Hi Bruce, I believe that we used the command recon-all to create cluster1_roi.mgz. When opened in freeview along with colin, it appears to be in alignment. I'm not clear on where our cluster1_roi.dat file originated from though - I'll look into that. ________________________________________ 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, July 23, 2014 1:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label
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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@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 >>> 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 >>> >>> ____________________________________________________________________________ >>> 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 >>> >>> >> >> _______________________________________________ >> 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 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
