Hi Sarah
how did you create cluster1_roi.mgz? Is it in register with colin? Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote:
Hi Bruce,
To create the .mgh, we used the following command: mri_vol2surf --src cluster1_roi.mgz --srcreg cluster1_roi.dat --hemi rh --o ./test-rh.mgh --out_type mgh --float2int tkregister
I can view both the .nii and the .mgz in Freeview but the /test-rh.mgh does not appear to have any nonzero vertices. Any thoughts on why this might be? ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 12:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label
Hi Sarah
how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume?
Bruce
p.s. can you remind me where you got the FS-processed colin data?
On Wed, 23 Jul 2014, Weiss, Sarah wrote:
Hi Bruce,
Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) --> this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations
When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is "test-rh.mgh," the resultant value is ** 0.000000 **.
Do I need to create a "test-rh.dat" file? How would I go about doing that? Should my template brain colin have a curvature file?
Again, thank you for any inputs or suggestions!
-- Sarah ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label
Hi Sarah
Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok?
cheers Bruce
On Wed, 23 Jul 2014, Weiss, Sarah wrote:
Hi all, We are still struggling with this issue - any ideas? Here is some more information:
- The surface that we are trying to label is the subject colin, as found
here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in).
- We first tried to create a surface to overlay from our .nii file (which
does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface!
- We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id
- In Freeview with our .nii file loaded, we verified that our volume of
interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File > Load label value file > cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389
We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space?
Thank you!
-- Sarah Weiss
From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label
Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain.
Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 9389 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label...
Why does it say that 0 nonzero vertices have been found, yet it selects 9389 vertices? Is there an additional option that we should be utilizing? Is a label the correct way to create what we are looking for, or would an overlay be more appropriate? If the latter is the case, should we be using mri_vol2surf?
Thank you in advance for your assistance!
Best,
Sarah Weiss and Robert Kim
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