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 1. 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