[Freesurfer] mri_convert --out_orientation with inhomogeneous volumes
Dear FS Listers, mri_convert isn't giving me quite what I expected when I use it to reorient an inhomogeneous volume. I apologize in advance if it is my misunderstanding or something that has been covered before. These orientation issues make my head spin (as they do the subject data ;-). Consider the following example: % mri_info volume.mgz : dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 : Orientation : PIL Primary Slice Direction: sagittal : I take this volume and reorient it with mri_convert to LIA orientation. % mri_convert --out_orientation LIA volume.mgz volume_LIA.mgz But what it gives me back is unexpected. % mri_info volume_LIA.mgh : dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 : Orientation : LIA Primary Slice Direction: coronal I was first surprised first that mri_convert was resorting to trilinear interpolation. It seems like this kind of transformation could be done with 100% fidelity using nearest neighbor. But the bigger concern is I would have also expected the output dimensions to be 128x256x256 with the voxel sizes 1.33, 1.00, 1.00. It seems like if you reorient a non cubic volume with mri_convert, it arbitrarily cuts some of the data out from the posterior and anterior. tkmedit display seems to confirm this. To put it another way, I would expect: mri_convert --out_orientation PIL volume_LIA.mgz volume_PIL.mgz to generate at volume_PIL.mgz file that was voxel identical to the original volume.mgz. Thanks for your time. Ray ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] new Intel Mac freesurfer distribution
This was (still is) great news! Is the 3.0.4 stable release a Mac OS X Universal Binary? Thank you, Ray @ now using 2006.10.30 Intel dev release On Oct 6, 2006, at 7:27 PM, Nick Schmansky wrote: Intel Mac owners, This distribution is from our 'dev' (development) code base, so it is slightly different from the normal publicly distributed 'stable' release. A stable build release of this Intel Mac distribution (with associated install GUI) will coincide with the next stable build release (next month, hopefully). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Intel Mac
Four months. Time to check in. Any developments on this front? See you in four months at Christmas. Hopefully Santa has a Mac Pro in his sleigh for Bruce. :-) Ray On Apr 23, 2006, at 10:52 PM, Ray Fix wrote: Hello, Any plans for a Mac OS X Tiger Intel release? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Intel Mac
Hello, Any plans for a Mac OS X Tiger Intel release? Ray ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MINC tools for Mac OS X
http://www.bic.mni.mcgill.ca/software/distribution/#osx from the message below (from Vicka earlier this year) might help you. http://www.mail-archive.com/[EMAIL PROTECTED]/ msg00936.html You probably saw Tosa's dependency list earlier today. Knowing that that will probably help you too. Ray On Oct 19, 2004, at 3:22 PM, Kushal Koolwal wrote: hi, Well I am running into some serious problems while running csurf on my Mac machine Can someone suggest a good source where I can download the MIN/MINC tools that are required for running csurf. I mean I want to use the mri_montion_correct utility as mentioned in the Freesurfer tutorial. Can someone suggest a good source for downloading the MINC tools which are required for the above purpose.? thanks, Kushal ___ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_montion_correct command not found on Mac OS X
Hi Kushal, Exhibit A: On Oct 18, 2004, at 4:32 PM, Bruce Fischl wrote: what happens when you run it on a Linux machine? You might expect a response like this from some random joker on the mailing list (such as me). Take a moment and consider the source here. Hmmm Exhibit B: On Oct 18, 2004, at 6:17 PM, Doug Greve wrote: I don't know that much about Macs. I assume that they have a /tmp that is writable? Albeit an honest, thoughtful, well meaning response, however, are some warning bells starting to ring? Here's the awful truth ... well, okay, just my personal advice to you. If you plan to do anything serious with FreeSurfer, do it on Linux or don't do it at all. You will save yourself a lot of grief.This is coming from my personal experience. I would recommend getting some ugly, headless Linux box and running it from X from your Mac. You might even be able to get away with doing a little manual editing on the Mac. It isn't ideal but considering FreeSurfer is closed source and is only very lightly tested on the Mac (if at all) it might be the best way to go. What is your most important goal: A) an accurate cortical reconstruction or B) getting FreeSurfer to work natively on the Mac? In my case, A outweighed B 1000 to 1 so there was no question. Ray Fix @ Mac/Linux ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit question
Hello Brian, I found this email fascinating because I didn't know FS had the ability to measure hippocampal volumes. Naively, I tried your suggestion, but found that the mri/aseg directory doesn't exist. How is that normally created? At this point I am using a somewhat archaic (year old ... but stable) version of FS so that might be the problem. Any hints you can give would be greatly appreciated. Best regards, Ray Fix On Sep 28, 2004, at 3:57 PM, Brian T. Quinn wrote: mri_label_volume -s subject_name -l logfile segdir labelvalue(s) will output to the logfile the volumes for each of the labelvalue(s) you list. example: mri_label_volume -s s126 -l s126hipps.log $SUBJECTS_DIR/s126/mri/aseg 17 53 will output the hippocampal volumes for subject s126. -- brian t. quinn On Tue, 28 Sep 2004, George Papadimitriou wrote: Hi all, How can I compute the volume of a label created using tkmedit? Is there a program to do this, or is it sufficient to count the number of points listed in the label file and multiply by the volume per voxel? (And if so, is the volume per voxel the voxel size for my original 40 slice axial volume, or the voxel size for the 256 slice resampled volume that tkmedit displays?) Thanks, George P. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: question about average7...
Thanks for the info Doug. My comments below. On Mar 10, 2004, at 1:19 PM, Doug Greve wrote: Ray Fix wrote: Hello List, Question 1: Where does the sample average7 come from? I searched through the manuals, googled, searched around a little but was unable to find any info. For example, is this the averaged brains of 7 male subjects in there 40s? It's a 7th order icosahedron (163842 vertices). I think the orig coordinates are supposed to be talariach coordinates averaged over some subjects (but it does not overlay very well on the talairach brain). Bruce can give you more details. Wow. Interesting. I never would have guessed. Thanks. (Aside: Let's see ... 20 * 7^2 is only 980 faces so I am not sure where all of those vertices are coming from. Probably some different definition of order 7.) Question 2: My plan is to create my own ICBM labels using average7 and then apply them via mri_label2label to two groups of subjects (which happen to be pediatric data). Does this stand any chance of working? I would be very interested if their are any other approaches you recommend. It all depends on how you're going to map the labels. What coordinate system are the ICBM labels in? I guess I have to look into this more. Any suggestion on what coordinate system should I use? Perhaps talairach. To be honest my only knowledge about labels comes from looking at the recon-all script and the one Faq-O-Matic page. I was told that the labels in FreeSurfer are sort of non-standard. The whole motivation for reporting results in terms of ICBM labels is to make the results meaningful a large audience without getting into a huge discussion about label definitions. That said, it is likely that deep consideration was given in coming up with the current default labeling scheme. Maybe someone would like to refute my assertion that they are non-standard. It is something I would like to learn more about but am not sure how to find out. Thank you very much for your comments. Ray Fix ___ Freesurfer mailing list [EMAIL PROTECTED] http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
