Hi, I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?
Thank you, Anna mri_label2label --sd /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel Testing1N.label --regmethod volume srclabel = Testing.label srcsubject = segfs trgsubject = segfs trglabel = Testing1N.label regmethod = volume usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label FREESURFER_HOME /tools/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file Testing.label No such file or directory ERROR reading Testing.label ________________________________________ 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 6:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Co-registering different source data 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). 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. If the reader of this message is not the intended >>>>> recipient or the >>>>> employee or agent responsible for delivering the message to the intended >>>>> recipient, you >>>>> are hereby notified that any dissemination, distribution or copying of >>>>> this >>>>> communication is strictly prohibited. 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 >>>> >>>> >>>> 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. >>>> >>>> >>>> =================================== >>>> >>>> >>>> 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. If the reader of this message is not the intended >>>> recipient or the employee or agent responsible for delivering the message >>>> to the intended recipient, you are hereby notified that any dissemination, >>>> distribution or copying of this communication is strictly prohibited. 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. If the reader of this message is not the intended >>> recipient or the employee or agent responsible for delivering the message >>> to the intended recipient, you are hereby notified that any dissemination, >>> distribution or copying of this communication is strictly prohibited. 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. If the reader of this message is not the intended recipient >> or the employee or agent responsible for delivering the message to the >> intended recipient, you are hereby notified that any dissemination, >> distribution or copying of this communication is strictly prohibited. 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. If the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the intended > recipient, you are hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. 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. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. 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
