Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data
Why do you need that? The reason for the slice increase is that the image
is rotated into ACPC space and so the slice plane is different.
Peace,
Matt.
On 7/24/18, 4:20 PM, "Sang-Young Kim" wrote:
>Hi, Matt:
>
>Thanks for your prompt response.
>
>Yes, I can use
>${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
>warp the data to structural space.
>But the problem is that I want to keep the same number of slice as
>original fMRI data (e.g., N slice=72).
>
>Once I warped rfMRI data to structural space using 2 mm reference volume,
>the number of slice for the output is 91.
>
>Is there a way to solve this issue? Also the warp field for
>standard2rfMRI_REST1_LR.nii.gz is not released, right? The reason is, as
>you mentioned, that there is no need to go to original fMRI space?
>
>Any comments would be appreciated.
>
>Best,
>
>Sang-Young
>
>
>
>> On Jul 24, 2018, at 3:03 PM, Glasser, Matthew
>>wrote:
>>
>> There is no need to go to original fMRI space in most cases. If you
>>want
>> data in the native physical space of the subject you can use
>> ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
>> warp the data to structural space (and can use a 2mm reference volume in
>> that space if you wish to keep it at the same resolution).
>>
>> Peace,
>>
>> Matt.
>>
>> On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf
>>of
>> Sang-Young Kim" > sykim...@gmail.com> wrote:
>>
>>> Dear HCP experts:
>>>
>>> I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>>> Data".
>>> The downloaded data was just preprocessed for resting state fMRI using
>>> fMRIVolume and fMRISurface pipeline.
>>>
>>> But I cannot find warp field to transform MNI space data to original
>>>fMRI
>>> space, which is normally located in ${Subject}/MNINonLinear/xfms after
>>> fMRIVolume pipeline.
>>>
>>> Could you please let me know where to find it?
>>>
>>> Thanks.
>>>
>>> Sang-Young Kim, Ph.D.
>>>
>>> Postdoctoral Fellow
>>> Department of Radiology
>>> University of Pittsburgh
>>> ___
>>> 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.
>
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Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data
Hi, Matt:
Thanks for your prompt response.
Yes, I can use
${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to warp the
data to structural space.
But the problem is that I want to keep the same number of slice as original
fMRI data (e.g., N slice=72).
Once I warped rfMRI data to structural space using 2 mm reference volume, the
number of slice for the output is 91.
Is there a way to solve this issue? Also the warp field for
standard2rfMRI_REST1_LR.nii.gz is not released, right? The reason is, as you
mentioned, that there is no need to go to original fMRI space?
Any comments would be appreciated.
Best,
Sang-Young
> On Jul 24, 2018, at 3:03 PM, Glasser, Matthew wrote:
>
> There is no need to go to original fMRI space in most cases. If you want
> data in the native physical space of the subject you can use
> ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
> warp the data to structural space (and can use a 2mm reference volume in
> that space if you wish to keep it at the same resolution).
>
> Peace,
>
> Matt.
>
> On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> Sang-Young Kim" sykim...@gmail.com> wrote:
>
>> Dear HCP experts:
>>
>> I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>> Data".
>> The downloaded data was just preprocessed for resting state fMRI using
>> fMRIVolume and fMRISurface pipeline.
>>
>> But I cannot find warp field to transform MNI space data to original fMRI
>> space, which is normally located in ${Subject}/MNINonLinear/xfms after
>> fMRIVolume pipeline.
>>
>> Could you please let me know where to find it?
>>
>> Thanks.
>>
>> Sang-Young Kim, Ph.D.
>>
>> Postdoctoral Fellow
>> Department of Radiology
>> University of Pittsburgh
>> ___
>> 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.
___
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Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data
There is no need to go to original fMRI space in most cases. If you want
data in the native physical space of the subject you can use
${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
warp the data to structural space (and can use a 2mm reference volume in
that space if you wish to keep it at the same resolution).
Peace,
Matt.
On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim" wrote:
>Dear HCP experts:
>
>I have downloaded a HCP data from "S1200 Extensively Processed fMRI
>Data".
>The downloaded data was just preprocessed for resting state fMRI using
>fMRIVolume and fMRISurface pipeline.
>
>But I cannot find warp field to transform MNI space data to original fMRI
>space, which is normally located in ${Subject}/MNINonLinear/xfms after
>fMRIVolume pipeline.
>
>Could you please let me know where to find it?
>
>Thanks.
>
>Sang-Young Kim, Ph.D.
>
>Postdoctoral Fellow
>Department of Radiology
>University of Pittsburgh
>___
>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.
___
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[HCP-Users] Where to find warp field from standard to original resting state fMRI data
Dear HCP experts:
I have downloaded a HCP data from "S1200 Extensively Processed fMRI Data".
The downloaded data was just preprocessed for resting state fMRI using
fMRIVolume and fMRISurface pipeline.
But I cannot find warp field to transform MNI space data to original fMRI
space, which is normally located in ${Subject}/MNINonLinear/xfms after
fMRIVolume pipeline.
Could you please let me know where to find it?
Thanks.
Sang-Young Kim, Ph.D.
Postdoctoral Fellow
Department of Radiology
University of Pittsburgh
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