Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
Hi Brian,
this is a bug that Tosa has fixed. He has a new Mac version of tksurfer that he'll send you shortly.
cheers, Bruce
On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote:
Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sounds good. Thanks. Brian
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Stats and viewing parcellation problem
Hi Brian,
this is a bug that Tosa has fixed. He has a new Mac version of tksurfer that he'll send you shortly.
cheers, Bruce
On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote:
Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Fixed MacOSX version of tksurfer is available on our ftp page.
$ ftp surfer.nmr.mgh.harvard.edu
username: anonymous passwd: (your email address) cd /transfer/outgoing/birn/tosa/Update/Mac bin get tksurfer
I verified this works under Powerbook G4 running Panther. Should work for G5 (not compatible with G3). If you have problems, let me know.
Tosa
Brian Schweinsburg, Ph.D. wrote:
Sounds good. Thanks. Brian
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Stats and viewing parcellation problem
Hi Brian,
this is a bug that Tosa has fixed. He has a new Mac version of tksurfer that he'll send you shortly.
cheers, Bruce
On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote:
Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
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
Just a quick question, will this update be incorporated if I use the UPDATER script from the afni website? I don't necessarily mean right now, but upon the next upgrade. Thanks.
Xander
On Tue, 2004-12-07 at 11:44, Yasunari Tosa wrote:
Fixed MacOSX version of tksurfer is available on our ftp page.
$ ftp surfer.nmr.mgh.harvard.edu
username: anonymous passwd: (your email address) cd /transfer/outgoing/birn/tosa/Update/Mac bin get tksurfer
I verified this works under Powerbook G4 running Panther. Should work for G5 (not compatible with G3). If you have problems, let me know.
Tosa
Brian Schweinsburg, Ph.D. wrote:
Sounds good. Thanks. Brian
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Stats and viewing parcellation problem
Hi Brian,
this is a bug that Tosa has fixed. He has a new Mac version of tksurfer that he'll send you shortly.
cheers, Bruce
On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote:
Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
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
This is just a bug fix for tksurfer, reading annotation file. Nothing related to afni script.
Tosa
Xander Meadow wrote:
Just a quick question, will this update be incorporated if I use the UPDATER script from the afni website? I don't necessarily mean right now, but upon the next upgrade. Thanks.
Xander
On Tue, 2004-12-07 at 11:44, Yasunari Tosa wrote:
Fixed MacOSX version of tksurfer is available on our ftp page.
$ ftp surfer.nmr.mgh.harvard.edu
username: anonymous passwd: (your email address) cd /transfer/outgoing/birn/tosa/Update/Mac bin get tksurfer
I verified this works under Powerbook G4 running Panther. Should work for G5 (not compatible with G3). If you have problems, let me know.
Tosa
Brian Schweinsburg, Ph.D. wrote:
Sounds good. Thanks. Brian
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Tue, 7 Dec 2004 11:50:50 -0500 (EST) To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Stats and viewing parcellation problem
Hi Brian,
this is a bug that Tosa has fixed. He has a new Mac version of tksurfer that he'll send you shortly.
cheers, Bruce
On Mon, 6 Dec 2004, Brian Schweinsburg, Ph.D. wrote:
Hi All,
I am having problems computing stats using the parcellation file. In addition, when I try to display the parcellation results in tksurfer (File -> Label -> Import Annotation -> rh.aparc.annot), which were completed without an error message using parcellate_subject-rh, I get an error message. I am not sure how to procede. Any hints?
In both error logs, there is a reference to an older location of the Simple_surface_labels2002.txt file, which never existed on my machine. Is that related to the problem?
My machine is a powerbook G4, OS X 10.3.6 with freesurfer-20040218.
I appreciate any assistance. Brian
####### mris_anatomical_stats error message ####### mris_anatomical_stats -b -a $SUBJECTS_DIR/SC002/label/rh.aparc.annot SC002 rh computing statistics for each annotation in /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/label/rh.aparc.anno t. reading volume /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/wm... reading input surface /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/surf/rh.white... Computing inter-vertex distance
computing second fundamental form...reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[3284]: arguments too large: 3221219760,520 CTABreadFrom: could not allocate -1073747536 bin table Cannot allocate memory Bus error
####### Tksurfer error message ####### reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) *** malloc_zone_calloc[3290]: arguments too large: 3221210304, 520 CTABreadFrom: could not allocate -1073756992 bin table Cannot allocate memory
Command Finished
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
Hi Tosa, Is it true that tksurfer must have tcl/tk 8.3? I get an error message stating that there is a package conflict because I have version 8.4. I didn't receive this message with the old tksurfer version, so I must have something set up wrong. The new tksurfer also couldn't find the following shared libaries: libBLT.2, libtix8.1.8.4, libtk8.4, and libglut.3. Once I specified these, I got the error message below on my powerbook G4.
Thanks for the help. Brian
##error log### surfer: current subjects dir: /unix-apps/freesurfer-20040218/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3 surfer: /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/T1/COR-.info INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. surfer: vertices=151063, faces=302122 Tcl_Init failed: Can't find a usable init.tcl in the following directories: /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3 /usr/local/fsl/lib/tcl8.4
/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl: version conflict for package "Tcl": have 8.4, need 8.3 version conflict for package "Tcl": have 8.4, need 8.3 while executing "package require -exact Tcl 8.3" (file "/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl" line 19) invoked from within "source /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $tclfile]"
This probably means that Tcl wasn't installed properly.
Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/local/fsl/lib/tix8.1 /unix-apps/freesurfer-20040218/freesurfer/local/lib/Darwin/tix4.1
This probably means that Tix wasn't installed properly.
surfer: using interface /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tksurfer.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_common.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/fsgdfPlot.tcl surfer: couldn't dis/enable menu set 0: can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 1: can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 2: can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 4: can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable surfer: couldn't dis/enable menu set 5: can't read "glMenuGroups(mg_OverlayLoaded)": no such variable surfer: couldn't dis/enable menu set 6: can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable surfer: couldn't dis/enable menu set 7: can't read "glMenuGroups(mg_LabelLoaded)": no such variable surfer: couldn't dis/enable menu set 8: can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable surfer: couldn't dis/enable menu set 9: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable
Hi, Brian and others Mac users:
I understand the problems.
We are moving to a new way of building binaries without using the older tcl/tk ... I did not realize that the older version had the "explicit" link to the tcl/tk...
Please be patient while we sort the problems out. It may take a few days.
Tosa
Brian Schweinsburg, Ph.D. wrote:
Hi Tosa, Is it true that tksurfer must have tcl/tk 8.3? I get an error message stating that there is a package conflict because I have version 8.4. I didn't receive this message with the old tksurfer version, so I must have something set up wrong. The new tksurfer also couldn't find the following shared libaries: libBLT.2, libtix8.1.8.4, libtk8.4, and libglut.3. Once I specified these, I got the error message below on my powerbook G4.
Thanks for the help. Brian
##error log### surfer: current subjects dir: /unix-apps/freesurfer-20040218/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3 surfer: /unix-apps/freesurfer-20040218/freesurfer/subjects/SC002/mri/T1/COR-.info INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_2018/orig_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. surfer: vertices=151063, faces=302122 Tcl_Init failed: Can't find a usable init.tcl in the following directories: /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3 /usr/local/fsl/lib/tcl8.4
/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl: version conflict for package "Tcl": have 8.4, need 8.3 version conflict for package "Tcl": have 8.4, need 8.3 while executing "package require -exact Tcl 8.3" (file "/unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl" line 19) invoked from within "source /unix-apps/freesurfer-20040218/freesurfer/local/lib/tcl8.3/init.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $tclfile]"
This probably means that Tcl wasn't installed properly.
Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/local/fsl/lib/tix8.1 /unix-apps/freesurfer-20040218/freesurfer/local/lib/Darwin/tix4.1
This probably means that Tix wasn't installed properly.
surfer: using interface /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tksurfer.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_common.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /unix-apps/freesurfer-20040218/freesurfer/lib/tcl/fsgdfPlot.tcl surfer: couldn't dis/enable menu set 0: can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 1: can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 2: can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable surfer: couldn't dis/enable menu set 4: can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable surfer: couldn't dis/enable menu set 5: can't read "glMenuGroups(mg_OverlayLoaded)": no such variable surfer: couldn't dis/enable menu set 6: can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable surfer: couldn't dis/enable menu set 7: can't read "glMenuGroups(mg_LabelLoaded)": no such variable surfer: couldn't dis/enable menu set 8: can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable surfer: couldn't dis/enable menu set 9: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable
freesurfer@nmr.mgh.harvard.edu
-
Brian Schweinsburg, Ph.D. -
Bruce Fischl -
Xander Meadow -
Yasunari Tosa