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help > RE: Lesion Segmentation
Mar 16, 2021 12:03 AM | Alana Batista
RE: Lesion Segmentation
Hi Alfonso,
I'm a Brazilian Phd student and I work with Stroke patients too. I'm trying to modify the TPM file with the script that you suggested on another before I read this post. I tried to use the command conn_createtpm with different images and I found the same error message:
>> conn_createtpm
Select mask file
Select structural file
Error using conn_getinfo (line 148)
File type not implemented
Error in conn_file (line 11)
[nV,str,icon,filename]=conn_getinfo(filename,doconvert);
Error in conn_createtpm (line 50)
structural=conn_file(conn_fullfile(structural)); structural=structural{1};
My Best,
Alana Batista
Originally posted by Alfonso Nieto-Castanon:
I'm a Brazilian Phd student and I work with Stroke patients too. I'm trying to modify the TPM file with the script that you suggested on another before I read this post. I tried to use the command conn_createtpm with different images and I found the same error message:
>> conn_createtpm
Select mask file
Select structural file
Error using conn_getinfo (line 148)
File type not implemented
Error in conn_file (line 11)
[nV,str,icon,filename]=conn_getinfo(filename,doconvert);
Error in conn_createtpm (line 50)
structural=conn_file(conn_fullfile(structural)); structural=structural{1};
My Best,
Alana Batista
Originally posted by Alfonso Nieto-Castanon:
Hi Matthew
In the latest release there is also a (still in development) possible way to create new TPM files informed by a lesion mask. For that you may simply use the syntax:
conn_createtpm( lesionfile, anatfile)
where 'lesionfile' is your lesion mask, and 'anatfile' is an anatomical image of the same subject and in the same space as your lesion mask. This will create a new TPM.nii file (named by default lesionTPM.nii and located in your current directory) that includes a 7th tissue class (in addition to the standard gray/white/csf/bone/soft/air categories) characterizing the lesion. You can then use this new lesionTPM.nii file during segmentation (and normalization) to make sure that the lesion is properly taken into account during the combined normalization/segmentation procedure. See "help conn_createspm" for additional details, and this is still a work in progress so if you have a chance to try this out please let me know how it goes and/or if you run into any issues
Best
Alfonso
Originally posted by Matthew Heard:
In the latest release there is also a (still in development) possible way to create new TPM files informed by a lesion mask. For that you may simply use the syntax:
conn_createtpm( lesionfile, anatfile)
where 'lesionfile' is your lesion mask, and 'anatfile' is an anatomical image of the same subject and in the same space as your lesion mask. This will create a new TPM.nii file (named by default lesionTPM.nii and located in your current directory) that includes a 7th tissue class (in addition to the standard gray/white/csf/bone/soft/air categories) characterizing the lesion. You can then use this new lesionTPM.nii file during segmentation (and normalization) to make sure that the lesion is properly taken into account during the combined normalization/segmentation procedure. See "help conn_createspm" for additional details, and this is still a work in progress so if you have a chance to try this out please let me know how it goes and/or if you run into any issues
Best
Alfonso
Originally posted by Matthew Heard:
Hi Jeff,
Any luck solving using lesion masks in CONN? I saw elsewhere on this forum that you need to modify the TPM.nii file, but I haven't found any sources on how to do so: https://www.nitrc.org/forum/message.php?msg_id=26112
So far, all I have found is a paper demonstrating that masking a lesion is crucial to analyzing functional connectivity in a brain with a lesion: https://journals.sagepub.com/doi/abs/10....
Thanks,
Matthew
Any luck solving using lesion masks in CONN? I saw elsewhere on this forum that you need to modify the TPM.nii file, but I haven't found any sources on how to do so: https://www.nitrc.org/forum/message.php?msg_id=26112
So far, all I have found is a paper demonstrating that masking a lesion is crucial to analyzing functional connectivity in a brain with a lesion: https://journals.sagepub.com/doi/abs/10....
Thanks,
Matthew
Threaded View
| Title | Author | Date |
|---|---|---|
| kjacobs | Feb 14, 2018 | |
| Marcela Takahashi | Apr 18, 2018 | |
| Jeff Browndyke | Apr 18, 2018 | |
| Matthew Heard | Jan 21, 2019 | |
| Alfonso Nieto-Castanon | Feb 19, 2020 | |
| Alana Batista | Mar 16, 2021 | |
| Jeff Browndyke | Jan 22, 2019 | |