Hi Anna freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview
cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > Hi, > > i created a test ROI which saves as a label. Every time I try to load it as a > label on the surface (inflated), it crashed FreeView. I'm not sure why it > won't load there. I noticed this happens with some other ore-made labels as > well. What could be the cause of this? > > I also tried doing mri_label2vol (to then do vol2surf), but I am getting an > errorL option unknown. I did the following: > > mri_label2vol \ --label Testing.label \ --temp ../mri/brainmask.mgz > > among other similar variations. Am I just inputting it wrong or am I just > missing information? > > Thank you, > Anna > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 26, 2016 4:23 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > scuba is very old and deprecated. Try using freeview instead > > cheers > Bruce > On Mon, 26 Sep > 2016, Crawford, Anna wrote: > >> To create the volume ROI, I found something that said to use: >> >> scuba -v $filename >> >> to then make a new ROI. >> >> I got en error that I could not open scuba. Is this the correct way to go >> about this, or is there some other means that I should be doing not 'scuba'? >> >> Thank you, >> Anna >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, September 26, 2016 1:52 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> yes, create a volume ROI and you can map it onto the surface using >> mri_vol2surf >> >> cheers >> Bruce >> On Mon, 26 Sep 2016, Crawford, Anna wrote: >> >>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new >>> to this and am just trying to figure out how to get the basic process >>> first.) Eventually, I will want it related to another signal such as the >>> EEG from an epilepsy subject for example. In that case, it would be the >>> active region that I want to capture and then map it to the surface. First, >>> I want to be sure that I can get an ROI that I can then project to the >>> surface (which I assume would be something like mri_vol2surf) if that makes >>> sense. So i first need to be able to create the volume or label. >>> >>> Thank you, >>> Anna >>> ________________________________________ >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 26, 2016 1:16 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> can you explain what the ROI is supposed to represent? If you can create >>> it in the volume, you can use mri_vol2surf to map it onto the surface. >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Sep 2016, Crawford, Anna wrote: >>> >>>> Hi, >>>> >>>> I am having trouble figuring out how to create my own ROI. I can visualize >>>> the anatomical ROI created automatically. How do I create a new ROI? >>>> >>>> Thanks, >>>> Anna >>>> ________________________________________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...@nmr.mgh.harvard.edu] >>>> Sent: Monday, September 26, 2016 10:44 AM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Co-registering different source data >>>> >>>> Hi Anna >>>> >>>> I'm not exactly sure what you mean, but if you register EEG electrodes to >>>> the white or pial surface, then you can visualize them on the inflated >>>> surface trivially. That is, you can create your ROI on any surface of the >>>> same hemisphere/subject and visualize it on any other >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 26 Sep 2016, Crawford, Anna >>>> wrote: >>>> >>>>> Hello, >>>>> >>>>> I am trying to create a new surface area on the inflated brain given by >>>>> freesurfer >>>>> using recon-all. I make to create my own ROI that is co-registered onto >>>>> this surfer. >>>>> Ultimately, I want to be able to take information from a different data >>>>> source such as >>>>> EEG and have it co-registered onto the inflated surface. How do I go >>>>> about creating >>>>> this new ROI surface? >>>>> >>>>> Thanks, >>>>> Anna >>>>> >>>>> =================================== >>>>> >>>>> Please consider the environment before printing this e-mail >>>>> >>>>> Cleveland Clinic is ranked as one of the top hospitals in America by >>>>> U.S.News & World >>>>> Report (2015). 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If >>> you have received this communication in error, please contact the sender >>> immediately and destroy the material in its entirety, whether electronic or >>> hard copy. >>> >>> Thank you. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World Report (2015). >> Visit us online at http://www.clevelandclinic.org for a complete listing of >> our services, staff and locations. >> >> >> Confidentiality Note: This message is intended for use only by the >> individual or entity to which it is addressed and may contain information >> that is privileged, confidential, and exempt from disclosure under >> applicable law. 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If >> you have received this communication in error, please contact the sender >> immediately and destroy the material in its entirety, whether electronic or >> hard copy. >> >> Thank you. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News > & World Report (2015). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the > individual or entity to which it is addressed and may contain information > that is privileged, confidential, and exempt from disclosure under applicable > law. 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