Do you mind sharing how did you end up calling xtract for HCP data? Any thoughts on the images, do they look reasonable?
On Tue, 23 Apr 2024 20:50:10 +0000, Glasser, Matt <[log in to unmask]> wrote:
>I see, this seems like a different function than we ran.
>
>Matt.
>
>On 4/23/24, 2:12 PM, "FSL - FMRIB's Software Library on behalf of Estephan J. Moana-Filho" <[log in to unmask] <mailto:[log in to unmask]> on behalf of [log in to unmask] <mailto:[log in to unmask]>> wrote:
>
>
>In case it helps, I ran xtract as implemented in the QuNex container: https://qunex.readthedocs.io/en/latest/api/gmri/dwi_xtract.html <https://qunex.readthedocs.io/en/latest/api/gmri/dwi_xtract.html>
>
>
>I attached the log file for an example participant (10001, same as some of the pictures I shared). From the xtract output, I then ran xtract_blueprint.
>
>
>On Tue, 23 Apr 2024 19:57:30 +0100, Estephan J. Moana-Filho <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
>
>>Hi Matt, xtract ran fine on my dataset and the xtract_qc output seemed reasonable. It is the xtract_blueprint command for the connectivity blueprint that I'm curious about. I tried to attached some example images here in a previous message, but for some reason the message was never posted (I wonder if the mailing list places restrictions on attachments?). I reduced the picture file sizes, let's see if it goes now. Thanks.
>>
>>Estephan
>>
>>
>>On Tue, 23 Apr 2024 18:22:05 +0000, Glasser, Matt <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>>>Hi Estephan,
>>>
>>>We have successfully run xtract on HCP-YA data after some trial and error.
>>>
>>>I don't believe xtract is cortical surface aware, but perhaps you can post some images of what you are seeing.
>>>
>>>Matt.
>>>
>>>On 4/23/24, 1:03 PM, "FSL - FMRIB's Software Library on behalf of Estephan J. Moana-Filho" <[log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>> on behalf of [log in to unmask] <mailto:[log in to unmask]> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>>>
>>>
>>>
>>>Hello, I ran xtract_blueprint on my HCP-like DWI data, which was pre-processed using the HCP pipelines. I would like to check with you experts if the output images I got are reasonable. This is the command used for a given individual:
>>>
>>>
>>>xtract_blueprint -bpx /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/T1w/Diffusion.bedpostX -xtract /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/T1w/xtract -out /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/T1w/xtract/blueprint_wm-only -seeds /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/fsaverage_LR32k/10001.L.white.32k_fs_LR.surf.gii,/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/fsaverage_LR32k/10001.R.white.32k_fs_LR.surf.gii -target /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/T1w/xtract/blueprint_tempfiles/wm-only.nii.gz -warps /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/T1w_restore_brain.nii.gz /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/xfms/acpc_dc2standard.nii.gz /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/xfms/standard2acpc_dc.nii.gz -rois /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/fsaverage_LR32k/10001.L.atlasroi.32k_fs_LR.shape.gii,/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/MNINonLinear/fsaverage_LR32k/10001.R.atlasroi.32k_fs_LR.shape.gii -subseed /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/hcp/10001/T1w/xtract/blueprint_tempfiles/subseed.txt -gpu -stage 0 -thr 0.001 -nsamples 1000 -res 1.5
>>>
>>>
>>>The output BP.LR.dscalar.nii for some of the tracts do not have data in the whole cortical surface. They also seem to have somewhat of a pattern, where the output is mostly located in sulci, and less in gyri (specially dorsal).
>>>
>>>
>>>So my questions are:
>>>1. Does the xtract_blueprint command look reasonable for HCP-like pre-processed data?
>>>2. What are your thoughts on the output images, is this what is expect at the individual tract level?
>>>
>>>
>>>Thank you.
>>>
>>>
>>>Estephan
>>>
>>>
>>>########################################################################
>>>
>>>
>>>To unsubscribe from the FSL list, click the following link:
>>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1;>
>>>
>>>
>>>This message was issued to members of http://www.jiscmail.ac.uk/FSL <http://www.jiscmail.ac.uk/FSL> <http://www.jiscmail.ac.uk/FSL> <http://www.jiscmail.ac.uk/FSL;>, a mailing list hosted by http://www.jiscmail.ac.uk/ <http://www.jiscmail.ac.uk/> <http://www.jiscmail.ac.uk/> <http://www.jiscmail.ac.uk/;>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/> <https://www.jiscmail.ac.uk/policyandsecurity/> <https://www.jiscmail.ac.uk/policyandsecurity/;>
>>>
>>>
>>>
>>>
>>>________________________________
>>>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.
>>>
>>>########################################################################
>>>
>>>To unsubscribe from the FSL list, click the following link:
>>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1>
>>>
>>>This message was issued to members of http://www.jiscmail.ac.uk/FSL <http://www.jiscmail.ac.uk/FSL>, a mailing list hosted by http://www.jiscmail.ac.uk/ <http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
>>
>>
>>########################################################################
>>
>>To unsubscribe from the FSL list, click the following link:
>>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1>
>>
>>This message was issued to members of http://www.jiscmail.ac.uk/FSL <http://www.jiscmail.ac.uk/FSL>, a mailing list hosted by http://www.jiscmail.ac.uk/ <http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
>>
>
>
>
>
>########################################################################
>
>
>To unsubscribe from the FSL list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1>
>
>
>This message was issued to members of http://www.jiscmail.ac.uk/FSL <http://www.jiscmail.ac.uk/FSL>, a mailing list hosted by http://www.jiscmail.ac.uk/ <http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
>
>
>
>
>________________________________
>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.
>
>########################################################################
>
>To unsubscribe from the FSL list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1
>
>This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1
This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
|