Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Thank you so much! I understand it better now. best regards Jaime El mié., 29 may. 2019 a las 21:43, Timothy Coalson () escribió: > Yes, it is a similar problem to working in "image space", basically the > FSL tools work in a space resulting from taking the voxel indices and > multiplying them by the voxel dimensions, so a particular corner voxel > always has coordinates of (0, 0, 0)mm. Because of the transition from > origin-less ANALYZE volume format to a completely defined coordinate space > in NIfTI, different software has ended up with different quirks as to > whether it properly handles NIfTI coordinates. I think ANTs does use the > full NIfTI coordinate specification, though internally they flip it to the > ITK convention (which only matters if you need to interpret ANTs transforms > yourself, as the identity transform still does the right thing). > Unfortunately, FSL continued to use the ANALYZE coordinate specification > when doing registration and resampling of NIfTI volumes. > > We started connectome workbench much more recently than FSL started, and > although workbench inherited some code from caret5 (which also used the > full NIfTI coordinate specification, but also supported ANALYZE and other > formats, leading to some issues), its volume code was rewritten from > scratch, and only supports NIfTI volumes, so we were able to avoid legacy > issues and use the full NIfTI coordinates from day 1. FSL didn't have this > luxury, as they started before NIfTI even existed. > > As to your situation, when using FSL tools to resample to a different > voxel grid, you have to either carefully generate your volume spaces in > advance to have their corners aligned in NIfTI space the same way that FSL > assumes they align in its ANALYZE-like space, or you have to deal with FSL > adding translations to your voxel coordinates every time you resample > between these voxel spaces (by using affine files containing the opposite > translations). > > The different MNI template resolutions we use in the pipelines have these > special corner voxels aligned already in their NIfTI coordinates, so for > the pipelines we can tolerate the quirks of FSL resampling tools (and their > more advanced tools don't seem to have equivalents in other software > packages, and we work with them on improvements), but I can't recommend FSL > resampling tools to the unwary as the first choice for a new task in an > unknown volume space. > > Tim > > > On Wed, May 29, 2019 at 1:16 PM Jaime Caballero > wrote: > >> Thank you, Timothy >> >> I did the resampling with ANTs' WarpImageMultiTransform, as I thought the >> software used for this didn't matter. I have now done the same with >> wb_command as you suggested and the resulting ROIs are exactly the same. >> >> I could not make FSL's applywarp work, so I cannot tell by now what would >> come out from that. Anyway I'm not sure I understand why would it fail. Is >> it something related to rounding coordinates or working directly in image >> space? >> >> Regards, >> Jaime >> >> El mar., 28 may. 2019 a las 20:46, Timothy Coalson () >> escribió: >> >>> If you need to preserve the mm coordinates of the ROI, I would not trust >>> FSL's resampling with an identity transform to get it right, because that >>> will produce a different shift depending on what coordinates a particular >>> corner voxel is at in each image (as I understand it, FSL's conventions >>> come from originally handling ANALYZE format images). Instead, wb_command >>> -volume-affine-resample, given an identity matrix (and NOT specifying >>> -flirt) will do the resampling via nifti mm coordinates, with no guesswork. >>> >>> Tim >>> >>> >>> On Tue, May 28, 2019 at 8:08 AM Jaime Caballero >>> wrote: >>> >>>> Thank you so much! >>>> >>>> It worked fine, and the resulting ROIs are were they are suposed to be. >>>> >>>> Regards, >>>> Jaime >>>> >>>> El lun., 27 may. 2019 22:20, Glasser, Matthew >>>> escribió: >>>> >>>>> That file does exist in the structural package then. >>>>> >>>>> >>>>> >>>>> Matt. >>>>> >>>>> >>>>> >>>>> *From: *Jaime Caballero >>>>> *Date: *Monday, May 27, 2019 at 3:20 PM >>>>> *To: *"Glasser, Matthew" >>>>> *Cc: *"hcp-users@humanconnectome.org" >>>>> *Subject: *
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Yes, it is a similar problem to working in "image space", basically the FSL tools work in a space resulting from taking the voxel indices and multiplying them by the voxel dimensions, so a particular corner voxel always has coordinates of (0, 0, 0)mm. Because of the transition from origin-less ANALYZE volume format to a completely defined coordinate space in NIfTI, different software has ended up with different quirks as to whether it properly handles NIfTI coordinates. I think ANTs does use the full NIfTI coordinate specification, though internally they flip it to the ITK convention (which only matters if you need to interpret ANTs transforms yourself, as the identity transform still does the right thing). Unfortunately, FSL continued to use the ANALYZE coordinate specification when doing registration and resampling of NIfTI volumes. We started connectome workbench much more recently than FSL started, and although workbench inherited some code from caret5 (which also used the full NIfTI coordinate specification, but also supported ANALYZE and other formats, leading to some issues), its volume code was rewritten from scratch, and only supports NIfTI volumes, so we were able to avoid legacy issues and use the full NIfTI coordinates from day 1. FSL didn't have this luxury, as they started before NIfTI even existed. As to your situation, when using FSL tools to resample to a different voxel grid, you have to either carefully generate your volume spaces in advance to have their corners aligned in NIfTI space the same way that FSL assumes they align in its ANALYZE-like space, or you have to deal with FSL adding translations to your voxel coordinates every time you resample between these voxel spaces (by using affine files containing the opposite translations). The different MNI template resolutions we use in the pipelines have these special corner voxels aligned already in their NIfTI coordinates, so for the pipelines we can tolerate the quirks of FSL resampling tools (and their more advanced tools don't seem to have equivalents in other software packages, and we work with them on improvements), but I can't recommend FSL resampling tools to the unwary as the first choice for a new task in an unknown volume space. Tim On Wed, May 29, 2019 at 1:16 PM Jaime Caballero wrote: > Thank you, Timothy > > I did the resampling with ANTs' WarpImageMultiTransform, as I thought the > software used for this didn't matter. I have now done the same with > wb_command as you suggested and the resulting ROIs are exactly the same. > > I could not make FSL's applywarp work, so I cannot tell by now what would > come out from that. Anyway I'm not sure I understand why would it fail. Is > it something related to rounding coordinates or working directly in image > space? > > Regards, > Jaime > > El mar., 28 may. 2019 a las 20:46, Timothy Coalson () > escribió: > >> If you need to preserve the mm coordinates of the ROI, I would not trust >> FSL's resampling with an identity transform to get it right, because that >> will produce a different shift depending on what coordinates a particular >> corner voxel is at in each image (as I understand it, FSL's conventions >> come from originally handling ANALYZE format images). Instead, wb_command >> -volume-affine-resample, given an identity matrix (and NOT specifying >> -flirt) will do the resampling via nifti mm coordinates, with no guesswork. >> >> Tim >> >> >> On Tue, May 28, 2019 at 8:08 AM Jaime Caballero >> wrote: >> >>> Thank you so much! >>> >>> It worked fine, and the resulting ROIs are were they are suposed to be. >>> >>> Regards, >>> Jaime >>> >>> El lun., 27 may. 2019 22:20, Glasser, Matthew >>> escribió: >>> >>>> That file does exist in the structural package then. >>>> >>>> >>>> >>>> Matt. >>>> >>>> >>>> >>>> *From: *Jaime Caballero >>>> *Date: *Monday, May 27, 2019 at 3:20 PM >>>> *To: *"Glasser, Matthew" >>>> *Cc: *"hcp-users@humanconnectome.org" >>>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format >>>> (subcortical) >>>> >>>> >>>> >>>> Sorry for the confusion. >>>> >>>> >>>> >>>> Locally acquired data wasn't processed using the HCP pipelines, it is >>>> in a different resolution and it was processed in volume space, no problem >>>> there. >>>> >>>> >>>> >>>> I want to use Choi's parcellation with HCP data. All
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Thank you, Timothy
I did the resampling with ANTs' WarpImageMultiTransform, as I thought the
software used for this didn't matter. I have now done the same with
wb_command as you suggested and the resulting ROIs are exactly the same.
I could not make FSL's applywarp work, so I cannot tell by now what would
come out from that. Anyway I'm not sure I understand why would it fail. Is
it something related to rounding coordinates or working directly in image
space?
Regards,
Jaime
El mar., 28 may. 2019 a las 20:46, Timothy Coalson ()
escribió:
> If you need to preserve the mm coordinates of the ROI, I would not trust
> FSL's resampling with an identity transform to get it right, because that
> will produce a different shift depending on what coordinates a particular
> corner voxel is at in each image (as I understand it, FSL's conventions
> come from originally handling ANALYZE format images). Instead, wb_command
> -volume-affine-resample, given an identity matrix (and NOT specifying
> -flirt) will do the resampling via nifti mm coordinates, with no guesswork.
>
> Tim
>
>
> On Tue, May 28, 2019 at 8:08 AM Jaime Caballero
> wrote:
>
>> Thank you so much!
>>
>> It worked fine, and the resulting ROIs are were they are suposed to be.
>>
>> Regards,
>> Jaime
>>
>> El lun., 27 may. 2019 22:20, Glasser, Matthew
>> escribió:
>>
>>> That file does exist in the structural package then.
>>>
>>>
>>>
>>> Matt.
>>>
>>>
>>>
>>> *From: *Jaime Caballero
>>> *Date: *Monday, May 27, 2019 at 3:20 PM
>>> *To: *"Glasser, Matthew"
>>> *Cc: *"hcp-users@humanconnectome.org"
>>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>>> (subcortical)
>>>
>>>
>>>
>>> Sorry for the confusion.
>>>
>>>
>>>
>>> Locally acquired data wasn't processed using the HCP pipelines, it is in
>>> a different resolution and it was processed in volume space, no problem
>>> there.
>>>
>>>
>>>
>>> I want to use Choi's parcellation with HCP data. All the process I
>>> described is mi workaround to adapt Choi files to HCP files.
>>>
>>>
>>>
>>> Jaime
>>>
>>>
>>>
>>> El lun., 27 may. 2019 22:12, Glasser, Matthew
>>> escribió:
>>>
>>> I thought you said you were using a locally collected sample you ran the
>>> HCP Pipelines on?
>>>
>>> Matt.
>>>
>>>
>>>
>>> *From: *Jaime Caballero
>>> *Date: *Monday, May 27, 2019 at 3:10 PM
>>> *To: *"Glasser, Matthew"
>>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>>> (subcortical)
>>>
>>>
>>>
>>> Ok, thank you! I will try that.
>>>
>>>
>>>
>>> I asume the reference image
>>> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
>>> downloaded with the structural package?
>>>
>>>
>>>
>>> Regards,
>>>
>>> Jaime
>>>
>>>
>>>
>>> El lun., 27 may. 2019 a las 21:00, Glasser, Matthew ()
>>> escribió:
>>>
>>> To make the .dscalar.nii file, you seem to be on the right track. If
>>> the Choi ROIs are properly in MNI space, hopefully you could simply use
>>> applywarp --interp=nn -i -r
>>> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
>>> and then the wb_command -cifti-create-dense-from-template you
>>> mention.
>>>
>>>
>>>
>>> Matt.
>>>
>>>
>>>
>>> *From: *Jaime Caballero
>>> *Date: *Monday, May 27, 2019 at 12:56 PM
>>> *To: *"Glasser, Matthew"
>>> *Cc: *"hcp-users@humanconnectome.org"
>>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>>> (subcortical)
>>>
>>>
>>>
>>> The objective is to extract functional connectivity between cortical and
>>> striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
>>>
>>>
>>>
>>> Up to this point I have imported each subject's dtseries.nii file into
>>> MATLAB, and also the previously defined ROIs in an HCP-compatible format.
>>> For the dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1
>>> matrix containing a mask, which I use to extract the time series I&#
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
If you need to preserve the mm coordinates of the ROI, I would not trust
FSL's resampling with an identity transform to get it right, because that
will produce a different shift depending on what coordinates a particular
corner voxel is at in each image (as I understand it, FSL's conventions
come from originally handling ANALYZE format images). Instead, wb_command
-volume-affine-resample, given an identity matrix (and NOT specifying
-flirt) will do the resampling via nifti mm coordinates, with no guesswork.
Tim
On Tue, May 28, 2019 at 8:08 AM Jaime Caballero wrote:
> Thank you so much!
>
> It worked fine, and the resulting ROIs are were they are suposed to be.
>
> Regards,
> Jaime
>
> El lun., 27 may. 2019 22:20, Glasser, Matthew
> escribió:
>
>> That file does exist in the structural package then.
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: *Jaime Caballero
>> *Date: *Monday, May 27, 2019 at 3:20 PM
>> *To: *"Glasser, Matthew"
>> *Cc: *"hcp-users@humanconnectome.org"
>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>> (subcortical)
>>
>>
>>
>> Sorry for the confusion.
>>
>>
>>
>> Locally acquired data wasn't processed using the HCP pipelines, it is in
>> a different resolution and it was processed in volume space, no problem
>> there.
>>
>>
>>
>> I want to use Choi's parcellation with HCP data. All the process I
>> described is mi workaround to adapt Choi files to HCP files.
>>
>>
>>
>> Jaime
>>
>>
>>
>> El lun., 27 may. 2019 22:12, Glasser, Matthew
>> escribió:
>>
>> I thought you said you were using a locally collected sample you ran the
>> HCP Pipelines on?
>>
>> Matt.
>>
>>
>>
>> *From: *Jaime Caballero
>> *Date: *Monday, May 27, 2019 at 3:10 PM
>> *To: *"Glasser, Matthew"
>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>> (subcortical)
>>
>>
>>
>> Ok, thank you! I will try that.
>>
>>
>>
>> I asume the reference image
>> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
>> downloaded with the structural package?
>>
>>
>>
>> Regards,
>>
>> Jaime
>>
>>
>>
>> El lun., 27 may. 2019 a las 21:00, Glasser, Matthew ()
>> escribió:
>>
>> To make the .dscalar.nii file, you seem to be on the right track. If the
>> Choi ROIs are properly in MNI space, hopefully you could simply use
>> applywarp --interp=nn -i -r
>> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
>> and then the wb_command -cifti-create-dense-from-template you
>> mention.
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: *Jaime Caballero
>> *Date: *Monday, May 27, 2019 at 12:56 PM
>> *To: *"Glasser, Matthew"
>> *Cc: *"hcp-users@humanconnectome.org"
>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>> (subcortical)
>>
>>
>>
>> The objective is to extract functional connectivity between cortical and
>> striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
>>
>>
>>
>> Up to this point I have imported each subject's dtseries.nii file into
>> MATLAB, and also the previously defined ROIs in an HCP-compatible format.
>> For the dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1
>> matrix containing a mask, which I use to extract the time series I'm
>> interested in for further processing.
>>
>>
>>
>> Jaime
>>
>>
>>
>>
>>
>> El lun., 27 may. 2019 a las 19:14, Glasser, Matthew ()
>> escribió:
>>
>> What do you plan to do with the file?
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: *Jaime Caballero
>> *Date: *Monday, May 27, 2019 at 12:08 PM
>> *To: *"Glasser, Matthew"
>> *Cc: *"hcp-users@humanconnectome.org"
>> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
>> (subcortical)
>>
>>
>>
>> A .dscalar.nii output, I think. Basically I want an equivalent of the
>> nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI,
>> 0 if outside. Would a dlabel file be better for this application?
>>
>>
>>
>> El lun., 27 may. 2019 a las 19:03, Glasser, Matthew ()
>> escribió:
>>
>> Are you wanting a .dlabel.nii output or a .dscalar.nii output?
>>
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Thank you so much!
It worked fine, and the resulting ROIs are were they are suposed to be.
Regards,
Jaime
El lun., 27 may. 2019 22:20, Glasser, Matthew escribió:
> That file does exist in the structural package then.
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 3:20 PM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> Sorry for the confusion.
>
>
>
> Locally acquired data wasn't processed using the HCP pipelines, it is in a
> different resolution and it was processed in volume space, no problem there.
>
>
>
> I want to use Choi's parcellation with HCP data. All the process I
> described is mi workaround to adapt Choi files to HCP files.
>
>
>
> Jaime
>
>
>
> El lun., 27 may. 2019 22:12, Glasser, Matthew
> escribió:
>
> I thought you said you were using a locally collected sample you ran the
> HCP Pipelines on?
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 3:10 PM
> *To: *"Glasser, Matthew"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> Ok, thank you! I will try that.
>
>
>
> I asume the reference image
> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
> downloaded with the structural package?
>
>
>
> Regards,
>
> Jaime
>
>
>
> El lun., 27 may. 2019 a las 21:00, Glasser, Matthew ()
> escribió:
>
> To make the .dscalar.nii file, you seem to be on the right track. If the
> Choi ROIs are properly in MNI space, hopefully you could simply use
> applywarp --interp=nn -i -r
> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
> and then the wb_command -cifti-create-dense-from-template you
> mention.
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 12:56 PM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> The objective is to extract functional connectivity between cortical and
> striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
>
>
>
> Up to this point I have imported each subject's dtseries.nii file into
> MATLAB, and also the previously defined ROIs in an HCP-compatible format.
> For the dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1
> matrix containing a mask, which I use to extract the time series I'm
> interested in for further processing.
>
>
>
> Jaime
>
>
>
>
>
> El lun., 27 may. 2019 a las 19:14, Glasser, Matthew ()
> escribió:
>
> What do you plan to do with the file?
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 12:08 PM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> A .dscalar.nii output, I think. Basically I want an equivalent of the
> nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI,
> 0 if outside. Would a dlabel file be better for this application?
>
>
>
> El lun., 27 may. 2019 a las 19:03, Glasser, Matthew ()
> escribió:
>
> Are you wanting a .dlabel.nii output or a .dscalar.nii output?
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Jaime
> Caballero
> *Date: *Monday, May 27, 2019 at 10:37 AM
> *To: *"hcp-users@humanconnectome.org"
> *Subject: *[HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
>
>
>
> Dear experts
>
>
>
> In my center we are studying cortico-striatal functional connectivity, and
> cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample.
> For that we are using Choi's functional parcellation, distributed as a
> volumetric NIFTI file, in MNI152 space. We want to validate our measures
> with a subset of the S1200 release (resting state, 3T). Specifically I have
> used the ICA-FIX cleaned and MSM-all registered files, i.e.:
>
>
> /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
>
>
>
> The thing is I have doubts on the way to convert nifti ROIs to cifti
> format in this case.
>
>
>
> My first approach:
>
>
>
> 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi
> file is a volume containing 0s and 1s.
>
> 2. Use the inverse of the NIFTI'
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
That file does exist in the structural package then.
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 3:20 PM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Sorry for the confusion.
Locally acquired data wasn't processed using the HCP pipelines, it is in a
different resolution and it was processed in volume space, no problem there.
I want to use Choi's parcellation with HCP data. All the process I described is
mi workaround to adapt Choi files to HCP files.
Jaime
El lun., 27 may. 2019 22:12, Glasser, Matthew
mailto:glass...@wustl.edu>> escribió:
I thought you said you were using a locally collected sample you ran the HCP
Pipelines on?
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 3:10 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Ok, thank you! I will try that.
I asume the reference image
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
downloaded with the structural package?
Regards,
Jaime
El lun., 27 may. 2019 a las 21:00, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
To make the .dscalar.nii file, you seem to be on the right track. If the Choi
ROIs are properly in MNI space, hopefully you could simply use applywarp
--interp=nn -i -r
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
and then the wb_command -cifti-create-dense-from-template you mention.
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:56 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
The objective is to extract functional connectivity between cortical and
striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
Up to this point I have imported each subject's dtseries.nii file into MATLAB,
and also the previously defined ROIs in an HCP-compatible format. For the
dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1 matrix
containing a mask, which I use to extract the time series I'm interested in for
further processing.
Jaime
El lun., 27 may. 2019 a las 19:14, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
What do you plan to do with the file?
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:08 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an equivalent of the nifti
ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if
outside. Would a dlabel file be better for this application?
El lun., 27 may. 2019 a las 19:03, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
Are you wanting a .dlabel.nii output or a .dscalar.nii output?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 10:37 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts
In my center we are studying cortico-striatal functional connectivity, and
cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For
that we are using Choi's functional parcellation, distributed as a volumetric
NIFTI file, in MNI152 space. We want to validate our measures with a subset of
the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX
cleaned and MSM-all registered files, i.e.:
/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
The thing is I have doubts on the way to convert nifti ROIs to cifti format in
this case.
My first approach:
1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is
a volume containing 0s and 1s.
2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ
coordinates in MNI space from each grayordinate to XYZ coordinates in the
NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based
matrix indexing)
3. The values of the NIFTI volume for the obtained coordinates define the ROI
in the output cifti.
4. Keep only the grayordinates that are set to one by my method and t
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Sorry for the confusion.
Locally acquired data wasn't processed using the HCP pipelines, it is in a
different resolution and it was processed in volume space, no problem there.
I want to use Choi's parcellation with HCP data. All the process I
described is mi workaround to adapt Choi files to HCP files.
Jaime
El lun., 27 may. 2019 22:12, Glasser, Matthew escribió:
> I thought you said you were using a locally collected sample you ran the
> HCP Pipelines on?
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 3:10 PM
> *To: *"Glasser, Matthew"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> Ok, thank you! I will try that.
>
>
>
> I asume the reference image
> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
> downloaded with the structural package?
>
>
>
> Regards,
>
> Jaime
>
>
>
> El lun., 27 may. 2019 a las 21:00, Glasser, Matthew ()
> escribió:
>
> To make the .dscalar.nii file, you seem to be on the right track. If the
> Choi ROIs are properly in MNI space, hopefully you could simply use
> applywarp --interp=nn -i -r
> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
> and then the wb_command -cifti-create-dense-from-template you
> mention.
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 12:56 PM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> The objective is to extract functional connectivity between cortical and
> striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
>
>
>
> Up to this point I have imported each subject's dtseries.nii file into
> MATLAB, and also the previously defined ROIs in an HCP-compatible format.
> For the dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1
> matrix containing a mask, which I use to extract the time series I'm
> interested in for further processing.
>
>
>
> Jaime
>
>
>
>
>
> El lun., 27 may. 2019 a las 19:14, Glasser, Matthew ()
> escribió:
>
> What do you plan to do with the file?
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero
> *Date: *Monday, May 27, 2019 at 12:08 PM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> A .dscalar.nii output, I think. Basically I want an equivalent of the
> nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI,
> 0 if outside. Would a dlabel file be better for this application?
>
>
>
> El lun., 27 may. 2019 a las 19:03, Glasser, Matthew ()
> escribió:
>
> Are you wanting a .dlabel.nii output or a .dscalar.nii output?
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Jaime
> Caballero
> *Date: *Monday, May 27, 2019 at 10:37 AM
> *To: *"hcp-users@humanconnectome.org"
> *Subject: *[HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
>
>
>
> Dear experts
>
>
>
> In my center we are studying cortico-striatal functional connectivity, and
> cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample.
> For that we are using Choi's functional parcellation, distributed as a
> volumetric NIFTI file, in MNI152 space. We want to validate our measures
> with a subset of the S1200 release (resting state, 3T). Specifically I have
> used the ICA-FIX cleaned and MSM-all registered files, i.e.:
>
>
> /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
>
>
>
> The thing is I have doubts on the way to convert nifti ROIs to cifti
> format in this case.
>
>
>
> My first approach:
>
>
>
> 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi
> file is a volume containing 0s and 1s.
>
> 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ
> coordinates in MNI space from each grayordinate to XYZ coordinates in the
> NIFTI'S volume space. (The matrix is corrected to account for MATLAB's
> 1-based matrix indexing)
>
> 3. The values of the NIFTI volume for the obtained coordinates define the
> ROI in the output cifti.
>
> 4. Keep only the grayordinates that are set to one by my method and that
> are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti
> files.
>
>
>
> This aproach is rather hand-made, and I wonder if I am missing something
> important.
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
I thought you said you were using a locally collected sample you ran the HCP
Pipelines on?
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 3:10 PM
To: "Glasser, Matthew"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Ok, thank you! I will try that.
I asume the reference image
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
downloaded with the structural package?
Regards,
Jaime
El lun., 27 may. 2019 a las 21:00, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
To make the .dscalar.nii file, you seem to be on the right track. If the Choi
ROIs are properly in MNI space, hopefully you could simply use applywarp
--interp=nn -i -r
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
and then the wb_command -cifti-create-dense-from-template you mention.
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:56 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
The objective is to extract functional connectivity between cortical and
striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
Up to this point I have imported each subject's dtseries.nii file into MATLAB,
and also the previously defined ROIs in an HCP-compatible format. For the
dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1 matrix
containing a mask, which I use to extract the time series I'm interested in for
further processing.
Jaime
El lun., 27 may. 2019 a las 19:14, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
What do you plan to do with the file?
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:08 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an equivalent of the nifti
ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if
outside. Would a dlabel file be better for this application?
El lun., 27 may. 2019 a las 19:03, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
Are you wanting a .dlabel.nii output or a .dscalar.nii output?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 10:37 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts
In my center we are studying cortico-striatal functional connectivity, and
cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For
that we are using Choi's functional parcellation, distributed as a volumetric
NIFTI file, in MNI152 space. We want to validate our measures with a subset of
the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX
cleaned and MSM-all registered files, i.e.:
/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
The thing is I have doubts on the way to convert nifti ROIs to cifti format in
this case.
My first approach:
1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is
a volume containing 0s and 1s.
2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ
coordinates in MNI space from each grayordinate to XYZ coordinates in the
NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based
matrix indexing)
3. The values of the NIFTI volume for the obtained coordinates define the ROI
in the output cifti.
4. Keep only the grayordinates that are set to one by my method and that are
labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files.
This aproach is rather hand-made, and I wonder if I am missing something
important. Conceptually it looks correct to me, but the ROIs appear slightly
displaced to the right, which might affect the results.
To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose
works well (it reads the grayordinate positions and labels), and to load the
NIFTIs I use Freesurfer's load_nifti( ).
Is this method correct, or is there something important I'm not taking into
account?
Now I'm trying to do the same with wb_command to compare, but I cannot get it
working. The procedure I use is:
# Resample the ROI file to 2x2x2 resolution with ANT
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
To make the .dscalar.nii file, you seem to be on the right track. If the Choi
ROIs are properly in MNI space, hopefully you could simply use applywarp
--interp=nn -i -r
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o
and then the wb_command -cifti-create-dense-from-template you mention.
Matt.
From: Jaime Caballero
Date: Monday, May 27, 2019 at 12:56 PM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
The objective is to extract functional connectivity between cortical and
striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
Up to this point I have imported each subject's dtseries.nii file into MATLAB,
and also the previously defined ROIs in an HCP-compatible format. For the
dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1 matrix
containing a mask, which I use to extract the time series I'm interested in for
further processing.
Jaime
El lun., 27 may. 2019 a las 19:14, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
What do you plan to do with the file?
Matt.
From: Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:08 PM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an equivalent of the nifti
ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if
outside. Would a dlabel file be better for this application?
El lun., 27 may. 2019 a las 19:03, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
Are you wanting a .dlabel.nii output or a .dscalar.nii output?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Jaime Caballero mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 10:37 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts
In my center we are studying cortico-striatal functional connectivity, and
cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For
that we are using Choi's functional parcellation, distributed as a volumetric
NIFTI file, in MNI152 space. We want to validate our measures with a subset of
the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX
cleaned and MSM-all registered files, i.e.:
/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
The thing is I have doubts on the way to convert nifti ROIs to cifti format in
this case.
My first approach:
1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is
a volume containing 0s and 1s.
2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ
coordinates in MNI space from each grayordinate to XYZ coordinates in the
NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based
matrix indexing)
3. The values of the NIFTI volume for the obtained coordinates define the ROI
in the output cifti.
4. Keep only the grayordinates that are set to one by my method and that are
labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files.
This aproach is rather hand-made, and I wonder if I am missing something
important. Conceptually it looks correct to me, but the ROIs appear slightly
displaced to the right, which might affect the results.
To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose
works well (it reads the grayordinate positions and labels), and to load the
NIFTIs I use Freesurfer's load_nifti( ).
Is this method correct, or is there something important I'm not taking into
account?
Now I'm trying to do the same with wb_command to compare, but I cannot get it
working. The procedure I use is:
# Resample the ROI file to 2x2x2 resolution with ANTs:
ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0
# Convert the obtained nifti to cifti:
wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile"
"$CiftiOut" -volume-all "$NiftiFileResampled"
Which outputs the error: -volume-all specifies a volume file that doesn't match
the volume space of the template cifti file
Is there anything wrong with my way of doing this procedure?
Thanks in advance,
Best regards,
Jaime Caballero-Insaurriaga
___
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Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
The objective is to extract functional connectivity between cortical and striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs. Up to this point I have imported each subject's dtseries.nii file into MATLAB, and also the previously defined ROIs in an HCP-compatible format. For the dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1 matrix containing a mask, which I use to extract the time series I'm interested in for further processing. Jaime El lun., 27 may. 2019 a las 19:14, Glasser, Matthew () escribió: > What do you plan to do with the file? > > > > Matt. > > > > *From: *Jaime Caballero > *Date: *Monday, May 27, 2019 at 12:08 PM > *To: *"Glasser, Matthew" > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format > (subcortical) > > > > A .dscalar.nii output, I think. Basically I want an equivalent of the > nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, > 0 if outside. Would a dlabel file be better for this application? > > > > El lun., 27 may. 2019 a las 19:03, Glasser, Matthew () > escribió: > > Are you wanting a .dlabel.nii output or a .dscalar.nii output? > > > > Matt. > > > > *From: * on behalf of Jaime > Caballero > *Date: *Monday, May 27, 2019 at 10:37 AM > *To: *"hcp-users@humanconnectome.org" > *Subject: *[HCP-Users] Convert nifti-ROIs to cifti format (subcortical) > > > > Dear experts > > > > In my center we are studying cortico-striatal functional connectivity, and > cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. > For that we are using Choi's functional parcellation, distributed as a > volumetric NIFTI file, in MNI152 space. We want to validate our measures > with a subset of the S1200 release (resting state, 3T). Specifically I have > used the ICA-FIX cleaned and MSM-all registered files, i.e.: > > > /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii > > > > The thing is I have doubts on the way to convert nifti ROIs to cifti > format in this case. > > > > My first approach: > > > > 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi > file is a volume containing 0s and 1s. > > 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ > coordinates in MNI space from each grayordinate to XYZ coordinates in the > NIFTI'S volume space. (The matrix is corrected to account for MATLAB's > 1-based matrix indexing) > > 3. The values of the NIFTI volume for the obtained coordinates define the > ROI in the output cifti. > > 4. Keep only the grayordinates that are set to one by my method and that > are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti > files. > > > > This aproach is rather hand-made, and I wonder if I am missing something > important. Conceptually it looks correct to me, but the ROIs appear > slightly displaced to the right, which might affect the results. > > To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this > purpose works well (it reads the grayordinate positions and labels), and to > load the NIFTIs I use Freesurfer's load_nifti( ). > > Is this method correct, or is there something important I'm not taking > into account? > > > > Now I'm trying to do the same with wb_command to compare, but I cannot get > it working. The procedure I use is: > > > > # Resample the ROI file to 2x2x2 resolution with ANTs: > > ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0 > > # Convert the obtained nifti to cifti: > > wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile" > "$CiftiOut" -volume-all "$NiftiFileResampled" > > > > Which outputs the error: -volume-all specifies a volume file that doesn't > match the volume space of the template cifti file > > Is there anything wrong with my way of doing this procedure? > > > > Thanks in advance, > > > > Best regards, > > Jaime Caballero-Insaurriaga > > ___ > 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 relian
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
What do you plan to do with the file? Matt. From: Jaime Caballero Date: Monday, May 27, 2019 at 12:08 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) A .dscalar.nii output, I think. Basically I want an equivalent of the nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if outside. Would a dlabel file be better for this application? El lun., 27 may. 2019 a las 19:03, Glasser, Matthew (mailto:glass...@wustl.edu>>) escribió: Are you wanting a .dlabel.nii output or a .dscalar.nii output? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Jaime Caballero mailto:jcabai...@gmail.com>> Date: Monday, May 27, 2019 at 10:37 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) Dear experts In my center we are studying cortico-striatal functional connectivity, and cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For that we are using Choi's functional parcellation, distributed as a volumetric NIFTI file, in MNI152 space. We want to validate our measures with a subset of the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX cleaned and MSM-all registered files, i.e.: /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii The thing is I have doubts on the way to convert nifti ROIs to cifti format in this case. My first approach: 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is a volume containing 0s and 1s. 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ coordinates in MNI space from each grayordinate to XYZ coordinates in the NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based matrix indexing) 3. The values of the NIFTI volume for the obtained coordinates define the ROI in the output cifti. 4. Keep only the grayordinates that are set to one by my method and that are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files. This aproach is rather hand-made, and I wonder if I am missing something important. Conceptually it looks correct to me, but the ROIs appear slightly displaced to the right, which might affect the results. To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose works well (it reads the grayordinate positions and labels), and to load the NIFTIs I use Freesurfer's load_nifti( ). Is this method correct, or is there something important I'm not taking into account? Now I'm trying to do the same with wb_command to compare, but I cannot get it working. The procedure I use is: # Resample the ROI file to 2x2x2 resolution with ANTs: ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0 # Convert the obtained nifti to cifti: wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile" "$CiftiOut" -volume-all "$NiftiFileResampled" Which outputs the error: -volume-all specifies a volume file that doesn't match the volume space of the template cifti file Is there anything wrong with my way of doing this procedure? Thanks in advance, Best regards, Jaime Caballero-Insaurriaga ___ 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an equivalent of the nifti ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if outside. Would a dlabel file be better for this application? El lun., 27 may. 2019 a las 19:03, Glasser, Matthew () escribió: > Are you wanting a .dlabel.nii output or a .dscalar.nii output? > > > > Matt. > > > > *From: * on behalf of Jaime > Caballero > *Date: *Monday, May 27, 2019 at 10:37 AM > *To: *"hcp-users@humanconnectome.org" > *Subject: *[HCP-Users] Convert nifti-ROIs to cifti format (subcortical) > > > > Dear experts > > > > In my center we are studying cortico-striatal functional connectivity, and > cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. > For that we are using Choi's functional parcellation, distributed as a > volumetric NIFTI file, in MNI152 space. We want to validate our measures > with a subset of the S1200 release (resting state, 3T). Specifically I have > used the ICA-FIX cleaned and MSM-all registered files, i.e.: > > > /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii > > > > The thing is I have doubts on the way to convert nifti ROIs to cifti > format in this case. > > > > My first approach: > > > > 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi > file is a volume containing 0s and 1s. > > 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ > coordinates in MNI space from each grayordinate to XYZ coordinates in the > NIFTI'S volume space. (The matrix is corrected to account for MATLAB's > 1-based matrix indexing) > > 3. The values of the NIFTI volume for the obtained coordinates define the > ROI in the output cifti. > > 4. Keep only the grayordinates that are set to one by my method and that > are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti > files. > > > > This aproach is rather hand-made, and I wonder if I am missing something > important. Conceptually it looks correct to me, but the ROIs appear > slightly displaced to the right, which might affect the results. > > To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this > purpose works well (it reads the grayordinate positions and labels), and to > load the NIFTIs I use Freesurfer's load_nifti( ). > > Is this method correct, or is there something important I'm not taking > into account? > > > > Now I'm trying to do the same with wb_command to compare, but I cannot get > it working. The procedure I use is: > > > > # Resample the ROI file to 2x2x2 resolution with ANTs: > > ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0 > > # Convert the obtained nifti to cifti: > > wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile" > "$CiftiOut" -volume-all "$NiftiFileResampled" > > > > Which outputs the error: -volume-all specifies a volume file that doesn't > match the volume space of the template cifti file > > Is there anything wrong with my way of doing this procedure? > > > > Thanks in advance, > > > > Best regards, > > Jaime Caballero-Insaurriaga > > ___ > 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
Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Are you wanting a .dlabel.nii output or a .dscalar.nii output? Matt. From: on behalf of Jaime Caballero Date: Monday, May 27, 2019 at 10:37 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) Dear experts In my center we are studying cortico-striatal functional connectivity, and cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For that we are using Choi's functional parcellation, distributed as a volumetric NIFTI file, in MNI152 space. We want to validate our measures with a subset of the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX cleaned and MSM-all registered files, i.e.: /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii The thing is I have doubts on the way to convert nifti ROIs to cifti format in this case. My first approach: 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is a volume containing 0s and 1s. 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ coordinates in MNI space from each grayordinate to XYZ coordinates in the NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based matrix indexing) 3. The values of the NIFTI volume for the obtained coordinates define the ROI in the output cifti. 4. Keep only the grayordinates that are set to one by my method and that are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files. This aproach is rather hand-made, and I wonder if I am missing something important. Conceptually it looks correct to me, but the ROIs appear slightly displaced to the right, which might affect the results. To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose works well (it reads the grayordinate positions and labels), and to load the NIFTIs I use Freesurfer's load_nifti( ). Is this method correct, or is there something important I'm not taking into account? Now I'm trying to do the same with wb_command to compare, but I cannot get it working. The procedure I use is: # Resample the ROI file to 2x2x2 resolution with ANTs: ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0 # Convert the obtained nifti to cifti: wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile" "$CiftiOut" -volume-all "$NiftiFileResampled" Which outputs the error: -volume-all specifies a volume file that doesn't match the volume space of the template cifti file Is there anything wrong with my way of doing this procedure? Thanks in advance, Best regards, Jaime Caballero-Insaurriaga ___ 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
[HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts In my center we are studying cortico-striatal functional connectivity, and cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For that we are using Choi's functional parcellation, distributed as a volumetric NIFTI file, in MNI152 space. We want to validate our measures with a subset of the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX cleaned and MSM-all registered files, i.e.: /MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii The thing is I have doubts on the way to convert nifti ROIs to cifti format in this case. My first approach: 1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is a volume containing 0s and 1s. 2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ coordinates in MNI space from each grayordinate to XYZ coordinates in the NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based matrix indexing) 3. The values of the NIFTI volume for the obtained coordinates define the ROI in the output cifti. 4. Keep only the grayordinates that are set to one by my method and that are labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files. This aproach is rather hand-made, and I wonder if I am missing something important. Conceptually it looks correct to me, but the ROIs appear slightly displaced to the right, which might affect the results. To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose works well (it reads the grayordinate positions and labels), and to load the NIFTIs I use Freesurfer's load_nifti( ). Is this method correct, or is there something important I'm not taking into account? Now I'm trying to do the same with wb_command to compare, but I cannot get it working. The procedure I use is: # Resample the ROI file to 2x2x2 resolution with ANTs: ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0 # Convert the obtained nifti to cifti: wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile" "$CiftiOut" -volume-all "$NiftiFileResampled" Which outputs the error: -volume-all specifies a volume file that doesn't match the volume space of the template cifti file Is there anything wrong with my way of doing this procedure? Thanks in advance, Best regards, Jaime Caballero-Insaurriaga ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
