[Freesurfer] map parcellations into DWI space?
External Email - Use Caution Dear FreeSurfer experts: I am trying to map ./mri/aparc.a2009s+aseg.mgz and ./mri/aparc+aseg.mgz into DTI file. Let's say, we have a DTI file with its b-vectors: ./bvals ./bvecs ./data.nii.gz I am trying to use the command from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat So I used the command : mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o dk-in-rawavg.mgz --regheader aparc+aseg.mgz The output file seems not very reasonable. Could you help me with this? Yerong == Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: [Hide Quoted Text] External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] map parcellations into DWI space?
External Email - Use Caution Yes, this is super-helpful. Thank you so much. Yerong Quoting "Greve, Douglas N.,Ph.D." : > you might try this page > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 > > On 12/30/18 1:45 AM, Yerong Li wrote: >> External Email - Use Caution >> Dear FreeSurfer experts: >> I am trying to map ./mri/aparc.a2009s+aseg.mgz and >> ./mri/aparc+aseg.mgz into DTI file. >> Let's say, we have a DTI file with its b-vectors: >> ./bvals >> ./bvecs >> ./data.nii.gz >> >> I am trying to use the command from this webpage: >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >> >> So I used the command : >> mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o >> dk-in-rawavg.mgz --regheader aparc+aseg.mgz >> >> The output file seems not very reasonable. Could you help me with this? >> >> Yerong >> == >> Can you be more specific about which files you want to map into your DWI >> space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You >> will need a registration file which you can obtain with bbregister >> >> >> On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: >>> >>> External Email - Use Caution >>> >>> Dear FreeSurfer experts, >>> I have a parcellation and a whole brain white matter files which are >>> the outputs of FreeSurfer. >>> I want to register them to my DWI. I mean I want my parcellation and >>> white matter to be in the physical space of my DWI. >>> Can FreeSurfer do it for me? >>> If not , can you suggest me a toolbox that can do it fast? >>> I would be grateful if u could help me. >>> Cheers, >>> Maedeh, >>> >>> >> > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] On relationship between aparc+aseg.mgz and ?h.aparc.annot
External Email - Use Caution Dear Freesurfer experts: I am on ROI analysis tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0 And I am trying to understand the relationship between: /label/?h.aparc.annot and /mri/aparc+aseg.mgz /label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany atlas" and its labels have 35 different labels (except unknown 0), while in several cases you mentioned that "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas", which I DO NOT understand. "/mri/aparc+aseg.mgz" to me are subcortical segmentations while "/label/?h.aparc.annot" are cortical(surface) parcellations. "Desikan-Killiany atlas" should mean "cortical (surface) parcellations". That's why I do not understand why "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"? Could anyone help me understand this? Yerong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] On relationship between aparc+aseg.mgz and ?h.aparc.annot
External Email - Use Caution
Dear Bruce:
Thank you.
So my question would be if aparc+aseg.mgz is from ?h.aparc.annot and
aparc.a2009s+aseg.mgz is from
?h.aparc.a2009s.annot.
Then how I can find the mapping between labels in aparc+aseg.mgz to
labels in ?h.aparc.annot?
The labels in ?h.aparc.annot are
06500 660700 1316060 1326300
1351760 2146559
2647065 3296035 3302420 3302560 3957880
3988500 3988540
4924360 6553700 6558940 7874740 8204875
9180240 9180300
9182740 9211105 9221140 9221340 9231540
1051148510542100
1114631011832480131457501442310014433500
1446422014474380
they have naming:
{'unknown' }
{'bankssts'}
{'caudalanteriorcingulate' }
{'caudalmiddlefrontal' }
{'corpuscallosum' }
{'cuneus' }
{'entorhinal' }
{'fusiform'}
{'inferiorparietal'}
{'inferiortemporal'}
{'isthmuscingulate'}
{'lateraloccipital'}
{'lateralorbitofrontal'}
{'lingual' }
{'medialorbitofrontal' }
{'middletemporal' }
{'parahippocampal' }
{'paracentral' }
{'parsopercularis' }
{'parsorbitalis' }
{'parstriangularis'}
{'pericalcarine' }
{'postcentral' }
{'posteriorcingulate' }
{'precentral' }
{'precuneus' }
{'rostralanteriorcingulate'}
{'rostralmiddlefrontal'}
{'superiorfrontal' }
{'superiorparietal'}
{'superiortemporal'}
{'supramarginal' }
{'frontalpole' }
{'temporalpole'}
{'transversetemporal' }
{'insula' }
The labels in aparc+aseg.mgz are from 0-2035 and most of them are under 88.
And in lookup tables, labels in aparc+aseg.mgz have different naming.
Do you know how to do find relationship between volumtic labels and
surface labels?
Yerong
Quoting Bruce Fischl :
> Hi Yerong
>
> the parcellations are done on the surface to generate the annot files.
> These are then sampled into the cortical ribbon to extend the aseg so that
> every voxel in the cortex is given a label from the corresponding annot
> file (aparc+aseg.mgz from aparc.annot and aparc.a2009s+aseg.mgz from
> aparc.a2009s.annot)
>
> cheers
> Bruce
>
>
> On
> Tue, 8 Jan 2019, Yerong Li wrote:
>
>>External Email - Use Caution
>>
>> Dear Freesurfer experts:
>>
>> I am on ROI analysis tutorial:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0
>>
>> And I am trying to understand the relationship between:
>>
>>/label/?h.aparc.annot and /mri/aparc+aseg.mgz
>>/label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz
>>
>> I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany
>> atlas" and its labels have 35 different labels (except unknown 0),
>> while in several cases you mentioned that "/mri/aparc+aseg.mgz"
>> corresponds to "Desikan-Killiany atlas", which I DO NOT understand.
>>"/mri/aparc+aseg.mgz" to me are subcortical segmentations while
>> "/label/?h.aparc.annot" are cortical(surface) parcellations.
>> "Desikan-Killiany atlas" should mean "cortical (surface)
>> parcellations". That's why I do not understand why
>> "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"?
>>
>> Could anyone help me understand this?
>>
>> Yerong
>>
>>
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>>
>>
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[Freesurfer] Programs samples two surface parcellation into volumetric segmentation
External Email - Use Caution Dear Freesurfer experts: In notice "mris_sample_parc" samples a volumetric parcellation onto a surface, I am trying to find a program that samples "annot" files to volumetric parcellations. I need to know the connection between labels in [lh.aparc.annot, rh.aparc.annot] and labels in [aparc+aseg.mgz]. I am expecting a program with two inputs [lh.aparc.annot, rh.aparc.annot] and output [aparc+aseg.mgz] ** Basically I have fibers from tracking algorithms and I am reconstructing connectivity matrices on the surface parcellation, that's why I need the subcortical segmentation file aparc+aseg.mgz. Yerong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
