Er, I messed up the loop, I have 180 time points so it should be
tic
A=zeros([64,64,40,180]);
for t=1:180
V=spm_vol_nifti('Test4D.nii',t);
A(:,:,:,t)=spm_read_vols(V);
end
mean(A,4);
toc
% Elapsed time is 1.883952 seconds.
and it's of course slower.
-Tom
On Mon, Jul 11, 2016 at 7:10 PM, Thomas Nichols <[email protected]>
wrote:
> 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
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> or, via email, send a message with subject or body 'help' to
>> [email protected]
>>
>> You can reach the person managing the list at
>> [email protected]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of HCP-Users digest..."
>>
>>
>> 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 --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160711/28e85fdd/attachment-0001.html
>>
>> ------------------------------
>>
>> 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 --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160711/c23eca09/attachment-0001.html
>>
>> ------------------------------
>>
>> 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
>> > >
>> >
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160711/8697979f/attachment-0001.html
>>
>> ------------------------------
>>
>> 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
>> > > >
>> > >
>> > >
>> >
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160711/89545fd5/attachment-0001.html
>>
>> ------------------------------
>>
>> 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
>> ****************************************
>>
>> _______________________________________________
>> HCP-Users mailing list
>> [email protected]
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>> Spam detection software, running on the system "mailman02.nrg.mir", has
>> identified this incoming email as possible spam. The original message
>> has been attached to this so you can view it (if it isn't spam) or label
>> similar future email. If you have any questions, see
>> @@CONTACT_ADDRESS@@ for details.
>>
>> 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
>> ---- ----------------------
>> --------------------------------------------------
>> 2.0 DEAR_SOMETHING BODY: Contains 'Dear (something)'
>> 2.7 FRT_ROLEX BODY: ReplaceTags: Rolex
>> 0.4 MIME_HTML_MOSTLY BODY: Multipart message mostly text/html MIME
>> 0.0 HTML_MESSAGE BODY: HTML included in message
>>
>>
>>
>>
>
>
> --
> __________________________________________________________
> 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
>
>
--
__________________________________________________________
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
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
