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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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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