I think you SUBJECTS_DIR might be set incorrectly, /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I suspect the value should be: /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ or possibly something else: ${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with Testing.label hth d On 9/27/16 11:58 AM, Crawford, Anna wrote: > Th output is below: > > aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label > rh.BA4p.label > aparc.annot.ctab lh.BA45.thresh.label > rh.aparc.a2009s.annot rh.BA4p.thresh.label > aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot > rh.BA6.label > BA.ctab lh.BA4a.thresh.label > rh.aparc.DKTatlas40.annot rh.BA6.thresh.label > BA.thresh.ctab lh.BA4p.label rh.BA1.label > rh.BA.annot > lh.aparc.a2009s.annot lh.BA4p.thresh.label rh.BA1.thresh.label > rh.BA.thresh.annot > lh.aparc.annot lh.BA6.label rh.BA2.label > rh.cortex.label > lh.aparc.DKTatlas40.annot lh.BA6.thresh.label rh.BA2.thresh.label > rh.entorhinal_exvivo.label > lh.BA1.label lh.BA.annot rh.BA3a.label > rh.MT.label > lh.BA1.thresh.label lh.BA.thresh.annot rh.BA3a.thresh.label > rh.MT.thresh.label > lh.BA2.label lh.cortex.label rh.BA3b.label > rh.perirhinal.label > lh.BA2.thresh.label lh.entorhinal_exvivo.label rh.BA3b.thresh.label > rh.V1.label > lh.BA3a.label lh.MT.label rh.BA44.label > rh.V1.thresh.label > lh.BA3a.thresh.label lh.MT.thresh.label rh.BA44.thresh.label > rh.V2.label > lh.BA3b.label lh.perirhinal.label rh.BA45.label > rh.V2.thresh.label > lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label > Testing1.label > lh.BA44.label lh.V1.thresh.label rh.BA4a.label > Testing.label > lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label > > Thanks, > Anna > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw > [dgwake...@gmail.com] > Sent: Tuesday, September 27, 2016 11:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > what is the output of "ls"? > > > On 9/27/16 11:50 AM, Crawford, Anna wrote: >> Thank you. That worked for changing the default directory. When I run >> mri_label2label, I am still getting the same error that there is no such >> file or directory for the label. >> >> Anna >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw >> [dgwake...@gmail.com] >> Sent: Tuesday, September 27, 2016 11:36 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> Anna, if you are using bash the command is: >> >> export SUBJECTS_DIR=<path> >> >> >> On 9/27/16 11:31 AM, Crawford, Anna wrote: >>> I also tried doing setenv SUBJECTS_DIR <path> but that did not work either. >>> >>> bash: setenv: command not found >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: Crawford, Anna >>> Sent: Tuesday, September 27, 2016 11:12 AM >>> To: Freesurfer support list >>> Subject: RE: [Freesurfer] Co-registering different source data >>> >>> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR >>> /tools/freesurfer/subjects) which is not where my data is located. >>> >>> Thanks, >>> Anna >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Tuesday, September 27, 2016 10:50 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Co-registering different source data >>> >>> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that >>> is already set properly, then do not use the --sd. >>> >>> >>> On 9/27/16 9:38 AM, Crawford, Anna wrote: >>>> 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. 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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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