Re: [Freesurfer] tksurfer curvature and overlay displays
At 11/24/2014 08:23 AM, Bruce Fischl wrote: Hi Graham have you tried freeview? We stopped development on the tktools some time ago. cheers Bruce Hi Bruce, thanks for replying. Yes, I did proceed to try the same task in Freeview (which in general has a nicer UI, to be sure). Some notes: Test case: For subject bert, display principal curvature k1 (of smoothwm) on smoothwm and on inflated. Using Freeview latest version, in Linux Mint 15. Freeview Problems/Bugs --- 1. The Threshold frequency histogram widget with color adjustment handles is a great idea, but has several problems. a. Horizontal range of the freq hist defaults to entire range of the variable, which, for k1, is one to two orders of magnitude larger than the range of the bulk of the data. Consequence: the bulk of the data appears compressed to a tiny range near zero, in a tiny number of bins, and it's impossible to set the adjustment handles. This mechanism needs to accept manual upper and lower limits (and options to clip outliers to that value, or exclude them). b. The Use percentile checkbox doesn't seem to do anything that I could discover. c. The mouse hit detection for selecting and dragging the color adjustment handles often doesn't work. This is some combination of: -- The target area of the handles is too small. -- Clicking the handle but missing instead moves some other handle to the clicked location -- Sometimes the hit detection seems to think you're pressing/clicking on the mirror-image side of the graph. Press at +10, and it's like you pressed at -10. 2. It would be great to be able to clone (or save/load) display settings associated with one surface onto another. This way, time spent configuring the display of a particular variable on, say, smoothwm, would not have to be redone (inevitably imperfectly) to display the same variable on another surface like inflated, which is a frequent need. mris_convert - 3. crv-text, text-crv. I didn't find a tool that would convert between crv and text format and back, to make it easy to use some other tool to clip k1 to tractable limits. Maybe mris_convert does this, but if so, the help for that program could use some revision: --- Usage: mris_convert [options] input file output file ... -c scalar file input is scalar curv overlay file (must still specify surface) --- a. 'curv' perhaps also includes 'crv'? b. Why is 'surface' needed? The curv/crv files contain everything they need for conversion. Requiring surface makes it seem like the conversion is going to do something more elaborate than just convert binary -- text. c. And does 'surface' mean just an argument like 'orig' or 'pial', or the name of a surface file? Perhaps it just means that mris_convert still looks for an input file argument, but doesn't use it? Anyhow, I didn't trust that this was going to do what I intended. --- I DID end up getting the display I wanted: I inspected a k1.crv file in a hex editor, discovered it was the same as old new .curv format, and wrote some python code to read/write/filter such a file. With this I could produce a clipped version of k1, which did work tractably in Freeview and produced a nice display. -- Graham ___ 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] tksurfer curvature and overlay displays
Hi all, I'm having some issues (some possibly mine, some possibly tksurfer's) getting tksurfer (5.3c6) to display curvature the way I think it should be able to. I am using the bert sample data. The Curvature display - If I use the Show Curvature button in the UI control panel, I get the familiar gyrus=green; sulcus=red pattern applied to the displayed brain. The Configure Curvature Display is a bit of a shambles, and I think should be fixed. First, it is virtually impossible to set midpoint using the slider, because the values it pushes to the adjacent textbox are way too coarse. Typing values into the midpoint textbox works, in that it affects the balance of red and green in the display. However the textbox does not affect the position of the slider, suggesting that it actually does not work. That said, there's no actual adjustment of the threshold size. Indeed, it's not clear that there actually IS a threshold -- perhaps there isn't. Maybe threshold midpoint just sets the midpoint of the color range? And then there's a a textbox labeled threshold slope. I'm pretty sure that's nonsensical phrase. What this box appears to do is set the ratio of color to curvature value. Ie: Color intensity. Bottom line -- this dialog only partially fits the purpose at hand, and is so confusingly wording that ones attempts to use it are pretty much random. It may even be that some UI elements or functionality that was once there has gone missing accidentally? Finally, I wanted a colorbar for the curvature display, and so far as I can tell there isn't one. I can turn on a colorbar, but it's the one for overlays. Using a Curvature variable as an overlay I next tried to read in the k1.crv variable as an overlay. This sort of works, but gives a very mottled display (except using heat map color scheme), I think because even in definite sulcus and gyrus regions, the curvature values straddle the border of the grey range of color, and I'm not sure how to adjust it sensibly. -- I couldn't figure out how to set the overall color range, that is to say the extremes of the colorbar. These seem stubbornly stuck at 5.0 and -5.0. In particular, the Theshhold Max setting doesn't seem to affect the extremes of the color range. -- I couldn't figure out how to eliminate the large grey range in the middle of the color range. I noted that the Threshhold Min setting can be used to make the grey range larger, but setting Min below 1.5 (for example, zero) does not eliminate the grey between 0 and +/-1.5. Anybody have any helpful clues on these items! Thanks! -- Graham ___ 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] CVS crashing consistently
Hi MGH folks, I am attempting to download the source via CVS as described here: http://freesurfer.net/fswiki/ReadOnlyCVS using: cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r release_5_3_0 dev (ie: 5.3.0 source) The CVS process is consistently stopping about 760 files into the process, with the final lines of output being: cvs checkout: Updating dev/distribution/trctrain U dev/distribution/trctrain/Makefile.am Terminated with fatal signal 9 After the first attempt got stuck here, I attempted to run the checkout command again. CVS quickly displays a bunch of Updating x where x is all the directories already downloaded, then gets to trctrain and stops indefinitely. (I then killed it using Ctl-C) I then created a new local directory and restarted from scratch. The checkout proceeded apace, and then got stuck at the same place (trctrain), with same failure message. So... I'm thinking it might be something at your end, maybe disk problems in whatever files come next after the last one above? FWIW, I'm using cvs as installed with Mint 15, which is 1.12.13-MirDebian-9 (client/server) -- Graham ___ 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] CUDA install; libcudart; 64-bit detection
Hi all, probably mostly Bruce and co., I've just got a new linux box set up and am able to run all graphical tools and recon-all OK. Linux Mint 15 x64 RC (based on Ubuntu 13) Intel i5 Ivy Bridge nVidia GTX 650 Ti nVidia drivers: Selected from System Device Drivers; nvidia-313-updates; automatically installed. Freesurfer 5.3 Centos 6 version Now I'm hoping to get CUDA working. The proximate problem is that when I run Freesurfer's cudadetect I get: error while loading shared libraries: libcudart.so.5: cannot open shared object file: No such file or directory Indeed, searching the file system, there appears to be no libcudart.* anywhere. But there do appear to be CUDA components installed with the installation of the nvidia video driver: /usr/lib/nvidia-313-updates/libcuda.so 10.4 MB (plus some version-named links to same) So, my current model is that nvidia has installed what it considers to be the necessary components for an application to use to operate the CUDA hardware. Googling around, there seem to be some mentions that libcudart.so.* is something that would be supplied with a particular application (in this case Freesurfer). I'm not sure I believe that, but... The only other alternative I see is to download the nvidia CUDA developer kit and install that. However I'm very loath to do that because it replaces the video driver along with installing a lot of other unneeded apparatus. I have no idea the extent to which that installation works with or against the Ubuntu/Mint installation scheme, and what would happen on next video driver update. Not to mention that the latest Ubuntu-compatible package nvidia has is for 11.10, while my Mint is based on Ubuntu 13. Any idea how to proceed? Any chance of getting libcudart.so.5 a la carte? SIDE NOTE ON 64-bit detection in cuda_setup I see that in script cuda_setup there's a section which detects 64-bit by looking for directory: /usr/lib64 However, on Mint (so I assume Ubuntu and Debian) 64-bit, there is no such directory. Instead, there are: /usr/lib /usr/lib32 Suggestions for other ways to detect 64-bit: http://stackoverflow.com/questions/246007/how-to-determine-whether-a-given-linux-is-32-bit-or-64-bit I'm pretty sure this is not pertinent to the hunt for missing libcudart.so, but seems like that needs to be fixed too for Ubuntu/Mint. Thanks, -- Graham ___ 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] Freesurfer on Ubuntu/Mint/Debian?
Hi all, My System Recommendations? post of a few days ago got some useful and interesting input on hardware and software. For Linux flavor, Nick S. commented that Centos was the OS of choice at home base. My question for today -- is Ubuntu, Mint or Debian equally satisfactory for Freesurfer and related software, both in terms of installation, and of use? Or are awkward obstacles encountered? Thanks, Graham ___ 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] surfer.nmr.mgh.harvard.edu down?
Hi MGH-ers, From where I sit (San Diego), http://surfer.nmr.mgh.harvard.edu/ seems to have been non-responsive at least since about 4 pm west-coast time. It's now 4:40 pm. http://nmr.mgh.harvard.edu is working fine. Perhaps you are already on top of this, but in case not... Thanks, -- Graham ___ 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] System recommendations for Freesurfer
Hi all, I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools. I have read the generic recommendations here: http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirementsclient=firefox-ahl=engl=usstrip=1 Feel free to point me to existing email threads if I've missed the place where this was definitively covered! I'd like any more detailed input such as: CPU: Intel vs AMD, and the extent to which more cores increase performance. Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code? Hard drive: Does SSD make much difference while running recon-all? Linux distro: Which are favored for use with Freesurfer, FSL, etc? Thanks! -- Graham ___ 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.
Re: [Freesurfer] Content of .tif files
Hi Anderson, This might be helpful (beware datedness though). https://surfer.nmr.mgh.harvard.edu/fswiki/TemplateTifImageFiles The data at the time I did that goc was evidently stored in 32-bit float format... that could lead to your wild number range if you interpret it as int-32. -- Graham At 3/21/2011 12:44 PM, Anderson Winkler wrote: Means and variances are large too, around 1,000,000,000 for all 3 sets. I'm using imread in Matlab and I don't seem to find options to set endianess. The numbers apparently get less badly behaved (e.g. mean ~21,000 and var ~15,000) if I convert to PNG with ImageMagick, but I'm unfamiliar with these ranges anyway. The scaling, even in PNG, doesn't seem linear, but logarithmic. Regardless..., knowing what is in each frame already solves what is needed... Thanks! Anderson On 03/21/2011 03:11 PM, Bruce Fischl wrote: are they? I thought they were just stored as straight variances. Are the means large too? Make sure there are no byte-swapping issues On Mon, 21 Mar 2011, Anderson Winkler wrote: Hi Bruce, Thanks! They appear to be stored as 32-bits integers and when I open I get very large numbers. How could I scale them back to the actual means/vars/dofs? I just tried to find a linear relation for the dof, but I get a non-integer result... maybe it's a log function (?) Thanks again! All the best, Anderson On 03/21/2011 02:00 PM, Bruce Fischl wrote: Hi Anderson, there are 3 sets of 3 frames each. In each set I store: Frame 1: means Frame 2: variances Frame 3: dofs (actually, there is only 1 dof for the whole map) these are stored for curv, sulc and inflated curvature. cheers Bruce On Mon, 21 Mar 2011, Anderson Winkler wrote: Hi all, The .tif files (templates) contain 9 pages each, which seem to be organized as 3+3+3. I think I understand that they are equirectangular projections of the latitude/longitude of curvature and sulcal depth, is this correct? But what exactly each of these 9 frames contain? Thanks! Anderson ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] automating tkmedit
... also if anyone might find these helpful, there's an article that may be of interested here: http://surfer.nmr.mgh.harvard.edu/fswiki/QaImageScripts This shows tcl scripts to do something substantial in tkmedit and tksurfer, and bash scripts to activate FreeSurfer and the tcl scripts. Hope that helps, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer tcl
What caption are you refering to? Graham At 3/4/2008 07:44 AM, you wrote: Hello, Is there a way to adjust the caption (at least turn it on and off) in a tcl script. I couldn't find any information on the wiki. Cheers, Dan -- ___ 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
Re: [Freesurfer] tksurfer tcl
Hmmm, well since the menus are implemented in tksurfer.tcl, it might be possible to add some tcl to that file (actually it already has code to daisy-chain to user-provided extra code on startup), to implement some means to control caption on/off by a later script. Not known by me: how the normal tksurfer mechanism to run a user script interacts with tksurfer.tcl. But it should be easy to discover. Graham At 3/4/2008 02:44 PM, Daniel Wakeman wrote: Hi, Sorry, As in ViewCaption. In the menu bar. Thanks Dan What caption are you refering to? Graham At 3/4/2008 07:44 AM, you wrote: Hello, Is there a way to adjust the caption (at least turn it on and off) in a tcl script. I couldn't find any information on the wiki. Cheers, Dan -- ___ 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
Re: [Freesurfer] RE: annotation binary files into ascii format
Hi Teddy: If you're investigating that area, you might also be interested in: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_5flabeledit Graham At 2/28/2008 05:09 PM, you wrote: Hi everyone, Thanks again for your help from my previous query. I had a question about how to convert the binary format of the annotation file to ascii format, similar to using mris_convert to surface files from binary to ascii. Is there an equivalent program that does the same thing for annotation files? Thanks very much, -Teddy Youn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] which image is the best
Hi: Your description of the problem looks to me like there's some trouble with the interpretation of the 1404 mm dimension. It seems very unlikely that you have a scan that actually covers 1404 mm, so there must be a problem here. I would advise reading the header of the scan, which might require some program to read and interpret the header for you. Perhaps the header actually contains sensible information, such as: 1404 slices at 0.2 mmm -- ~ 280 mm field of view in that direction or 304 slices (or some other sensible number) instead of 1404. Anyhow, if you see this, it would suggest that the scan is OK, but FreeSurfer is having trouble loading it. A possible strategy in that case is to load the scan into some other software, resample to a grid closer to 1 mm grid, and trim/pad to make it 256 x 256 x 256. Software which might help there is AFNI. Also MRICro (Chris Rorden) might be useful, and even my GWRawMRIView for inspecting what your dealing with. http://grahamwideman.com/gw/brain/tools/gworc/index.htm Hope that helps, Graham At 1/25/2008 11:32 AM, you wrote: Hi, I have a problem about which image is the best to run. I had ran the 1.5T data in freesurfer. Because the contrast of the 1.5T data was too bad, I use the 3T data and rerun again. When I run, it says the warning, WARNING The physical sizes are (1404.00 mm, 256.00 mm, 256.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 1404 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==== This problem confused me. What can I do? Could you tell me what image is freesurfer I can run and get the best results? (about dimension¡K. ) ___ 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
Re: [Freesurfer] Creating one's own average sphere/template
Doug and Bruce:
Bruce says:
mris_make_template creates an average sphere.reg (actually a bunch
of means and variances of different geometric features. To make a new
gcs file use mris_ca_train.
Side point -- the bunch of means and variances... that sounds more like the
template or GCS file than the average sphere.reg, which I thought was a mesh,
right?)
Doug says:
I've included hooks into make_average_subject and recon-all to make this
much easier. make_average_subject will create the template (.tif) files
from the subjects you specify, then you just run recon-all with
-surfreg-to-subject averagesubjectname.
Are these two suggestions alternates or complementary in some way? A major gap
for me is this:
Supposing we start with 10 subjects, to be used in creating a new average
sphere, tif and gcs for labels, later to be used for many more subjects. These
initial 10 subjects are processed by freesurfer, and hence have all their
surfaces, (along with ?h.sphere.reg and annot files, courtesy of the default
average sphere, tif and label gcs --- which we don't want to use ultimately.)
What then are the steps to create a *new* average sphere and tif?
My assumption has been that some program reads the 10 individuals' ?h.sphere
(not reg) files, plus their curv and sulc files, and by clever average, warp
and whatever on spherical surface, it produces an average ?h.sphere along with
corresponding average curv and sulc tif file. I'm expecting these to be done in
one step, because without a curv/sulc tif file the new average sphere is
meaningless I think.
I'm specifically *not* expecting that the process involves averaging the
individual white surfaces (possibly including talairaching), followed by
inflating the average white surface to a sphere. And because I have the
impression that this is the kind of thing that make_average_surfaces (called by
make_average_subject) does, I'm resistant to thinking that make_average_subject
is part of the answer here.
So... I'm all ready to think that mris_make_template is the program to do the
job... but I don't see anywhere in the source code where it writes out a
surface.
(FWIW I do see that mris_ca_train is used to create the GCS file -- I don't
have any questions on that part.)
And finally:
Bruce wrote:
average is a catch-all for various average files, like volume
statistics, tal atlases, etc..., fsaverage is the subject made
from averaging our 40 manually labeled subjects
...so I'm getting the impression that some of the {fshome}/average files are
not related to the fsaverage subjects (such as mni 305 files), and some perhaps
are (like lh.average.curvature.filled.buckner40.tif)... and some others... not
sure.
On this point, mainly I'm trying to understand what common sphere and tif file
are used in a normal recon-all run, and where they came from (and trying to
follow recon-all call's args into mris_register is puzzling).
Thanks,
Graham
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[Freesurfer] Creating one's own average sphere/template
Folks: I'm trying to get a complete picture of what's entailed in creating our own atlas, including our own average reference sphere, so if there's a doc on this specific subject I'd love to see it. Absent that, below are questions to fill in some gaps: 1. Normal spherical reg: mris_register's command-line params don't include all files it must read, so I'm looking for a list of all the files that it reads under the usual circumstances (ie: registration to ref sphere; registration to opposite hemi), and how it decides *which* files to read. (Amongst other discrepancies, when recon-all runs, mris_register doesn't seem to read ?h.curv, whereas various postings suggest that it does.) 2. Normal labeling with mris_ca_label: Presumably this only works if subjects are registered to the same average sphere mesh as was used to create the chosen GCS file, right? Yet mris_ca_label doesn't need to read that actual ?h.sphere.reg file because equivalent position-on-sphere info is contained in the GCS file... right? 3. Creating one's own average reference sphere: What progam(s) does one use to create the average ?h.sphere(.reg?) file (presumably from each subject's ?h.sphere file)? and average curvature file (ie: the tif file)? FWIW, it looks like mris_make_template is somehow involved here, but it's entire documentation consists of just This program will add a template into an average surface (what does that mean?), and the source code looks like it only produces the tif file containing average sulc and curv data. (From which I conclude the here, template refers to just that file.) 4. What, if any, is the relationship between .../freesurfer/average and .../freesurfer/subjects/fsaverage Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Zen of label editing in tksurfer
Folks: We notice that when we try editing labels in tksurfer (eg: draw an outline, fill with new label value), this results in tksurfer's control panel showing two labels everywhere (even where we didn't edit), with the second one saying 1 additional label (or something like that... don't have it running at the moment). Further exploration has us puzzled about deletion, saving and so on. What is the model that tksurfer is following here? If you load one label file, and then start editing, is that like tksurfer introduces another layer (ie: a second label slot for every vertex?). How do you load a label file and explicitly edit that data instead of creating new data? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Freesurfer Digest, Vol 47, Issue 2 (Visual Inspection)
Simon: If you are running a bunch of cases and then want to do basic visual inspection QA, it can be helpful to script tkmedit and tksurfer to generate screen caps at various angles and positions which you can then view rapidly. I've just posted some sample scripts to do this: https://surfer.nmr.mgh.harvard.edu/fswiki/QaImageScripts Hope that helps, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Folding Index question
Folks: We're wondering about how FS's folding index corresponds to Van Essen's calculation (J Neurosci, 1997 Sept 15). In particular, do the FI values for each region factor out the area of the region or not. When we plot them the FI values look extremely correlated to area, but that doesn't make sense for an index. Ultimately we're wanting to know how to aggregate FIs for individual parcellations into larger regions. Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit scripting: control window size?
Folks: In a tcl script for tkmedit, is there a way to control the size of the graphics window? I see functions for all sorts of other aspects of the view, but not this -- maybe I'm missing something? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] New recon-all Files vs Steps doc posted
Folks: If you need to know what recon-all and its many steps are really doing you may be interested in a doc I've just posted tabulating file create/read/write/delete for each step: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps In case you've seen my previous similar effort, this one's a considerable improvement because it's based on monitoring an actual run (bert to the rescue!), rather than on documentation. Hope it shortens a few learning curves :-). Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Scripting: Feeding arguments and variables to script?
Folks: Basic scripting questions: 1. When you launch FS from command line and provide a -tcl command to invoke a tcl script, how do you supply arguments to that script (or is that even possible)? FWIW, I tried things along the lines of: set myvar [lindex $argv 1] ... and this gives an error about no such variable. 2. Once a script is running, what variables can it look at to find out: Current subject id Path to current subject Details about currently loaded surfaces: especially right or left 3. What assumptions, if any, can a script rely on as to current directory? Thanks, Graham ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Insula: Why no label in parcellation?
Folks: We see that parcellation has insula labelled as unknown. Is this by design and if so is there a discussion of the rationale? Thanks, Graham ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aparc - voxels program?
Folks: I'm hoping that there's an aparc -- voxels program. That program might be mri_aparc2aseg, but I wanted to check first if that's the best way to go and whether there are particular options to know about and so on. Basically I want a program that inputs a parcellation, and outputs a label mri where each voxel that's fully or partially between the white and pial surface gets labelled with the parcellation label from the vertex (white or pial) that it's closest to. (A variation that would also work for our purpose would label voxels even beyond that, possibly all voxels). This seems like it's probably already been done, hence my asking. I'm thinking that *might* be what mri_aparc2aseg does... but I'm not clear what the wiki description is trying to say: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_5faparc2aseg?action=highlightvalue=aparc First, it appears from Example 1 that mri_aparc2aseg does something interesting when run with basically no specific command line arguments, so presumably using default input files. But then what is the purpose of --ribbon? Then the description talks about the automatic segmentation volume as though it's an input separate from the ?h.ribbon, yet there are no parameters related to that. And finally the --noribbon flag is mentioned as turning something off, but it's not clear what it's turning off. Bottom line: I'd appreciate some clarification as to which program does what I want, and if it's mri_aparc2aseg, then what options are appropriate to do the simple version of the task where it ignores existing aseg and ribbon. Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparc - voxels program?
Doug: Thanks for your quick reply -- but I still have some big holes in understanding, probably because I'm having a hard time digesting the mri_aparc2aseg's wiki page. For the ribbon-related parameters we seem to have the 3 choices: no ribbon param ... or ... --ribbon ...or... --noribbon The Description presumably applies to using no ribbon parameter, and describes that *both* aseg *and* the surface-derived ?h.ribbon are used. If that's the case, then what does the --ribbon arg add? It goes on to say This can be turned off with --noribbon. What can be turned off? Use of ?h.ribbon? Or relabeling of the unknown voxels to zero (ie: aparc+aseg would have them labeled as cortex). Finally, for my task where I hope to ignore aseg entirely, is my solution to fake up an aseg volume filled with cortex voxels, and use that for input? (And I'm not seeing an argument to tell mri_aparc2aseg to use a different aseg...). Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit/tksurfer fail at startup: Followup
Nick and all: Followup on the earlier thread: tkmedit/tksurfer fail at startup with X BadValue I was not able to get to the root cause of this problem. However, conducting the installation for the latest nVidia display driver resulted in a system that now does run tkmedit (and glxgears, FWIW). (I was already running a version of the nVidia driver as up-to-date as the ones you recommended.) So, not sure whether the installation actually installed anything that fixed a previous bug relative to the particular video card, or whether it replaced some software component that was damaged or missing, or whether it replaced some setting in xorg.conf that was troublesome. Anyhow, progress has now resumed. Thanks for the suggestion to try glxgears -- I had thought that other software that was clearly running OK was sufficient evidence that video was OK, but apparently not. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit/tksurfer fail at startup with X BadValue errors
Nick: Still having the same trouble as reported last week. Several more tests to report: 1. I installed 3.0.4 -- same result. 2. In addition to several other GUI apps, I ran xclock as you suggested, looks fine. 3. I ldd'ed tkmedit. To get a realistic output I first did: source tkmedit ... to run the preparatory script that sets up environment variables as would normally be seen at the point that tkmedit.bin runs. Here's the ldd output: == [EMAIL PROTECTED] ~]$ ldd /brain-bin/fs_20061125/centos4/freesurfer/bin//tkmedit.bin libtix8.1.8.4.so = /brain-bin/fs_20061125/centos4/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x00f42000) libtk8.4.so = /brain-bin/fs_20061125/centos4/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x00bf7000) libtcl8.4.so = /brain-bin/fs_20061125/centos4/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x00111000) libglut.so.3 = /usr/lib/libglut.so.3 (0x00bb4000) libSM.so.6 = /usr/X11R6/lib/libSM.so.6 (0x00b5a000) libICE.so.6 = /usr/X11R6/lib/libICE.so.6 (0x00b65000) libXmu.so.6 = /usr/X11R6/lib/libXmu.so.6 (0x0067f000) libXi.so.6 = /usr/X11R6/lib/libXi.so.6 (0x00dee000) libGLU.so.1 = /usr/X11R6/lib/libGLU.so.1 (0x004f5000) libGL.so.1 = /usr/lib/libGL.so.1 (0x0056e000) libXext.so.6 = /usr/X11R6/lib/libXext.so.6 (0x00b24000) libdl.so.2 = /lib/libdl.so.2 (0x00b1e000) libX11.so.6 = /usr/X11R6/lib/libX11.so.6 (0x001aa000) libgsl.so.0 = /brain-bin/fs_20061125/centos4/freesurfer/lib/gsl/lib/libgsl.so.0 (0x00289000) libgslcblas.so.0 = /brain-bin/fs_20061125/centos4/freesurfer/lib/gsl/lib/libgslcblas.so.0 (0x00907000) libjpeg.so.62= /usr/lib/libjpeg.so.62 (0x003dd000) libtiff.so.3 = /usr/lib/libtiff.so.3 (0x03c6f000) libz.so.1= /usr/lib/libz.so.1 (0x00b34000) libm.so.6= /lib/tls/libm.so.6 (0x00af9000) libcrypt.so.1= /lib/libcrypt.so.1 (0x02f5d000) libc.so.6= /lib/tls/libc.so.6 (0x009cc000) libXxf86vm.so.1 = /usr/X11R6/lib/libXxf86vm.so.1 (0x00df8000) libXt.so.6 = /usr/X11R6/lib/libXt.so.6 (0x0062c000) libstdc++.so.6 = /usr/lib/libstdc++.so.6 (0x003fb000) libgcc_s.so.1= /lib/libgcc_s.so.1 (0x00ddf000) libGLcore.so.1 = /usr/lib/libGLcore.so.1 (0x065ea000) libnvidia-tls.so.1 = /usr/lib/tls/libnvidia-tls.so.1 (0x00ba) /lib/ld-linux.so.2 (0x009b3000) == Any ideas? Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit/tksurfer fail at startup with X BadValue errors
Nick: Thanks for the suggestions. It's looking like the problem is not specific to FS after all, but I'll recount the latest clues in case you hit this again. 1. NVidia version is 1.0-8765. 2. glxgears actually fails in same way as FS programs. Hmmm. 3. Color depth, as reported by GUI tools is supposedly millions of colors (presumably 24 bit). Anyhow, looks like I need to pursue this as a generic GL problem. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit/tksurfer fail at startup with X BadValue errors
Folks: On an installation that had been working, suddenly we're getting fatal errors on starting either tkmedit or tksurfer. These appear to be errors trying to perform X functions. Command lines and responses shown below. I am not aware of recent changes to the environment (new software installed etc) that would relate to this... but one never knows. 1. Anyone happen to know exactly what solves this? 2. Any clues as to how to troubleshoot would be helpful (eg: is there a log that these programs write into at this early of a stage in startup?) Thanks, Graham = Initialization = [EMAIL PROTECTED] ~]$ tcsh [EMAIL PROTECTED] ~]$ source /brain-bin/fs_20060528/centos4/freesurfer/SetUpFreeSurfer.csh freesurfer-Linux-centos4-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer FSFAST_HOME /brain-bin/fs_20060528/centos4/freesurfer/fsfast SUBJECTS_DIR/data/Structural/FreeSurfer_2007/segmixtest/bxbaseline FUNCTIONALS_DIR /brain-bin/fs_20060528/centos4/freesurfer/sessions MINC_BIN_DIR/brain-bin/fs_20060528/centos4/freesurfer/mni/bin MINC_LIB_DIR/brain-bin/fs_20060528/centos4/freesurfer/mni/lib PERL5LIB/brain-bin/fs_20060528/centos4/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /brain-bin/fs_20060528/centos4/freesurfer/lib/tcltktixblt/lib FSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/fsl = tkmedit: = [EMAIL PROTECTED] ~]$ which tkmedit /brain-bin/fs_20060528/centos4/freesurfer/bin//tkmedit [EMAIL PROTECTED] ~]$ tkmedit X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 78 (X_CreateColormap) Value in failed request: 0x0 Serial number of failed request: 15 Current serial number in output stream: 17 [EMAIL PROTECTED] ~]$ = tksurfer = [EMAIL PROTECTED] bxbaseline]$ tksurfer 85432 rh white surfer: current subjects dir: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: Reading header info from /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline/85432/mri/T1.mgz surfer: vertices=184105, faces=368206 surfer: single buffered window Received X error! Error code : 2 Request code : 78 Minor code : 0 Error text : 'BadValue (integer parameter out of range for operation)' Received X error! Error code : 12 Request code : 1 Minor code : 0 Error text : 'BadColor (invalid Colormap parameter)' ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit/tksurfer fail at startup with X BadValue errors
Nick: Thanks for the quick reply. Relating to the info you added, here's what I see: 1. DISPLAY is set to just :0 (ie: without the quotes, and no .0). Changing it to :0.0 -- the failures occur as before. 2. The logfiles you mention show the following: .xdebug_tkmedit: -- tkmedit started: Fri Jan 26 13:40:02 2007 tkmedit $Id: tkmedit.c,v 1.274.2.3 2006/04/15 00:13:10 nicks Exp $ $Name: stable3 $ -- .xdebug_tksurfer: empty So... nothing obvious seems to jump out here. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit/tksurfer fail at startup with X BadValue errors
Nick: At 1/26/2007 11:23 PM, Nick Schmansky wrote: Graham, Does an X app like 'xclock' work? If not, does xclock work if the Freesurfer setup script is not run? I haven't run xclock, and unfortunately (?) am no longer at work. However, -- Machine is running Centos 4.4 -- KDE works fine so far as I can tell -- I can run various GUI editors etc. -- I can run AFNI So, my main conclusion is that this is FS-specific. Later in the weekend, I'll try launching various apps from a terminal window after running FS setup script, and see if that disrupts anything. I'm also downloading FS 3.0.4 (was 3.0.3), and I'll see if that does anything for us. Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] processing steps
Claudia -- With your line of questioning, you may also might like to look at: http://grahamwideman.com/gw/brain/fs/index.htm ... particularly ... http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm Graham At 9/25/2006 10:29 AM, you wrote: Hi, I have just started to look at freesurfer and decided to run each step to try to understand what recon-all does. Well, after a bit of teething to put the data in the right orientation, we managed to start, but we have a few questions :-) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Quadrangle surface formats
Probably for Nick or Bruce? Is it the case that the quadrangle surface formats are obsolete, and only the triangle surface is currently used? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Odd brainmask.auto and brainmask data and behavior
Jenni: Thanks for your reply and explanation of the brainmask logic and rationale. As for this: Question 1: Is there a rationale for 255 values? (in the brainmask volume) I'm not sure where these are coming from in your volume - I assume you havent done any editting on this one. These subjects' data may well have been edited (not by me, hence my not knowing exactly what's what here). And I suppose it's the brainmask.mgz volume that would have been edited, and the act of editing it sets voxels to 255 perhaps? (The 255's are in the appropriate locations to add additional grey matter to the edges.) That leads me to believe that the answer to this: Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning masked brain, or mask using non-zero values to show where brain is. ... is that brainmask.mgz is used by subsequent steps as a mask in combination with some other image volume providing the actual image. In that case the actual intensities of brainmask.mgz are ignored. And I now see in the script that mri_ca_normalize does indeed use brainmask.mgz with the mask flag, so I guess I'm probably right that the actual intensities are unimportant. (And nu.mgz provides the actual image). Phew, I think I now have that straight... for this week :-) Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coordinate system clarification please
Folks: I am (still!) trying to get traction on some aspects of the current FS coordinate system(s). In the recon-all pipeline, am I right in assuming that from orig.mgz all the way through to aseg.mgz and then on to brain.mgz, wm.mgz and so on, that there's NO resampling to a new coordinate system (eg: the specific brain's data doesn't get resampled to rotate or talairach it)? Ie: if you overlay, for example, wm.mgz's data onto orig.mgz, it'll align properly? (Ie: overlay the raw voxel data, unmolested by any clever viewer transforms...) I *think* I'm right on this, but it's hard to be sure, because for example, mri_ca_normalize's docs say that it takes a gca transform file as input. But that *might* be so that mri_ca_normalize can resample some other standard file to match the specific brainmask.mgz file. scratching of head Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Odd brainmask.auto and brainmask data and behavior
Folks: I'd appreciate if someone could explain the brainmask.auto.mgz, and brainmask.mgz logic? Somewhat alarming is that in a brainmask volume, I'm seeing some full-brightness (255) values on the edge of the mask (border of brain and nothing), which are certainly not in the input volume T1.mgz volume. Question 0: Is the detailed image data in brainmask.mgz ever used, or is it simply a zero/not-zero mask? Ie: is the meaning masked brain, or mask using non-zero values to show where brain is. Question 1: Is there a rationale for 255 values? That led me to look at the brainmask.auto volume, and the bad values are not there either. The recon-all script is a bit puzzling and convoluted in this area -- Question 2: It appears that the Skull Stripping section of the script uses a -keep flag on mri_watershed. This isn't explained on the wiki doc page -- what does it do? (And why does mri_watershed get BMA and two BM's?) Question 3: In the normal case, does brainmask.auto.mgz just get copied to brainmask.mgz? If so it's a puzzle to me how these wind up different (in the cases I looked at the mgz files are not the same size). more scratching of head Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS using uncompressed (not mgz) MRI files?
Folks -- probably Nick? I'd like to be able to work with some FS sessions using uncompressed data, ie: not using mgz files. (Why? So that I can conveniently use some other tools for troubleshooting and inspection, tools that don't know how to uncompress mgz files). Questions: 1. If I just try to gunzip mgz files, some of their names collide with the directories that mksubjdirs has set up. Historically, most of these dirs used to act as containers for per-slice COR files, so they don't seem useful anymore. Can they just be deleted without consequence? 2. I'm assuming that the uncompressed files should be given the extension .mgh. Do the FS pipeline scripts and programs automatically adapt to uncompressed files? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS using uncompressed (not mgz) MRI files?
Doug and Nick: Thanks for the quick replies. Notes: Doug wrote: mri_convert orig.mgz orig.mgh Ah, good to know, and lets you rename in the same step, so avoids collision. At 9/6/2006 02:14 PM, you wrote: 1. You should keep the orig directory as that's where you store the the input data Yep, I knew about that one :-) Nick said: Yes, freesurfer recognizes the filename extension .mgh (and just doesnt do the gunzip on it internally). But Doug said: 2. I'm not sure that everything will run smoothly with mgh. I think a lot of stuff is hardcoded to work with mgz and/or COR Hmmm, so not sure what to make of that. Ideally programs would process the input based on the filename extension, and then produce same-format output. But that may not have been a priority. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_em_register args, ICV, etc
Folks: A couple of weeks ago, Bruce noted that: EM Registration with Skull is for generating ICV measures ... so I just got around to investigating where the ICV measures might be getting saved. Bottom line is I don't see what file that ICV measure is getting saved into. Details: I tried to figure out which program/script does this step, and what files it produces which might capture ICV. 1. Which commands correspond to the EM Registration with Skull step? Clue: wiki recon-all shows this step employs the noskull-lta step. Looking in recon-all script, this corresponds to the DoSkullLTA variable, and that in turn leads us to mri_em_register as the pertinent command. 2. Looking at docs for mri_em_register in the wiki shows 4 arguments, only one of which is flagged. Looking at actual help output from mri_em_register shows about 50 flagged arguments, none described. 3. The pertinent bit of script looks like this: set xopts = `fsr-getxopts mri_em_register $XOptsFile`; set cmd = (mri_em_register -skull -t transforms/talairach.lta \ $xopts nu_noneck.mgz $FREESURFER_HOME/average/$GCASkull \ transforms/talairach_with_skull.lta) 4. From all this, I don't see what output file mri_em_register might be placing the ICV into. Clues? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg, aparc regions reference table (aka data dictionary)?
Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the comments above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] The 5 mm limit on cortical thickness?
Bruce: Thanks for your reply -- actually the limit is in the thickness measurement, not the deformation. You can recreate the thickness files with mris_thickness -max $maxthick ... if you want a larger value. What's going wrong? Well we're trying to guess why the pial surface is somewhat consistently (across subjects) positioned short of the actual pial surface in certain instances, notably frontal medial temporal, and some other locations. We had wondered whether it was because of such a limit. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] The 5 mm limit on cortical thickness?
At 6/23/2006 06:57 PM, you wrote: probably not. Check the intensity of the white matter underlying the gray and see if it's significantly less than 110. If so, try putting a few control points there (make sure they aren't in partial-volumed wm) Bruce: You would recommend this, even though the white boundary looks more or less in the right place? One incongruity is that the aseg segmentation gets the grey pretty much right, but the pial surface is way inboard. (I do understand that the aseg grey is not used to find the surface, it just *looks* like it should be smarter!). And probably we shouldn't strain this discussion too far at this point... we need to take a closer look given that the 5 mm hypothesis is thrown out... Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Some FS input questions
Nick and Doug: Thanks guys for the thoughtful comments -- I need to do some further digesting. Nick: Yes I'll get a Wiki username. Both: Looks to me like I really need to understand what is the coordinate system of each input and output file in the pipeline -- this would greatly clarify what data is immediately compatible with what, or what transforms (and resampling tradeofss) are needed. And yes, after an initial conception that the subcortical seg and surface processing were completely separate, I did notice that output from the subcortical seg feeds into the preparation of volumes for the surface processes. (So thanks Doug for the further comments on that... again, still digesting!). Graham At 6/2/2006 09:51 AM, you wrote: Graham, It's tough to say just where you can begin processing with already ac-pc aligned brain extracted non-conformed input, [...] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to disable jumping tool windows? Environment variables?
Folks: Both tkmedit and tksurfer have tool windows which jump to a location below their respective main image windows whenever the image windows are moved or adjusted. This prevents the image windows from being enlarged to full screen height, because the tool windows then jump to bottom of screen, and behind the main window. Is there some way to signal these two apps not to move the tool windows? Also, if there is such a setting I'm suspecting it would be an environment variable. I looked at the Wiki, but didn't find a listing of useful environment variables -- is there one to be had? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mghWrite failure in mri_remove_neck
Folks: In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that: 1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz 2. But then appeared to perform the neck removal anyway and write the output 3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz ... and sure enough, there is no such file there. The recon-all.log for these steps is copied below. This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory. I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for? But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent writing output message suggesting success of this step (but no file to show for it). Clues? Thanks, Graham === #-- New invocation of recon-all Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $
Re: [Freesurfer] mghWrite failure in mri_remove_neck
Doug: There's over 200 gig space on that drive, and I have since test copied over 100 Meg to the mri directory (as the same user, so permissions seem OK). Questions: 1. Is mghWrite failure salient, or is this just mri_remove_neck checking for an existing file in order to delete it (ie: it's not really an error). 2. In general, does recon-all happily restart at wherever stage you tell it, and overwrite existing files, or is some special action necessary to deal with existing files? Thanks, Graham At 5/30/2006 10:10 AM, Doug Greve wrote: Can you verify that the disk was not full? doug Graham Wideman wrote: Folks: In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that: 1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz 2. But then appeared to perform the neck removal anyway and write the output 3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz ... and sure enough, there is no such file there. The recon-all.log for these steps is copied below. This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory. I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for? But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent writing output message suggesting success of this step (but no file to show for it). Clues? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mghWrite failure in mri_remove_neck
At 5/30/2006 01:41 PM, Bruce Fischl wrote: do you have gzip on your system? Yes... and just ran it to be sure. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mghWrite failure in mri_remove_neck
At 5/30/2006 01:38 PM, Doug Greve wrote: I've put a new Linux version of mri_remove_neck at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck Can you run this? It prints more info about why it's failing. doug Thanks Doug... here are the results, and it looks like Bruce's guess was in the right area :-) I ran: recon-all -autorecon2 -nogcareg -nocanorm -nocareg -nocareginv ... so as to run only the Remove Neck step, and here's what I get: #-- [EMAIL PROTECTED] Remove Neck Tue May 30 13:56:46 PDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam-type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue May 30 14:08:38 PDT 2006 Any ideas on this? I've not sure which program is issuing which error. Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mghWrite failure in mri_remove_neck
At 5/30/2006 03:25 PM, Doug Greve wrote: It was running out of memory. I've copied a new version into that ftp site. It might do a little better with the memory managment. First off -- thanks for the quick response with new versions of the program to try, and obviously the addition of the diagnostic output has really helped. Response with this version was basically the same as before... Cannot allocate memory (log excerpt below). FWIW here's more info: Linux box running FC4. Only half gig of memory, plus one gig swap space. While running these last couple of times I watched memory allocation in KInfoCenter's Memory monitor pane. With no FS script running: Physical memory: 432 Meg free Swap: 933 Meg free. With mri_remove_neck running: Physical memory: fluctuates between 5 Meg and 40 Meg free. Swap memory: Generally about 500 Meg free. So, clearly mri_remove_neck sucks up a lot of memory, and one path-of-least-resistance is a trip to Fry's for some more memory :-). Any other suggestions are welcome, of course. Graham ### #-- [EMAIL PROTECTED] Remove Neck Tue May 30 14:39:56 PDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam-type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue May 30 14:54:52 PDT 2006 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mghWrite failure in mri_remove_neck -- SOLVED
Doug and Bruce: Turns out that 2 gig of memory causes mri_remove_neck to work. (Not known whether 1 gig would do the trick.) Thanks for the crucial clues. Graham At 5/30/2006 04:44 PM, Doug Greve wrote: I don't know why the new version did not work. I free the morph before it tries to write. Maybe there was not enough contiguous space. Bruce Fischl wrote: oh, that's because it reads in the nonlinear morph which is big. I guess we need to recommend 1G/cpu from now on :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Some FS input questions
Most likely to Nick S, unless anyone else would like to chime in... I'm gearing up for some extensive use of FS... it's downloaded, installed, and initial tests run OK... so far with minimum of pain (yay team!). Now... I need to discover how to feed in data other than raw scanned files, because we want to try several alternatives to the initial processing, which we have in AFNI format, ac-pc aligned with iso-sided voxels but not 1 mm. I suspect I'll end up scouring the recon-all script, but a few hints would be helpful, mainly aimed at (a) taking advantage of processing that we have done by other methods, (b) minimizing resampling and (c) winding up with surfaces and segmentations that are most readily overlayed with our other processed data, tracings etc. 1. If we want to feed in already ac-pc aligned, brain-extracted input, at what stage of recon-all should we be looking to supply it? (I can figure out where in the directories to put the data, but not sure on the stage of processing to start at). 2. It used to be that FS's surface pipeline didn't insist on Talairaching the voxel data, and skipping that resulted in output that is true to original space. Is that still the case? 3. Does current FS proper require 256x256x256 1mm data, or can it take any shape brick and voxel size (ie: without resampling) these days? 4. If FS *does* want to work with 1mm voxels only: It used to be that though FS wanted 1mm input voxels, you could feed in some other sizes by do-it-yourself creation of the COR images, and FS was fine... is that still the case (but now with mgz format)? 4. Is it the case that the subcortical voxel-based parcellation *does* require the Talairaching step for correspondence with the probability atlas? 5. The surface and voxel-based pipelines are separate, not even sharing the white segmentation step, right? Thanks in advance, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Announcement: new stable release, v3.0
Nick: Congratulations! Graham At 3/6/2006 11:59 AM, you wrote: Freesurfer community, A new stable release, v3.0, is now available. The Release Notes page describing what's new, and a link to the download page, is here: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Video card/linux distro for 3D dual monitors: Recommendations?
Folks: Having developed high blood pressure due to the incredible time waste involved in trying to get anything other than lowest-common-denominator video running on linux... I thought I'd ask you all for recommendations that you know *do* work. So I'm looking for some combination of video card, drivers/libraries and linux distribution that can be installed and configured in time guaranteed to be less than infinite... 1. Must support dual monitors (ie: for 2560 x 1024 desktop). 2. Vid card must have some features that make 3D operations speedy. 3. Must have actual non-buggy drivers that allow FreeSurfer to drive the vid card's 3D features. 4. All should be relatively recent so that they don't preclude getting other things running due to being obsolete. Any suggestions? Thanks, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregistration?
Nate Parks wrote: Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI. AFNI coregistration program is 3dvolreg. See docs: http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html And if you are having trouble finding which AFNI program does what, you might like my all afni helps on one page: http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Distributions: which? ; Archives -- forbidden
Folks: I would like to get up-to-date on our FreeSurfer installation. Are there some notes which describe the various snapshots at: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ ? In particular, some of these downloads are much huger than others, which makes one wonder what's included in each. I also tried to see if there were some email messages covering this in the archives, but the archive seems to be broken currently: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/ ... returns Forbidden -- ie: permissions problem. Regards, Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] can left and right surfaces be flipped?
Peggy: I think mris_reverse will do the trick. But one cautionary note... I think when I investigated this there is a minor problem. The job of mris_reverse is to flip the sign of the RL coordinate on each of the vertices, and also to change the order of the vertices in the sets of three points that make up each triangle (because order of the three points is used to indicate inside and outside the brain). If you wish to have your flipped surfaces viewable in conjunction with your original COR volume you might be tempted to flip the input volume also (using for example AFNI or some other MRI software). However, 0,0,0 in the coordinate system used by FreeSurfer is not in the center of the COR volume, it's off by half a voxel. Ie: in the L-R direction, the center of a COR image (ie: between the two middle pixels) is at R = 0.5 mm. [*] The net result will be that the flipped surfaces will misregister with the flipped MRI volume by one voxel RL (ie: half + half). For some users this is no concern at all, for others its a problem. More details at: http://wideman-one.com/gw/brain/fs/coords/fscoords.htm Graham [*] Subject to the usual possibility of getting off-the-top-of-the-head details wrong in emails. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert and COR files
Kushal: You may benefit from my notes (now somewhat outdated) on getting FS going, including the Bert data and how it doesn't match the manual. wideman-one.com/gw/brain/fs/instvalid.htm Graham At 10/15/2004 03:27 PM, Kushal Koolwal wrote: Hi, I downloaded the raw data set for the subject called 'bert' and found 3 directories named 001 002 003 under it. And each of the directories contains files from COR-001 to COR-256. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
