Hi Joseph,

Thanks for your recommendation! 

All the best,
_______________
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons




On Feb 24, 2015, at 1:41 PM, An Vu <j...@umn.edu> wrote:

> Hi Marta,
> 
> Matt has the right idea here. To get the 1.6-2mm at 7T, I would recommend 
> using IPAT 2, partial fourier 6/8, TE ~20ms. Use the smallest MB factor that 
> will give you TR <= 1 second (should be MB <= 5).
> 
> Joseph
> 
>> On Feb 23, 2015, at 10:01 AM, hcp-users-requ...@humanconnectome.org wrote:
>> 
>> Send HCP-Users mailing list submissions to
>>      hcp-users@humanconnectome.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
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>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of HCP-Users digest..."
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>> 
>> Today's Topics:
>> 
>>  1. 7 tesla MRI (Marta Moreno)
>>  2. Re: 7 tesla MRI (Glasser, Matthew)
>>  3. Re: 7 tesla MRI (Marta Moreno)
>>  4. Re: Processing Diffusion MRI Data (Archer,Derek B)
>>  5. Re: Processing Diffusion MRI Data (Satrajit Ghosh)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Sun, 22 Feb 2015 20:26:29 -0500
>> From: Marta Moreno <mmorenoort...@icloud.com>
>> Subject: [HCP-Users] 7 tesla MRI
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <68a764ca-d62d-42cf-87ed-c9eb4be92...@icloud.com>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Hi users,
>> 
>> I am going to start acquiring data from 7 Tesla MRI (Siemens) and would like 
>> to know best option for resting state (carrying out whole brain shimming up 
>> to 2nd order). Which would be best protocol in your expert opinion? 
>> 
>> Thanks!
>> _______________
>> Marta Moreno-Ortega, Ph.D.
>> Postdoctoral Research Fellow 
>> Division of Experimental Therapeutics
>> New York State Psychiatric Institute
>> Department of Psychiatry
>> Columbia University College of Physicians and Surgeons
>> 
>> 
>> 
>> 
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>>  
>> 
>> ------------------------------
>> 
>> Message: 2
>> Date: Mon, 23 Feb 2015 01:37:22 +0000
>> From: "Glasser, Matthew" <glass...@wusm.wustl.edu>
>> Subject: Re: [HCP-Users] 7 tesla MRI
>> To: Marta Moreno <mmorenoort...@icloud.com>,
>>      "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <d10fe02a.e8a88%glass...@wusm.wustl.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> An HTML attachment was scrubbed...
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>>  
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Sun, 22 Feb 2015 21:35:37 -0500
>> From: Marta Moreno <mmorenoort...@icloud.com>
>> Subject: Re: [HCP-Users] 7 tesla MRI
>> To: "Glasser, Matthew" <glass...@wusm.wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <0b4de77d-556c-4ca4-99c1-50f830a4a...@icloud.com>
>> Content-Type: text/plain; charset="windows-1252"
>> 
>> Thank you very much, Matt! I am going to test both this week and chose best. 
>> Is there any other information I should be aware of in order to acquire my 
>> data best way and establish a final protocol? Will have this week for 
>> testing.
>> _______________
>> Marta Moreno-Ortega, Ph.D.
>> Postdoctoral Research Fellow
>> Division of Experimental Therapeutics
>> New York State Psychiatric Institute
>> Department of Psychiatry
>> Columbia University College of Physicians and Surgeons
>> 
>> 
>> 
>> 
>> On Feb 22, 2015, at 8:37 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> 
>> wrote:
>> 
>>> I?d get the best spatial resolution you can (e.g. 2mm-1.6mm) while keeping 
>>> the TR under 1 second (with multi-band EPI).  
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> From: Marta Moreno <mmorenoort...@icloud.com>
>>> Date: Sunday, February 22, 2015 at 7:26 PM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] 7 tesla MRI
>>> 
>>> Hi users,
>>> 
>>> I am going to start acquiring data from 7 Tesla MRI (Siemens) and would 
>>> like to know best option for resting state (carrying out whole brain 
>>> shimming up to 2nd order). Which would be best protocol in your expert 
>>> opinion? 
>>> 
>>> Thanks!
>>> _______________
>>> Marta Moreno-Ortega, Ph.D.
>>> Postdoctoral Research Fellow 
>>> Division of Experimental Therapeutics
>>> New York State Psychiatric Institute
>>> Department of Psychiatry
>>> Columbia University College of Physicians and Surgeons
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> 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.
>> 
>> -------------- next part --------------
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>>  
>> 
>> ------------------------------
>> 
>> Message: 4
>> Date: Mon, 23 Feb 2015 15:02:47 +0000
>> From: "Archer,Derek B" <arche...@ad.ufl.edu>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> To: "Glasser, Matthew" <glass...@wusm.wustl.edu>, Stamatios
>>      Sotiropoulos    <stamatios.sotiropou...@ndcn.ox.ac.uk>,
>>      "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID:
>>      <ff208477c5853f498cf288adb02491a34d9b3...@ufexch-mbxn03.ad.ufl.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Hi Matt,
>> 
>> Is it possible to use nipype for bedpost processing?  Will this allow me to 
>> use the grad_dev.nii.gz file?
>> 
>> I haven't seen any other people using bedpost via nipype within this forum, 
>> however, it is being recommended to use by the engineer working for the 
>> cluster.
>> 
>> Thanks,
>> Derek
>> 
>> From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
>> Sent: Tuesday, February 17, 2015 12:55 PM
>> To: Archer,Derek B; Stamatios Sotiropoulos; hcp-users@humanconnectome.org
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> 
>> Are you running the command on ${StudyFolder}/${Subject}/T1w/Diffusion ?
>> 
>> You'll need the latest version of FSL 5.0.8 on your cluster as well.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <Archer>, Derek B <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>>
>> Date: Tuesday, February 17, 2015 at 11:53 AM
>> To: Matt Glasser <glass...@wusm.wustl.edu<mailto:glass...@wusm.wustl.edu>>, 
>> Stamatios Sotiropoulos 
>> <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>,
>>  "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
>> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: RE: [HCP-Users] Processing Diffusion MRI Data
>> 
>> Hi Matt,
>> 
>> The exact command I'm using locally is (I tried this from Stam's input):
>> 
>> bedpostx <subject directory> -n 3 -model 2 -g -rician
>> 
>> Subject directory contents:
>>               bvals
>>               bvecs
>>               data.nii.gz
>>               nodif_brain_mask.nii.gz
>>               grad_dev.nii.gz
>> 
>> This works.  How long do you estimate this will take? Because the -g option 
>> is not available on the cluster I am working on (not sure why this is the 
>> case..), and I think that may be causing the issue.
>> 
>> Thanks,
>> Derek
>> From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
>> Sent: Tuesday, February 17, 2015 12:47 PM
>> To: Archer,Derek B; Stamatios Sotiropoulos; 
>> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> 
>> How about posting the exact command line you are using and a listing of the 
>> contents of <subject_directory>
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <Archer>, Derek B <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>>
>> Date: Tuesday, February 17, 2015 at 9:20 AM
>> To: Stamatios Sotiropoulos 
>> <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>,
>>  "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
>> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> 
>> 
>> Hi Matt and Stam,
>> 
>> I seem to still be having some sort of issue running bedpostx.  I'm using:
>> 
>> bedpostx <subject_directory> --cnonlinear --rician --model=2 --nf=3.
>> 
>> (The -g option is not available in my version of FSL (5.0.5).  I am on a 
>> cluster environment.)
>> 
>> So when I run this line of code, I get the following error:
>> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> ** ERROR: (nifti_image_read): cannot create nifty image from header 'data'
>> ** ERROR: nifti_image_open (data): bad header info
>> ** ERROR: failed to open file data
>> 
>> The error seems to be with data.nii.gz, but is there error actually 
>> occurring because I am not feeding in grad_dev.nii.gz via the -g option? Do 
>> I need a newer version of FSL?
>> 
>> Thanks,
>> Derek Archer
>> 
>> From: Stamatios Sotiropoulos [mailto:stamatios.sotiropou...@ndcn.ox.ac.uk]
>> Sent: Monday, February 16, 2015 12:48 PM
>> To: Archer,Derek B
>> Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> 
>> Hi Derek
>> 
>> Please notice that model=3 is not officially released yet in FSL. Also, 
>> there should be a future HCP release in the near future including bedpostx 
>> results, with the optimal parameters.
>> 
>> Stam
>> 
>> 
>> 
>> On 16 Feb 2015, at 16:25, Archer,Derek B 
>> <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>> wrote:
>> 
>> 
>> 
>> 
>> Matt,
>> 
>> Thanks for the fast reply.  I will use these three inputs in bedpostX.
>> 
>> Derek
>> 
>> From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
>> Sent: Monday, February 16, 2015 11:24 AM
>> To: Archer,Derek B; 
>> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> 
>> Why do you need to use FLIRT/FNIRT with already registered data?  As for the 
>> others and aside from the flags you already mention, I think the 
>> recommendation for bedpostX will include these flags:
>> 
>> -n 3 (for 3 fibers)
>> --cnonlinear
>> --rician
>> --model=3
>> 
>> Not all of this may yet be available in the public release (you might need 
>> to use --model=2 for now).
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: <Archer>, Derek B <arche...@ad.ufl.edu<mailto:arche...@ad.ufl.edu>>
>> Date: Monday, February 16, 2015 at 9:16 AM
>> To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
>> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] Processing Diffusion MRI Data
>> 
>> Hello,
>> 
>> I am trying to analyze the preprocessed diffusion data, however, I am having 
>> some difficulties. Is there some documentation that I could look at that 
>> outlines how to use bedpostx, FLIRT/FNIRT, DTIFIT and probtrackx with this 
>> data?
>> 
>>> From what I've found in the archives, I need to do the following:
>> 
>> Bedpostx:  include the -g option
>> FLIRT/FNIRT:  do I include any extra options here?
>> DTIFIT:  include the -gradnonlin option
>> 
>> Is this all that needs to be done to have this data ready for tractography? 
>> Or are there steps that I have missed?
>> 
>> Please let me know if there is any documentation I have failed to locate.
>> 
>> Thanks,
>> Derek Archer
>> 
>> 
>> 
>> 
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> 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.
>> 
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> 
>> 
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> 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/20150223/d981a45d/attachment-0001.html
>>  
>> 
>> ------------------------------
>> 
>> Message: 5
>> Date: Mon, 23 Feb 2015 11:01:37 -0500
>> From: Satrajit Ghosh <sa...@mit.edu>
>> Subject: Re: [HCP-Users] Processing Diffusion MRI Data
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID:
>>      <ca+a4wonsfg0qpfqcgco6qdjxnuautdfruzwny9q2nsnljog...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> hi derek,
>> 
>> i would recommend at this point to use the HCP pipelines. however, if you
>> are comfortable hacking the code, the bedpostx step itself can be replaced
>> by a corresponding call to a nipype workflow, or better still if you have a
>> GPU to use the nipype bedpostx GPU interface.
>> 
>> for standard bedpostx nipype simply parallelizes the operation across
>> slices, but is able to do so on any cluster environment
>> (SGE/LSF/PBS/SLURM). thus, you simply reduce the time by assigning a slice
>> to a core. how much you can parallelize depends on our cluster
>> configuration. while we haven't done this yet, the nipype bedpostx workflow
>> could easily be made to look exactly like the command line call, to be a
>> drop in replacement.
>> 
>> however, if you have an Nvidia GPU (such as a tesla or equivalent), you can
>> drastically reduce the compute time. for our standard sequences (about  70
>> directions, 60 slices), we can run bedpostx for a given participant on the
>> gpu in less than 10 minutes.
>> 
>> cheers,
>> 
>> satra
>> 
>> On Mon, Feb 23, 2015 at 10:02 AM, Archer,Derek B <arche...@ad.ufl.edu>
>> wrote:
>> 
>>> Hi Matt,
>>> 
>>> 
>>> 
>>> Is it possible to use nipype for bedpost processing?  Will this allow me
>>> to use the grad_dev.nii.gz file?
>>> 
>>> 
>>> 
>>> I haven?t seen any other people using bedpost via nipype within this
>>> forum, however, it is being recommended to use by the engineer working for
>>> the cluster.
>>> 
>>> 
>>> 
>>> Thanks,
>>> 
>>> Derek
>>> 
>>> 
>>> 
>>> *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
>>> *Sent:* Tuesday, February 17, 2015 12:55 PM
>>> 
>>> *To:* Archer,Derek B; Stamatios Sotiropoulos;
>>> hcp-users@humanconnectome.org
>>> *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> Are you running the command on ${StudyFolder}/${Subject}/T1w/Diffusion ?
>>> 
>>> 
>>> 
>>> You?ll need the latest version of FSL 5.0.8 on your cluster as well.
>>> 
>>> 
>>> 
>>> Peace,
>>> 
>>> 
>>> 
>>> Matt.
>>> 
>>> 
>>> 
>>> *From: *<Archer>, Derek B <arche...@ad.ufl.edu>
>>> *Date: *Tuesday, February 17, 2015 at 11:53 AM
>>> *To: *Matt Glasser <glass...@wusm.wustl.edu>, Stamatios Sotiropoulos <
>>> stamatios.sotiropou...@ndcn.ox.ac.uk>, "hcp-users@humanconnectome.org" <
>>> hcp-users@humanconnectome.org>
>>> *Subject: *RE: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> Hi Matt,
>>> 
>>> 
>>> 
>>> The exact command I?m using locally is (I tried this from Stam?s input):
>>> 
>>> 
>>> 
>>> bedpostx <subject directory> ?n 3 ?model 2 ?g ?rician
>>> 
>>> 
>>> 
>>> Subject directory contents:
>>> 
>>>               bvals
>>> 
>>>               bvecs
>>> 
>>>               data.nii.gz
>>> 
>>>               nodif_brain_mask.nii.gz
>>> 
>>>               grad_dev.nii.gz
>>> 
>>> 
>>> 
>>> This works.  How long do you estimate this will take? Because the ?g
>>> option is not available on the cluster I am working on (not sure why this
>>> is the case..), and I think that may be causing the issue.
>>> 
>>> 
>>> 
>>> Thanks,
>>> 
>>> Derek
>>> 
>>> *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu
>>> <glass...@wusm.wustl.edu>]
>>> *Sent:* Tuesday, February 17, 2015 12:47 PM
>>> *To:* Archer,Derek B; Stamatios Sotiropoulos;
>>> hcp-users@humanconnectome.org
>>> *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> How about posting the exact command line you are using and a listing of
>>> the contents of <subject_directory>
>>> 
>>> 
>>> 
>>> Peace,
>>> 
>>> 
>>> 
>>> Matt.
>>> 
>>> 
>>> 
>>> *From: *<Archer>, Derek B <arche...@ad.ufl.edu>
>>> *Date: *Tuesday, February 17, 2015 at 9:20 AM
>>> *To: *Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>, "
>>> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> *Subject: *Re: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Hi Matt and Stam,
>>> 
>>> 
>>> 
>>> I seem to still be having some sort of issue running bedpostx.  I?m using:
>>> 
>>> 
>>> 
>>> bedpostx <subject_directory> --cnonlinear --rician --model=2 --nf=3.
>>> 
>>> 
>>> 
>>> (The ?g option is not available in my version of FSL (5.0.5).  I am on a
>>> cluster environment.)
>>> 
>>> 
>>> 
>>> So when I run this line of code, I get the following error:
>>> 
>>> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>>> 
>>> ** ERROR: (nifti_image_read): cannot create nifty image from header ?data?
>>> 
>>> ** ERROR: nifti_image_open (data): bad header info
>>> 
>>> ** ERROR: failed to open file data
>>> 
>>> 
>>> 
>>> The error seems to be with data.nii.gz, but is there error actually
>>> occurring because I am not feeding in grad_dev.nii.gz via the ?g option? Do
>>> I need a newer version of FSL?
>>> 
>>> 
>>> 
>>> Thanks,
>>> 
>>> Derek Archer
>>> 
>>> 
>>> 
>>> *From:* Stamatios Sotiropoulos [
>>> mailto:stamatios.sotiropou...@ndcn.ox.ac.uk
>>> <stamatios.sotiropou...@ndcn.ox.ac.uk>]
>>> *Sent:* Monday, February 16, 2015 12:48 PM
>>> *To:* Archer,Derek B
>>> *Cc:* hcp-users@humanconnectome.org
>>> *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> Hi Derek
>>> 
>>> 
>>> 
>>> Please notice that model=3 is not officially released yet in FSL. Also,
>>> there should be a future HCP release in the near future including bedpostx
>>> results, with the optimal parameters.
>>> 
>>> 
>>> 
>>> Stam
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 16 Feb 2015, at 16:25, Archer,Derek B <arche...@ad.ufl.edu> wrote:
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Matt,
>>> 
>>> 
>>> Thanks for the fast reply.  I will use these three inputs in bedpostX.
>>> 
>>> 
>>> 
>>> Derek
>>> 
>>> 
>>> 
>>> *From:* Glasser, Matthew [mailto:glass...@wusm.wustl.edu
>>> <glass...@wusm.wustl.edu>]
>>> *Sent:* Monday, February 16, 2015 11:24 AM
>>> *To:* Archer,Derek B; hcp-users@humanconnectome.org
>>> *Subject:* Re: [HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> Why do you need to use FLIRT/FNIRT with already registered data?  As for
>>> the others and aside from the flags you already mention, I think the
>>> recommendation for bedpostX will include these flags:
>>> 
>>> 
>>> 
>>> -n 3 (for 3 fibers)
>>> 
>>> --cnonlinear
>>> 
>>> --rician
>>> 
>>> --model=3
>>> 
>>> 
>>> 
>>> Not all of this may yet be available in the public release (you might need
>>> to use --model=2 for now).
>>> 
>>> 
>>> 
>>> Peace,
>>> 
>>> 
>>> 
>>> Matt.
>>> 
>>> 
>>> 
>>> *From: *<Archer>, Derek B <arche...@ad.ufl.edu>
>>> *Date: *Monday, February 16, 2015 at 9:16 AM
>>> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> *Subject: *[HCP-Users] Processing Diffusion MRI Data
>>> 
>>> 
>>> 
>>> Hello,
>>> 
>>> 
>>> 
>>> I am trying to analyze the preprocessed diffusion data, however, I am
>>> having some difficulties. Is there some documentation that I could look at
>>> that outlines how to use bedpostx, FLIRT/FNIRT, DTIFIT and probtrackx with
>>> this data?
>>> 
>>> 
>>> 
>>> From what I?ve found in the archives, I need to do the following:
>>> 
>>> 
>>> 
>>> Bedpostx:  include the ?g option
>>> 
>>> FLIRT/FNIRT:  do I include any extra options here?
>>> 
>>> DTIFIT:  include the ?gradnonlin option
>>> 
>>> 
>>> 
>>> Is this all that needs to be done to have this data ready for
>>> tractography? Or are there steps that I have missed?
>>> 
>>> 
>>> 
>>> Please let me know if there is any documentation I have failed to locate.
>>> 
>>> 
>>> 
>>> Thanks,
>>> 
>>> Derek Archer
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> 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.
>>> 
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> 
>>> 
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