Try giving it the full path to the label, ie, --srclabel /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote: > Hi, > > Below is the command I entered with the output containing the error. I also > tried different variations on the path for the directory, but this is the one > I thought it should be. > > Thanks, > Anna > > mri_label2label --srcsubject segfs --srclabel Testing1.label --trgsubject > segfs --trglabel Testing1N.label --regmethod volume > > srclabel = Testing1.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/ > FREESURFER_HOME /tools/freesurfer > Loading source label. > No such file or directory > mri_label2label: could not open label file Testing1.label > No such file or directory > ERROR reading Testing1.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: Wednesday, September 28, 2016 3:11 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Co-registering different source data > > Hi Anna > > sorry, I've lost track of where this is at. Can you send us the full > screen output of the command you tried to run and the error it gives? > > thanks > Bruce > On > Tue, 27 Sep 2016, Crawford, Anna wrote: > >> I have tried multiple variations for my subject directory. I have had it end >> at study11074, S2sdt, segfs, and label. I suspected it should either be >> S2sdt or segfs. I get the same error in all cases still. When using a >> differnt function with the subject directory path, I had ended at S2sdt, the >> subject was segfs, and then the file I wanted to use. I thought it would be >> the same in the case in that regard, but it doesn't seem to be working that >> way. >> >> Thank you, >> 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 12:04 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Co-registering different source data >> >> 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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