way to measure the distance from Pial surface boundary with
> GM/WM boundary in freesurfer ?.
>
>
> Thanks
> Vasudev
>
> On 11 July 2016 at 17:25, Dierker, Donna <[email protected]> wrote:
>
> > Hi Vasudev,
> >
> > This question confuses me a bit, I confess, but I would use Freesurfer to
> > generate cortical thickness measurements from T1w volumes:
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki
> >
> > Donna
> >
> >
> > On Jul 11, 2016, at 5:20 AM, Dev vasu <
> > [email protected]> wrote:
> >
> > > Dear Sir,
> > >
> > >
> > > can we used myelin style as a mapping method for Volume to surface
> > mapping in wb_command to produce cortical thickness files,Unfortunately i
> > only have T1w images and we have not acquired T2w images, i would like to
> > use T1w images to generate Cortical thickness , could you please let me
> > know if its appropriate way generate them using
> > > wb_command -volume-to-surface-mapping command and Myelin style mapping
> > method ?.
> > >
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > >
> > >
> > > On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote:
> > >
> > > Hi,
> > > For statistical inference, I would recommend that you look into the
> PALM
> > tool.
> > >
> > > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> > >
> > >
> > > --
> > > Michael Harms, Ph.D.
> > > -----------------------------------------------------------
> > > Conte Center for the Neuroscience of Mental Disorders
> > > Washington University School of Medicine
> > > Department of Psychiatry, Box 8134
> > > 660 South Euclid Ave. Tel: 314-747-6173
> > > St. Louis, MO 63110 Email: [email protected]
> > >
> > > From: Dev vasu <[email protected]>
> > > Date: Friday, July 8, 2016 at 9:56 AM
> > > To: "Harms, Michael" <[email protected]>
> > > Cc: "<[email protected]>" <[email protected]>
> > > Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> > subjects in the same template space
> > >
> > > Dear Sir,
> > >
> > > Is there any way to quantify the changes in cortical thickness between
> > healthy controls and non healthy controls ?.
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote:
> > >
> > > HI,
> > > Cortical thickness maps on the surface mesh are already created for
> > you. You should analyze/view the thickness on the surface; not try to
> > project the thickness back onto the volume.
> > >
> > > cheers,
> > > -MH
> > >
> > > --
> > > Michael Harms, Ph.D.
> > > -----------------------------------------------------------
> > > Conte Center for the Neuroscience of Mental Disorders
> > > Washington University School of Medicine
> > > Department of Psychiatry, Box 8134
> > > 660 South Euclid Ave. Tel: 314-747-6173
> > > St. Louis, MO 63110 Email: [email protected]
> > >
> > > From: <[email protected]> on behalf of Dev vasu <
> > [email protected]>
> > > Date: Friday, July 8, 2016 at 9:35 AM
> > > To: "<[email protected]>" <[email protected]>
> > > Subject: [HCP-Users] create cortical thickness maps for multiple
> > subjects in the same template space
> > >
> > > Dear Sir /madam,
> > >
> > > I am able to successfully run Structural preprocessing pipeline on a
> > group of 24 subjects, I would like to know how i can create cortical
> > thickness maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> > >
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > >
> > > _______________________________________________
> > > HCP-Users mailing list
> > > [email protected]
> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > >
> > >
> > >
> > >
> > > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature. If you
> > are not the intended recipient, be advised that any unauthorized use,
> > disclosure, copying or the taking of any action in reliance on the
> contents
> > of this information is strictly prohibited. If you have received this
> email
> > in error, please immediately notify the sender via telephone or return
> mail.
> > >
> > >
> > >
> > >
> > >
> > > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature. If you
> > are not the intended recipient, be advised that any unauthorized use,
> > disclosure, copying or the taking of any action in reliance on the
> contents
> > of this information is strictly prohibited. If you have received this
> email
> > in error, please immediately notify the sender via telephone or return
> mail.
> > >
> > >
> > > _______________________________________________
> > > HCP-Users mailing list
> > > [email protected]
> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > >
> >
> >
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> ------------------------------
>
> Message: 5
> Date: Mon, 11 Jul 2016 15:40:32 +0000
> From: "Dierker, Donna" <[email protected]>
> Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> To: Dev vasu <[email protected]>
> Cc: "[email protected] Listserv"
> <[email protected]>, "Dierker, Donna" <
> [email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="us-ascii"
>
> I don't know of any software that does a better job at that task.
>
> You do need to run your subject through the Freesurfer pipeline, which
> does a lot of stuff. It segments into gray matter, white matter, CSF,
> etc. And yes -- it generates a map of cortical thickness (distance between
> gm/wm and pial).
>
> Spend some time digesting the Freesurfer wiki. If you want to do what you
> want to do, Freesurfer can help.
>
> But I still agree with Mike: If your controls and proband subjects were
> scanned on different scanners, you may have a difficult review process
> ahead of you when it comes time to publish your results. Something to
> consider sooner rather than later.
>
>
> On Jul 11, 2016, at 10:36 AM, Dev vasu <
> [email protected]> wrote:
>
> > Dear madam,
> >
> > Is there any way to measure the distance from Pial surface boundary with
> GM/WM boundary in freesurfer ?.
> >
> >
> > Thanks
> > Vasudev
> >
> > On 11 July 2016 at 17:25, Dierker, Donna <[email protected]> wrote:
> > Hi Vasudev,
> >
> > This question confuses me a bit, I confess, but I would use Freesurfer
> to generate cortical thickness measurements from T1w volumes:
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki
> >
> > Donna
> >
> >
> > On Jul 11, 2016, at 5:20 AM, Dev vasu <
> [email protected]> wrote:
> >
> > > Dear Sir,
> > >
> > >
> > > can we used myelin style as a mapping method for Volume to surface
> mapping in wb_command to produce cortical thickness files,Unfortunately i
> only have T1w images and we have not acquired T2w images, i would like to
> use T1w images to generate Cortical thickness , could you please let me
> know if its appropriate way generate them using
> > > wb_command -volume-to-surface-mapping command and Myelin style mapping
> method ?.
> > >
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > >
> > >
> > > On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote:
> > >
> > > Hi,
> > > For statistical inference, I would recommend that you look into the
> PALM tool.
> > >
> > > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> > >
> > >
> > > --
> > > Michael Harms, Ph.D.
> > > -----------------------------------------------------------
> > > Conte Center for the Neuroscience of Mental Disorders
> > > Washington University School of Medicine
> > > Department of Psychiatry, Box 8134
> > > 660 South Euclid Ave. Tel: 314-747-6173
> > > St. Louis, MO 63110 Email: [email protected]
> > >
> > > From: Dev vasu <[email protected]>
> > > Date: Friday, July 8, 2016 at 9:56 AM
> > > To: "Harms, Michael" <[email protected]>
> > > Cc: "<[email protected]>" <[email protected]>
> > > Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> > >
> > > Dear Sir,
> > >
> > > Is there any way to quantify the changes in cortical thickness between
> healthy controls and non healthy controls ?.
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote:
> > >
> > > HI,
> > > Cortical thickness maps on the surface mesh are already created for
> you. You should analyze/view the thickness on the surface; not try to
> project the thickness back onto the volume.
> > >
> > > cheers,
> > > -MH
> > >
> > > --
> > > Michael Harms, Ph.D.
> > > -----------------------------------------------------------
> > > Conte Center for the Neuroscience of Mental Disorders
> > > Washington University School of Medicine
> > > Department of Psychiatry, Box 8134
> > > 660 South Euclid Ave. Tel: 314-747-6173
> > > St. Louis, MO 63110 Email: [email protected]
> > >
> > > From: <[email protected]> on behalf of Dev vasu <
> [email protected]>
> > > Date: Friday, July 8, 2016 at 9:35 AM
> > > To: "<[email protected]>" <[email protected]>
> > > Subject: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> > >
> > > Dear Sir /madam,
> > >
> > > I am able to successfully run Structural preprocessing pipeline on a
> group of 24 subjects, I would like to know how i can create cortical
> thickness maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> > >
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > >
> > > _______________________________________________
> > > HCP-Users mailing list
> > > [email protected]
> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > >
> > >
> > >
> > >
> > > The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> > >
> > >
> > >
> > >
> > >
> > > The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> > >
> > >
> > > _______________________________________________
> > > HCP-Users mailing list
> > > [email protected]
> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > >
> >
> >
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 11 Jul 2016 17:48:56 +0200
> From: Dev vasu <[email protected]>
> Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> subjects in the same template space
> To: "Dierker, Donna" <[email protected]>
> Cc: "[email protected] Listserv"
> <[email protected]>
> Message-ID:
> <
> cakwynu_7vnxanu2ngxdttq8pouzrrhqjdzbjr1nx6-2whb8...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear madam,
>
>
> The healthy controls and Subjects are scanned on same scanner , I am not
> using HCP data .
>
>
>
> Thanks
>
> Vasudev
>
> On 11 July 2016 at 17:40, Dierker, Donna <[email protected]> wrote:
>
> > I don't know of any software that does a better job at that task.
> >
> > You do need to run your subject through the Freesurfer pipeline, which
> > does a lot of stuff. It segments into gray matter, white matter, CSF,
> > etc. And yes -- it generates a map of cortical thickness (distance
> between
> > gm/wm and pial).
> >
> > Spend some time digesting the Freesurfer wiki. If you want to do what
> you
> > want to do, Freesurfer can help.
> >
> > But I still agree with Mike: If your controls and proband subjects were
> > scanned on different scanners, you may have a difficult review process
> > ahead of you when it comes time to publish your results. Something to
> > consider sooner rather than later.
> >
> >
> > On Jul 11, 2016, at 10:36 AM, Dev vasu <
> > [email protected]> wrote:
> >
> > > Dear madam,
> > >
> > > Is there any way to measure the distance from Pial surface boundary
> with
> > GM/WM boundary in freesurfer ?.
> > >
> > >
> > > Thanks
> > > Vasudev
> > >
> > > On 11 July 2016 at 17:25, Dierker, Donna <[email protected]> wrote:
> > > Hi Vasudev,
> > >
> > > This question confuses me a bit, I confess, but I would use Freesurfer
> > to generate cortical thickness measurements from T1w volumes:
> > >
> > > https://surfer.nmr.mgh.harvard.edu/fswiki
> > >
> > > Donna
> > >
> > >
> > > On Jul 11, 2016, at 5:20 AM, Dev vasu <
> > [email protected]> wrote:
> > >
> > > > Dear Sir,
> > > >
> > > >
> > > > can we used myelin style as a mapping method for Volume to surface
> > mapping in wb_command to produce cortical thickness files,Unfortunately i
> > only have T1w images and we have not acquired T2w images, i would like to
> > use T1w images to generate Cortical thickness , could you please let me
> > know if its appropriate way generate them using
> > > > wb_command -volume-to-surface-mapping command and Myelin style
> mapping
> > method ?.
> > > >
> > > >
> > > >
> > > > Thanks
> > > > Vasudev
> > > >
> > > >
> > > >
> > > > On 8 July 2016 at 17:03, Harms, Michael <[email protected]> wrote:
> > > >
> > > > Hi,
> > > > For statistical inference, I would recommend that you look into the
> > PALM tool.
> > > >
> > > > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
> > > >
> > > >
> > > > --
> > > > Michael Harms, Ph.D.
> > > > -----------------------------------------------------------
> > > > Conte Center for the Neuroscience of Mental Disorders
> > > > Washington University School of Medicine
> > > > Department of Psychiatry, Box 8134
> > > > 660 South Euclid Ave. Tel: 314-747-6173
> > > > St. Louis, MO 63110 Email: [email protected]
> > > >
> > > > From: Dev vasu <[email protected]>
> > > > Date: Friday, July 8, 2016 at 9:56 AM
> > > > To: "Harms, Michael" <[email protected]>
> > > > Cc: "<[email protected]>" <[email protected]
> >
> > > > Subject: Re: [HCP-Users] create cortical thickness maps for multiple
> > subjects in the same template space
> > > >
> > > > Dear Sir,
> > > >
> > > > Is there any way to quantify the changes in cortical thickness
> between
> > healthy controls and non healthy controls ?.
> > > >
> > > >
> > > > Thanks
> > > > Vasudev
> > > >
> > > > On 8 July 2016 at 16:47, Harms, Michael <[email protected]> wrote:
> > > >
> > > > HI,
> > > > Cortical thickness maps on the surface mesh are already created for
> > you. You should analyze/view the thickness on the surface; not try to
> > project the thickness back onto the volume.
> > > >
> > > > cheers,
> > > > -MH
> > > >
> > > > --
> > > > Michael Harms, Ph.D.
> > > > -----------------------------------------------------------
> > > > Conte Center for the Neuroscience of Mental Disorders
> > > > Washington University School of Medicine
> > > > Department of Psychiatry, Box 8134
> > > > 660 South Euclid Ave. Tel: 314-747-6173
> > > > St. Louis, MO 63110 Email: [email protected]
> > > >
> > > > From: <[email protected]> on behalf of Dev vasu
> <
> > [email protected]>
> > > > Date: Friday, July 8, 2016 at 9:35 AM
> > > > To: "<[email protected]>" <[email protected]
> >
> > > > Subject: [HCP-Users] create cortical thickness maps for multiple
> > subjects in the same template space
> > > >
> > > > Dear Sir /madam,
> > > >
> > > > I am able to successfully run Structural preprocessing pipeline on a
> > group of 24 subjects, I would like to know how i can create cortical
> > thickness maps for all the subjects in MNI152_T1_0.7mm.nii.gz template.
> > > >
> > > >
> > > >
> > > > Thanks
> > > > Vasudev
> > > >
> > > >
> > > > _______________________________________________
> > > > HCP-Users mailing list
> > > > [email protected]
> > > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > > >
> > > >
> > > >
> > > >
> > > > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature. If you
> > are not the intended recipient, be advised that any unauthorized use,
> > disclosure, copying or the taking of any action in reliance on the
> contents
> > of this information is strictly prohibited. If you have received this
> email
> > in error, please immediately notify the sender via telephone or return
> mail.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > The materials in this message are private and may contain Protected
> > Healthcare Information or other information of a sensitive nature. If you
> > are not the intended recipient, be advised that any unauthorized use,
> > disclosure, copying or the taking of any action in reliance on the
> contents
> > of this information is strictly prohibited. If you have received this
> email
> > in error, please immediately notify the sender via telephone or return
> mail.
> > > >
> > > >
> > > > _______________________________________________
> > > > HCP-Users mailing list
> > > > [email protected]
> > > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> > > >
> > >
> > >
> >
> >
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> ------------------------------
>
> Message: 7
> Date: Mon, 11 Jul 2016 15:54:35 +0200
> From: Marcus Siems <[email protected]>
> Subject: [HCP-Users] demographic information on 95 hcp MEG dataset
> To: [email protected]
> Message-ID:
> <
> 20160711155435.horde.uwrxr0dkifsggzioi6d6...@webmail.uni-tuebingen.de>
>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
> Hey,
>
> I was wondering where I could find demographic information about the
> newest release of the MEG-hcp dataset (n=95).
>
> Best,
> Marcus
>
>
>
> ------------------------------
>
> _______________________________________________
> HCP-Users mailing list
> [email protected]
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> End of HCP-Users Digest, Vol 44, Issue 9
> ****************************************
>
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> Content preview: Hello David, What SPM functions are you using to read in
> the
> data? What does your script look like? The following loop below works,
> but
> is painfully slow. data = zeros(91,109,91,1200); % preallocate space for
> data (~4GB) for img = 1:1200 % loop through all images hdr =
> spm_vol_nifti('rfMRI_REST1_RL_hp2000_clean.nii',img);
> % get hdr information for current iter data(:,:,:,img) =
> spm_read_vols(hdr);
> % store values in 4D data matrix end [...]
>
> Content analysis details: (5.1 points, 5.0 required)
>
> pts rule name description
> ---- ----------------------
> --------------------------------------------------
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>
>
>
--
__________________________________________________________
Thomas Nichols, PhD
Professor, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick, Coventry CV4 7AL, United Kingdom
Web: http://warwick.ac.uk/tenichols
Email: [email protected]
Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
Fx, +44 24 7652 4532
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