Freesurfer January 2005

freesurfer@nmr.mgh.harvard.edu

23 participants
50 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

mris_twoclass
by Keyma Prince 28 Jan '05

28 Jan '05

Hello, I am trying to use mri_twoclass for the first time to do a simple comparision of means for the output from parcellate_subject(i.e. cortical thickness and cortical volume) between 2 groups. This the command line i'm using but I keep getting the following output: mris_twoclass -o average7 lh thickness c1_emot_104 c1_emot_106:c2_emot_101 c2_emot_103 -t .01 output: using average7 as output subject mris_twoclass: must spectify ':' between class lists location: /space/engram/6/users/emoaging/ Also is mri_twoclass better than mris_glm to use for comparing the parcellation results between 2 groups? thanks, -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

2 3

visualizing the parcellation 2
by Wan Park 28 Jan '05

28 Jan '05

This is the output for the parcellate_subject: [autologins-Computer:stem/freesurfer/subjects] wanpark% parcellate_subject cf1 reading atlas from /Users/wanpark/Desktop/FreeSurfer/freesurfer/average/ lh.atlas2002_simple.gcs reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 15065 changed, 190865 examined... 001: 3883 changed, 57322 examined... 002: 1317 changed, 20293 examined... 003: 629 changed, 7437 examined... 004: 333 changed, 3451 examined... 005: 187 changed, 1811 examined... 006: 108 changed, 1054 examined... 007: 60 changed, 594 examined... 008: 37 changed, 330 examined... 009: 23 changed, 206 examined... 010: 23 changed, 130 examined... 011: 11 changed, 117 examined... 012: 10 changed, 67 examined... 013: 6 changed, 44 examined... 014: 1 changed, 27 examined... 015: 0 changed, 5 examined... 000: 678 total segments, 566 labels (9496 vertices) changed 001: 180 total segments, 70 labels (776 vertices) changed 002: 115 total segments, 5 labels (366 vertices) changed 003: 110 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 167 changed) writing output to /Users/../Volumes/stem/freesurfer/subjects/cf1/label/lh.aparc.annot... writing colortable into annotation file... classification took 20 minutes and 46 seconds. reading atlas from /Users/wanpark/Desktop/FreeSurfer/freesurfer/average/ rh.atlas2002_simple.gcs reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 14686 changed, 187213 examined... 001: 3723 changed, 54710 examined... 002: 1228 changed, 19135 examined... 003: 543 changed, 6751 examined... 004: 305 changed, 3107 examined... 005: 171 changed, 1740 examined... 006: 92 changed, 948 examined... 007: 48 changed, 498 examined... 008: 26 changed, 256 examined... 009: 18 changed, 153 examined... 010: 11 changed, 85 examined... 011: 8 changed, 49 examined... 012: 1 changed, 36 examined... 013: 0 changed, 8 examined... 000: 586 total segments, 459 labels (8211 vertices) changed 001: 166 total segments, 45 labels (461 vertices) changed 002: 122 total segments, 2 labels (19 vertices) changed 003: 120 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 196 changed) writing output to /Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot... writing colortable into annotation file... classification took 18 minutes and 52 seconds. [autologins-Computer:stem/freesurfer/subjects] wanpark% and then the tksurfer cf1 rh inflated > file > label> import annotation > /Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot: [autologins-Computer:stem/freesurfer/subjects] wanpark% tksurfer cf1 rh inflated surfer: current subjects dir: /Users/../Volumes/stem/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Volumes/stem/freesurfer/subjects surfer: /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/T1/COR-.info ltMNIread: could not open file /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=187213, faces=375476 surfer: using interface /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tksurfer.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_common.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkUtils.tcl Read /Users/wanpark/Desktop/FreeSurfer/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % 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[1839]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error my machine is a mac dual 1 GHz PowerPC G4 2 MB L3 cache per processor, Memory 1.5 Gb SDRAM rh.annot.aparc is not a directory.. what i can do? thanks wan

1 0

visualizing the parcellation
by Wan Park 28 Jan '05

28 Jan '05

Hi, while I am solving the problems with the cutting planes, I am doing parcellation with the subjects that went through. After doing parcellate_subject cf1 I wanted to visualize it so I wrote tksurfer cf1 rh inflated and then I went to file>labels>annotation and wrote /Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot but nothing happened and this error occured: [autologins-Computer:stem/freesurfer/subjects] wanpark% tksurfer cf1 rh inflated surfer: current subjects dir: /Users/../Volumes/stem/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Volumes/stem/freesurfer/subjects surfer: /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/T1/COR-.info ltMNIread: could not open file /Users/../Volumes/stem/freesurfer/subjects/cf1/mri/transforms/ talairach.xfm No such file or directory surfer: Talairach xform file not found (ignored) surfer: vertices=187213, faces=375476 surfer: using interface /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tksurfer.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_common.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /Users/wanpark/Desktop/FreeSurfer/freesurfer/lib/tcl/tkUtils.tcl Read /Users/wanpark/Desktop/FreeSurfer/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % could not read annot file /Users/../Volumes/stem/freesurfer/subjects/cf1/label/rh.aparc.annot/ Not a directory surfer: WARNING: no labels imported; annotation was empty 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[1759]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error do you have any suggestions? thanks, wan

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Re: [Freesurfer] overlay of multiple *.w files onto the same surface
by Joongnam Yang 27 Jan '05

27 Jan '05

Thanks, Bruce, But that's what I already know. What I'd like to do is: overlay 1.w onto surface1 overlay 2.w onto surface1 with 1.w already on it. overlay 3.w onto surface1 with 1.w and 2.w already on it. ...... something like that. Is it possible? If not, any suggestions? Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 01/27/05 1:17 PM >>> you can load multiple w files into different overlay layers in tksurfer, then switch between them in view->overlay layer cheers, Bruce On Thu, 27 Jan 2005, Joongnam Yang wrote: > Hi, > > I know how to overlay a *.w file with a surface. Is it possible to overlay > multiple *.w files onto the same surface on TkSurfer? > If so, would someone let me know how to do it? > > Thanks. > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

overlay of multiple *.w files onto the same surface
by Joongnam Yang 27 Jan '05

27 Jan '05

Hi, I know how to overlay a *.w file with a surface. Is it possible to overlay multiple *.w files onto the same surface on TkSurfer? If so, would someone let me know how to do it? Thanks. Nam.

2 1

how to seed points 3
by Wan Park 27 Jan '05

27 Jan '05

Hi, To create the surface, I have to define the corpus callosum and the pons as well. I have been suggested to get a talairach transform first, so I did: (22970 is the subject folder) $ talairach 22970 but I have received this message: wpark% talairach 22970 registering 22970 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/local/mni/lib/mni_autoreg /System/Library/Perl/5.8.1/darwin-thread-multi-2level /System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level /Network/Library/Perl/5.8.1 /Network/Library/Perl .) at /usr/pubsw/packages/mni/bin/mritotal line 56. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/bin/mritotal line 56. Error: could not open file "/usr/local/freesurfer_package/freesurfer/subjects/22970/mri/ transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/usr/local/freesurfer_package/freesurfer/subjects/22970/mri/ transforms/talairach.xfm' No such file or directory [ogden:freesurfer_package/freesurfer/subjects] wpark% I checked and I have no talairach.xfm under transforms. what should i do? The COR-.info file in mri/wm does not have a line beginning with xform, so I added: xform /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/transforms/ talaraich.xfm and ran the talairach 22970 again, but I received the same message. Thanks!! Wan

2 2

how to seed points 2
by Wan Park 26 Jan '05

26 Jan '05

Hello, Because I had problems finding automatically the corpus callosum cutting plane, I loaded the wm volume, click in the center of the corpus in coronal view, switch to sagittal plane and used the volume RAS coordinates (tailarach coord says "none"). then I ran this line: recon-all -stage2 -cc-xyz -2.0 25.0 0.0 -subjid 22970 but it showed this: ... masking possible pons locations using cc cutting plane voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; brainstem (min, max) thickness = (15,35) brainstem min height = 25 min_delta_thickness = 6 min_cont_brainstem_thickness = 8 min_cont_brainstem_height = 3 Looking for area (min, max) = (350, 790) area[0] = 78 (min = 350, max = 790), aspect = 0.52 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... initial attempt at finding brainstem failed - initiating backup plan A.... brainstem (min, max) thickness = (15,35) brainstem min height = 25 min_delta_thickness = 6 min_cont_brainstem_thickness = 8 min_cont_brainstem_height = 3 Looking for area (min, max) = (350, 790) area[0] = 78 (min = 350, max = 790), aspect = 0.52 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (-2.00, 25.00, 0.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status ------------------------------------------ Filesystem 512-blocks Used Avail Capacity Mounted on /dev/disk0s9 320144448 98977240 220655208 31% / ------------------------------------------ recon-all exited with errors at Wed Jan 26 16:07:52 EST 2005 what could be the problem? thanks a lot. wan

2 1

functional overlay overlap
by Ramapriyan Pratiwadi 26 Jan '05

26 Jan '05

hi all - i've succeeded in displaying FSL z-maps on an inflated brain. however, i'm trying to find a way to display the overlap between two z-maps. i was able to get one to display in red, and the other in blue, with the overlap being purple. however, this doesn't look very convincing, and it would be more helpful to calculate the total number of points in each z-map, and then how many points are in common. is there a way to do this within the freesurfer environment, or even in matlab or idl ? thanks, Ram -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. MailScanner thanks transtec Computers for their support.

2 1

average of functional overlays across subjects
by Joongnam Yang 26 Jan '05

26 Jan '05

Hi All, Would someone point me to a place where I can get information on averaging of functional overlays across subjects? All the materials I have do not have any information about averaging.... Nam.

2 1

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Freesurfer January 2005