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
________________________________
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Sent: Monday, July 11, 2016 1:00:01 PM
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Subject: HCP-Users Digest, Vol 44, Issue 9
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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
> >
>
>
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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.
>
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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
------------------------------
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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 [...]
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