[Freesurfer] ages of subjecs in buckner_data-raw_dicoms.tar.gz
Hi there, we are trying to determine small atrophy changes based on novel analytic approaches. At this point of our project MPRAGE sequences were adquired in a group of MCI patients (65-85 yrs.) but we do not have healthy controls of the same age interval. For this purpose, I decided to download the file buckner_data-raw_dicoms.tar.gz, but I am unable to figure out the ages of each subject within the file. I was wondering if you wouldn´t mind to provide me with the ages for the 40 subjects contained in this file in order to test my algorithms by combining Freesurfer and Matlab functions. Thanks in advance. Best, Jose L. Cantero -- Jose Luis Cantero (Lorente), Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 Seville (Spain) Phone: +34 95 4348366 Fax: +34 95 4349151 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ages of subjecs in buckner_data-raw_dicoms.tar.gz
Hi Jose, you're better off getting the Oasis dataset from Dan Marcus and Randy Buckner. It's much bigger, well characterized and distributed on DVD. cheers, Bruce On Fri, 5 Jan 2007, Jose Luis Cantero wrote: Hi there, we are trying to determine small atrophy changes based on novel analytic approaches. At this point of our project MPRAGE sequences were adquired in a group of MCI patients (65-85 yrs.) but we do not have healthy controls of the same age interval. For this purpose, I decided to download the file buckner_data-raw_dicoms.tar.gz, but I am unable to figure out the ages of each subject within the file. I was wondering if you wouldn´t mind to provide me with the ages for the 40 subjects contained in this file in order to test my algorithms by combining Freesurfer and Matlab functions. Thanks in advance. Best, Jose L. Cantero ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] label
Hi All, When I ran mri_annotation2label --subject UNC_4 --hemi rh --labelbase ./labels/aparc-rh --table $FREESURFER_HOME/surface_labels.txt Some labels are always skipped such as 6,7... I also tried on tutorial data, the same thing happened. Any ideas? Is surface_labels.txt a complete label list I should use? I also want to add some own labels(not extract them from annot), and cannot figure it out. How can I do this? Thank you, Ran ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ca normalize
I have a subject that has gotten stuck on the CA Normalize step. I have tried running it several times and it always gets stuck in the same place, running away for days if I let it, using 99.9% of the CPU. We are running RH4-x86_64-R302. Is this something that has been observed / dealt with before? This is the screen output for the CA Normalize step up to the point of getting stuck: #-- [EMAIL PROTECTED] CA Normalize Fri Jan 5 11:02:19 PST 2007 /space/emc1/4/data/MMILDB/ADNI/Containers/FREESURFERRECON_005_S_0448_20060504.085355_1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.405 -0.358 0.038 35.157; 0.193 0.687 -0.595 80.138; 0.176 0.895 1.062 -269.933; 0.000 0.000 0.000 1.000; INFO: transform used _ Fixing up the home? Live Search can help http://imagine-windowslive.com/search/kits/default.aspx?kit=improve&locale=en-US&source=hmemailtaglinenov06&FORM=WLMTAG ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coloring problem after autorecon2
Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/color_failure.png I can also upload the dicoms to the drop box if this would help. Thanks! Niels Bergsland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ca normalize
Hi Don, I've never seen that happen. Can you send us the data? Bruce On Fri, 5 Jan 2007, Don Hagler wrote: I have a subject that has gotten stuck on the CA Normalize step. I have tried running it several times and it always gets stuck in the same place, running away for days if I let it, using 99.9% of the CPU. We are running RH4-x86_64-R302. Is this something that has been observed / dealt with before? This is the screen output for the CA Normalize step up to the point of getting stuck: #-- [EMAIL PROTECTED] CA Normalize Fri Jan 5 11:02:19 PST 2007 /space/emc1/4/data/MMILDB/ADNI/Containers/FREESURFERRECON_005_S_0448_20060504.085355_1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.405 -0.358 0.038 35.157; 0.193 0.687 -0.595 80.138; 0.176 0.895 1.062 -269.933; 0.000 0.000 0.000 1.000; INFO: transform used _ Fixing up the home? Live Search can help http://imagine-windowslive.com/search/kits/default.aspx?kit=improve&locale=en-US&source=hmemailtaglinenov06&FORM=WLMTAG ___ 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] Freesurfer Installation Problem
I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running
Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the
installation with the command "tkmedit bert orig.mgz":
$ tkmedit bert orig.mgz
Talairach transform
/autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm
The setup script ran flawlessly, producing the following output:
$ source SetUpFreeSurfer.csh
freesurfer-Linux-centos4-stable-pub-v3.0.4
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer
FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast
SUBJECTS_DIR /home/fmri/fmrihome/dti/software/freesurfer/subjects
MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni
GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl
FSL_DIR /home/fmri/fmrihome/fsl
I was able to locate the "missing" talairach.xfm file in the appropriate
directory.
On another note, I run into the following tcl/tk error when running tksurfer:
Tk_Init failed: Can't find a usable tk.tcl in the following directories:
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /home/
fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 ./li
b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't access "::tk::Priv.:::171.65.48.253:0": parent namespace doesn't exist
can't access "::tk::Priv.:::171.65.48.253:0": parent namespace doesn't exist
while executing
"upvar #0 ::tk::Priv.:::171.65.48.253:0 ::tk::Priv"
("uplevel" body line 1)
invoked from within
"uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv"
(procedure "tk::ScreenChanged" line 9)
invoked from within
"tk::ScreenChanged [winfo screen .]"
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 277)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't import command "mc": already exists
can't import command "mc": already exists
while executing
"namespace import ::msgcat::mc"
(in namespace eval "::tk::msgcat" script line 21)
invoked from within
"namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [catch {package require msgcat}]} {
# The msgcat..."
(in namespace eval "::tk" script line 3)
invoked from within
"namespace eval ::tk {
# Set up the msgcat commands
namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [..."
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 20)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
This probably means that tk wasn't installed properly.
I run into the same error when opening the FSL 3.3 GUI, so I assume the error
from FreeSurfer is related. I understood that the latest FreeSurfer is packaged
with the required tcl/tk libraries, so this shouldn't be an issue. Any thoughts?
Note: I also installed the standard CentOS 4 (non 64 bit) distribution, but
encountered the same problems.
Thanks,
Jaakko
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Re: [Freesurfer] Coloring problem after autorecon2
Hi Niels, This looks like what would happen to the aseg if it was run on a subject who was missing a cerebellum. Did you run the aseg before you manually fixed the cerebellum and not re-run it? If so, the aseg needs to be rerun (in fact, all of -autorecon2 does). Another thought is, how did you manually edit to fix the missing cerebellum? Did you use command line procedures, like increasing the preflooding height or using the option -wsatlas? Or did you do it by hand with the "edit voxels" tool in tkmedit? If you've done it by hand, were you on the appropriate volume (brainmask.mgz) and did you do it for every slice that there was missing cerebellum? My recommendation for fixing a completely missing cerebellum is always to use the command line. Increasing the preflooding height (or using the atlas flag) should work everytime: recon-all -skullstrip -wsthresh 35 -clean-bm -s recon-all -skullstrip -wsatlas -clean-bm -s Jenni On Fri, 5 Jan 2007, Niels Bergsland wrote: Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/color_failure.png I can also upload the dicoms to the drop box if this would help. Thanks! Niels Bergsland ___ 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] control points and white matter edits
Hi all, I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? Thanks, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] problem with mris_anatomical_stats
Abdel, Indeed mris_fix_topology had the same bug as mris_anatomical_stats (when running on Slackware Linux). I've posted a fixed version of mris_fix_topology here: http://surfer.nmr.mgh.harvard.edu/pub/dist/ named: mris_fix_topology.gz mv this to your $FREESURFER_HOME/bin, then type: gunzip mris_fix_topology.gz chmod a+x mris_fix_topology Let me know if you encounter similar bugs. This fixed binary will appear in the next release. Nick On Fri, 2007-01-05 at 14:43 +, Abdel Douiri wrote: > Hi Nick > We have done a new update to our Linux system and i have found the same error > that i report a while ago (see bellow) But this time is for mris_fix_topology > program. > Can you please check it again for mris_fix_topology.c file, the error that > you found was problem with sprintf! (sprintf(fname,"%s.mgz",fname) to > strcat(fname,".mgz") > ). > Thanks > Abdel > > > > > Abdel, > > Thanks for testing this. The bug fix will appear in an upcoming > release, but you can continue using the mris_anatomical_stats that you > have now. > > For those interested in the perils of testing a multi-platform app, the > buggy line of code was: > > sprintf(fname,"%s.mgz",fname) > > Here the source and destination are the same, which, according to glibc > docs for sprintf, is undefined behavior. The odd thing is that these > Linux variants: RedHat 7.3, RedHat 9, Centos4, Debian and SuSE; and Mac > OS X, all have a shared libc lib that handles the line of code properly. > The libc included with Slackware, however, did not (and understandably > so). libc.so is included not with Freesurfer, but with the OS, so this > means that testing even on a half-dozen different platforms doesn't > guarantee trouble-free performance on a seemingly identical platform. > > The proper code in this case is: > > strcat(fname,".mgz"); > > N. > > > On Fri, 2006-08-18 at 18:40 +0100, A. Douiri wrote: > > that s works! > > Cheers! > > > > > > At 01:51 18/08/2006, Nick Schmansky wrote: > > >Abdel, > > > > > >I don't think there is a matlab alternative to mris_anatomical_stats. > > > > > >However, there is a suspicious line of code in mris_anatomical_stats that > > >I have fixed, and I'm wondering if you can give a new binary a try. It is > > >found here: > > > > > > http://surfer.nmr.mgh.harvard.edu/pub/dist/ > > > > > >and named: > > > > > > mris_anatomical_stats.gz > > > > > >To install, after downloading: > > > > > > gunzip mris_anatomical_stats.gz > > > chmod o+x mris_anatomical_stats > > > mv mris_anatomical_stats $FREESURFER_HOME/bin > > > > > >While I cannot recreate the error you see, I do not have a Slackware > > >installation, and I am wondering if its core libs are revealing a bug in > > >our code. > > > > > >Let me know if it works. > > > > > >Thanks, > > > > > >Nick > > > > > > > > > > Hi Nick, > > > > Thanks in advance for your help and i would like to ask is there an > > > > alternative in matlab for example to do mris_anatomical_stats? > > > > The detail of the outjkputs is: > > > > > > > > the output of: > > > > $ mris_anatomical_stats --all-info > > > > ProgramName: mris_anatomical_stats ProgramArguments: --all-info > > > > ProgramVersion: $Name: stable3 $ TimeStamp: 06/08/17-10:28:55-GMT CVS: > > > > $Id: > > > > mris_anatomical_stats.c,v 1.35.2.1 2006/04/21 19:45:19 nicks Exp $ User: > > > > douiri Machine: img-179 Platform: Linux PlatformVersion: 2.6.16.22 > > > > CompilerName: GCC CompilerVersion: 30400 > > > > > > > > I tried with other subjects and also bert and i get the same problem: > > > > > > > > $ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a > > > > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab bert lh > > > > INFO: assuming MGZ format for volumes. > > > > computing statistics for each annotation in ../label/lh.aparc.annot. > > > > reading volume .mgz... > > > > zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: > > > > No > > > > such file or directory > > > > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, > > > > -1): > > > > read error > > > > mris_anatomical_stats: could not read input volume .mgz > > > > > > > > > > > > the freesurfer version > > > > $ cat $FREESURFER_HOME/build-stamp.txt > > > > freesurfer-Linux-centos4-stable-pub-v3.0.3 > > > > > > > > > > > > and the linux version is: > > > > $ cat /etc/slackware-version > > > > Slackware 10.2.0 > > > > > > > > > > > > > > > > > > > > > > > > -Original Message- > > > > From: [EMAIL PROTECTED] > > > > [mailto:[EMAIL PROTECTED] On Behalf Of Nick > > > > Schmansky > > > > Sent: 17 August 2006 00:06 > > > > To: Abdel Douiri > > > > Cc: Freesurfer Mailing List > > > > Subject: RE: [Freesurfer] problem with mris_anatomical_stats > > > > > > > > Abdel, > > > > > > > > This problem is truly strange. The filename seems to just disappear. > > > > > > > > Can you send me the output of: > > > > > > > > mris_anatomical_stats --all-info
RE: [Freesurfer] control points and white matter edits
Hi Paul, The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get. Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are supposed to be wm. While adding voxels to the wm volume will have some impact on where the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with intensity troubles that will likely trump any edits you've made. If you'd like to upload one of your subjects I am happy to take a look at it - although I will be out of town all next week so it might take me a while to get to it. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits Hi all, I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? Thanks, Paul ___ 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] FS-FAST: problem with extracting BOLD time courses with a tksurfer tcl script
Hi, I am trying to extract numerical values for BOLD time courses of (a large number of) ROIs. For this purpose I use a tksurfer tcl script. Everything works fine when I only have a small number (~6) of contrasts/stimulus categories (as defined in the paradigm files), but if I increase the number of stimulus categories to 14-18, the script dies without producing anything. I am able to produce the numerical tables semi-manually with the GUI/tcl shell even for the large number of stimulus categories so I do not quite figure what gives. However, doing this manually for all our data would be impossible. Any suggestions how I could circumvent this problem? (The visualization part in the script below, that draws the actual time course display, is not necessary for producing the numerical tables, but removing that part of the script does not help - it still dies.) Any suggestions much appreciated! Also if anyone needs the full script I am happy to send you a copy - however notice that currently one of the command lines only works in the developmental environment (nmr-dev-env). Cheers, Tommi Specs: on machine ai nmr-dev-env cd /space/cuzco/12/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage #Here is the part of the subroutine that does the extraction (to run the whole thing from the master script that sets the variable values, launch run-label-FIR-h.csh in the same directory): # Set curvature for lh set curv lh.curv read_binary_curv set curvflag 1 # Clear earlier labels labl_remove_all # Clear earlier timecourses func_clear_selection # Load new label (use actual path to label file instead of $lname if running the script by itself) labl_load $lpath/$lname.label # Load new timecourse. 3 = No registration needed. # (use actual path to time course file [e.g., bold//h-lh.bhdr] instead of $timecourse if running the script by itself) func_load_timecourse $timecourse 3 # Set timecourse to show average value across all vertices included in the label set gaLinkedVars(func_graph_avg_mode) 2 # Some draw command, dunno what it does really SendLinkedVarGroup graph # Select only some of the contrasts for display. Specifically, here turn off contrasts 4-6 # General format: set gGraphSetting(,visible) <0|1> # where is: Red/Green/Blue/Purple/Brown/Pink/Gray/LightBlue/Yellow/Orange # "Red" is condition zero (NULL), "Green" is condition one, etc. set gGraphSetting(Brown,visible) 0 set gGraphSetting(Pink,visible) 0 set gGraphSetting(Gray,visible) 0 # Adjust amplitude (y-axis, % BOLD signal change) scale from -1 to +2 .wwGraph.gwGraph.gwGraph axis config y -min -1 -max 2 # Pre-stimulus baseline correction (to turn OFF, use 0) set gbPreStimOffset 1 # Draw time course display (this command works only in nmr-DEV-env version!) Graph_SelectVerticesFromMode # Save text file listing the numerical time course values for all categories func_print_timecourse_selection $lpath/$lname-$aname-h.xls # Save time course display as postscript Graph_SaveToPS $lpath/$lname-$aname-h.ps ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
