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Dear FreeSurfer Developers,
Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8...).
On the other hand, unfortunately, it seems that it only works in 3d volume space.
So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag.
Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form?
Thank you in advance.
Kind Regards, Andy (Junghyun) Kim
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Hi Andy The zigzag comes because the lines have to connect vertices on the surface. How big is your rectangle? If it is pretty big I would think the zigzags would be relatively small (although still high-frequency since the vertices are about 1mm apart). I don't think we have anything that will do exactly what you want, but coding something up to find every vertex inside a rectangle should be pretty easy in matlab or python
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Friday, July 14, 2023 8:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?
External Email - Use Caution Dear FreeSurfer Developers,
Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1fXlyaExTk7SyGjd66N0GIhTs9XnixOU0mVN4qCljTWmf84...https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8qAugBQR0S6zkInLYQn1Xl3TOY0oJFkbI6RPoALUmxV8oGNWxHym5WLqi_7QJGx6lX_2lR2STOnJi8s5vxdZ04_fp6b35pehxBr4-l3lWS9mctgTSjBy8AoiErcgueL8xMXgwARppZnFQsp5XATWNDB0WoToTsJF83bHPyUNGu6Y5lPXBkaByhwQCqmvt868YGR7krXkrVJxtOzaK6CXTOosaqrURervPHT_5_uQcCLb2pTXaSosaJebFrwRElEgl4lxY-KXxNejDq39JdB4yHXidLiBk2g2KtN7BJOhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FRoiEdit).
On the other hand, unfortunately, it seems that it only works in 3d volume space.
So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag.
Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form?
Thank you in advance.
Kind Regards, Andy (Junghyun) Kim
External Email - Use Caution
I haven’t seen anyone answer this on the list, but I hope someone replied off-list.
If this a human subject, you might be able to convert the freesurfer output to something Connectome Workbench can read:
https://secure-web.cisco.com/17wlnsQY5z19UrxrrKl-L3S8ST1x7RPRyaM-ySwrNBbtKgf...
Then you can get your hands on a 32k_fs_LR flat map and draw on that. You can then view the borders on midthickness, inflated, or flat as desired.
Don’t know about the zig zag thing.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Andy Kim andyjh.kim@mail.utoronto.ca Date: Friday, July 14, 2023 at 7:45 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Can I use Freeview (tksurferfv) Tools on surface? * External Email - Caution *
External Email - Use Caution Dear FreeSurfer Developers,
Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CzOEVJLskuT1eBHdHWkZm9Uv9RdwguBc8D3xEjfGkDT12y...https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8qAugBQR0S6zkInLYQn1Xl3TOY0oJFkbI6RPoALUmxV8oGNWxHym5WLqi_7QJGx6lX_2lR2STOnJi8s5vxdZ04_fp6b35pehxBr4-l3lWS9mctgTSjBy8AoiErcgueL8xMXgwARppZnFQsp5XATWNDB0WoToTsJF83bHPyUNGu6Y5lPXBkaByhwQCqmvt868YGR7krXkrVJxtOzaK6CXTOosaqrURervPHT_5_uQcCLb2pTXaSosaJebFrwRElEgl4lxY-KXxNejDq39JdB4yHXidLiBk2g2KtN7BJOhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeviewGuide%2FFreeviewTools%2FRoiEdit).
On the other hand, unfortunately, it seems that it only works in 3d volume space.
So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag.
Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form?
Thank you in advance.
Kind Regards, Andy (Junghyun) Kim
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freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce R.,PHD