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
>>>>>>>>>
>>>>>>>>> ===================================
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