[Freesurfer] Problem with the parcellation
Hello, I have been running freesurfer in G5 Macs with Panther. I was able to parcellate and retrieve data of the different areas. However, recently we changed the OS from Panther to Tiger. Since then, I have the following problem: When I do mris_anatomical_stats: [ogden:freesurfer_package/freesurfer/subjects] wpark% mris_anatomical_stats -b -a 14649/label/rh.aparc.annot 14649 rh computing statistics for each annotation in 14649/label/rh.aparc.annot. reading volume /usr/local/freesurfer_package/freesurfer/subjects/14649/mri/wm... reading input surface /usr/local/freesurfer_package/freesurfer/subjects/14649/surf/rh.white... INFO: Volume /tmp/mritotal_2576/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. done. computing second fundamental form...reading colortable from annotation file... colortable with 0 entries read (originally ) done. total white matter volume = 509402 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 3758 2149 4165 1.950 +- 0.579 0.199 0.067 75.676 9.502 ** annotation 003c148c 2251 1174 3233 2.652 +- 0.702 0.200 0.081 67.771 6.118 ** annotation 00b43cb4 1285731 1674 2.284 +- 0.590 0.179 0.065 25.068 2.573 ** annotation 003cdc14 1282792 1629 2.076 +- 0.523 0.170 0.041 14.336 1.902 ** annotation 00dc3c65 1304794 1569 2.005 +- 0.501 0.190 0.044 19.070 2.299 ** annotation 008c1415 306137291 2.137 +- 0.534 0.147 0.0253.083 0.471 ** annotation 00b43c15 1604935 1722 1.840 +- 0.477 0.203 0.070 34.702 3.964 ** annotation 001414b4 2363 1479 3196 2.165 +- 0.602 0.160 0.035 27.198 3.101 ** annotation 00b46465 2602 1659 3292 1.968 +- 0.729 0.189 0.052 47.088 5.998 ** annotation 00b4b43f 2299 1339 3348 2.510 +- 0.575 0.192 0.051 50.159 4.279 ** annotation 00dcb4dc 548309766 2.469 +- 0.454 0.165 0.0435.623 0.997 ** annotation 00c8c80a 1015591 1455 2.481 +- 0.499 0.196 0.056 24.732 1.704 ** annotation 0064dc8c .. Instead of having the name of different areas, I receive annotation... Curiously, this does not happen if I do mris_anatomical_stats in previously parcellated brains (before the new installation). This happens when I parcellate_subject and then I try to get the info of the areas. This is what I got when I parcellate: [ogden:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 14649 reading atlas from /usr/local/freesurfer_package/freesurfer/average/lh.atlas2002_simple.gcs... reading color table from GCSA file 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: 9935 changed, 137093 examined... 001: 2397 changed, 37088 examined... 002:731 changed, 1 examined... 003:340 changed, 4117 examined... 004:155 changed, 1818 examined... 005: 88 changed, 871 examined... 006: 47 changed, 459 examined... 007: 28 changed, 255 examined... 008: 19 changed, 160 examined... 009: 12 changed, 97 examined... 010: 10 changed, 64 examined... 011: 5 changed, 64 examined... 012: 3 changed, 27 examined... 013: 2 changed, 19 examined... 014: 1 changed, 9 examined... 015: 0 changed, 6 examined... 000: 340 total segments, 238 labels (3015 vertices) changed 001: 123 total segments, 23 labels (316 vertices) changed 002: 104 total segments, 4 labels (20 vertices) changed 003: 100 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 164 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/14649/label/lh.aparc.annot... writing colortable into annotation file... classification took 3 minutes and 42 seconds. reading atlas from /usr/local/freesurfer_package/freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file 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: 9869 changed, 137521 examined... 001: 2399 changed, 36932 examined... 002:698 changed, 12235 examined... 003:282 changed, 3952 examined... 004:150 changed, 1565 examined... 005: 81 changed, 821 examined... 006: 58 changed, 453 examined... 007: 30 changed, 299 examined... 008: 10 changed, 170 examined... 009: 4 changed, 54 examined... 010: 4 changed, 26 examined...
[Freesurfer] check_subject
when i put check_subject 14456, i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% check_subject 14456 CHECKING SUBJECT 14456 WARN: lh.rh.sphere.reg is empty/missing [ogden:freesurfer_package/freesurfer/subjects] wpark% is there any problem? wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert
hi, i am trying to convert 124 slices of .dcm files COR, but when i put mri_convert E9042_S002_A0001_anon.dcm . (E9042_S002_A0001_anon.dcm is the first slice). i receive this message: %mri_convert E9042_S002_A0001_anon.dcm . mri_convert E9042_S002_A0001_anon.dcm . reading from E9042_S002_A0001_anon.dcm... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... Segmentation fault % could you please help me with this? thanks, wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem converting IMA files
Can I suggest to change the file name from .IMA to .ima? Wan On Apr 19, 2005, at 9:14 AM, Bruce Fischl wrote: Hi Kristine, you can send us a series and we'll look at them if you want. Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: Hi Bruce I tried -it siemens too (based on some list question) and that did't work either, but I see now that hey are named .IMA not .ima Sorry, the FW-disk I got them from likely caused the problem. Thanks, Kristine -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 4/19/2005 12:00 AM To: Kristine Beate Walhovd Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] Problem converting IMA files Hi Kristine, mri_convert should handle ima files. Have you tried -it siemens? Are they named .ima? cheers, Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: Hi I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command mri_convert -ot cor one filename in the sequence output file but it doesn't work. Gives an error message cannot parse... (see attached error message). I'd be grateful for any suggestions. Thanks, Kristine ___ 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] mri_convert orientation
Unfortunately I only have img/hdr files. when I put mri_info I have this message: [ash:14725/mri/orig] wpark% ls 14725.hdr 14725.img [ash:14725/mri/orig] wpark% mri_info 14725.img INFO: analyzeRead(): found 1 files for /usr/local/freesurfer_package/freesurfer subjects/14725/mri/orig/14725.img - INFO: could not find /usr/local/freesurfer_package/freesurfer/subjects/14725/mr /orig/14725.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default) INFO: if not valid, please provide the information in /usr/local/freesurfer_pac age/freesurfer/subjects/14725/mri/orig/14725.mat file - Volume information for 14725.img type: analyze3d dimensions: 256 x 256 x 124 voxel sizes: 0.7812, 0.7812, 1.5000 type: SHORT (4) fov: 0.000 xstart: 0.0, xend: 0.0 ystart: 0.0, yend: 0.0 zstart: 0.0, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degre s nframes: 1 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0.000 : x_a = 0., y_a = 1., z_a = 0., c_a = 0.000 : x_s = 0., y_s = 0., z_s = 1., c_s = 0.000 voxel to ras transform: -0.7812 0. 0. 100. 0. 0.7812 0. -100. 0. 0. 1.5000 -93. 0. 0. 0. 1. [ash:14725/mri/orig] wpark% I know that doing mri_convert -iid x_r x_a x_s -ijd y_r y_a y_s -ikd z_r z_a z_s I can change the orientation. In this case it would be mri_convert -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 14725.img . My questions: 1) Are these the default values that the mri_convert use if I do not specify anything? (mri_convert 14725.img .) 2) If I want to change, the possible values are -1 0 and 1? Thank you very much. Wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] parcellation
Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks! wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parcellation IV
Thanks Xiao Han! I worked finally! Cheers (see below) Now I have this question: I see there is a lot of regions. How do each region correspond to specific color in the visualization? Thanks a lot! Wan total white matter volume = 533145 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 2955 1803 6322 3.453 +- 0.875 0.204 0.080 71.570 9.042 G_parietal_inferior-Angular_part 3572 2241 6032 2.691 +- 0.894 0.192 0.060 59.096 9.520 S_intraparietal-and_Parietal_transverse 2379 1388 3665 2.599 +- 0.657 0.190 0.060 58.310 6.513 G_parietal_superior 1269713 1901 2.621 +- 1.066 0.208 0.087 33.729 5.435 G_occipital_middle 824464 1105 2.449 +- 1.013 0.159 0.057 14.657 1.930 S_occipital_superior_and_transversalis 5746 3588 9688 2.721 +- 0.785 0.153 0.043 60.049 8.714 S_temporal_superior 3950 2272 5219 2.285 +- 0.617 0.183 0.060 74.201 8.967 G_precentral 3509 1947 5172 2.636 +- 0.791 0.193 0.078 291.730 9.736 G_postcentral 4558 2846 6608 2.321 +- 0.553 0.170 0.043 54.653 7.641 S_central 3180 1931 5328 2.757 +- 0.611 0.147 0.037 30.201 4.109 S_postcentral 2393 1395 2388 1.717 +- 0.559 0.225 0.074 58.455 7.835 G_paracentral 465248684 2.720 +- 0.584 0.138 0.0405.397 1.079 S_intermedius_primus-Jensen 2626 1508 3646 2.381 +- 0.738 0.158 0.047 37.750 4.537 G_precuneus 2486 1441 3440 2.371 +- 0.824 0.214 0.088 68.986 9.620 Pole_occipital 1150831 1277 1.559 +- 0.531 0.201 0.059 13.629 3.664 G_occipital_superior 1045613 1346 2.158 +- 0.733 0.191 0.069 20.900 2.763 G_occipital_inferior 2403 1278 3600 2.793 +- 0.657 0.182 0.067 52.261 6.180 G_temporal_middle 1531921 2238 2.456 +- 0.524 0.197 0.055 26.134 2.962 S_precentral-Superior-part 1747926 2300 2.469 +- 0.746 0.165 0.065 26.462 4.279 G_parietal_inferior-Supramarginal_part 788441 1023 2.287 +- 0.956 0.205 0.097 16.175 3.575 S_occipital_middle_and_Lunatus 1694924 1989 2.253 +- 0.946 0.204 0.087 47.149 7.090 G_cuneus 301118243 2.046 +- 0.736 0.140 0.0594.324 0.713 S_occipital_inferior 770453 1140 2.513 +- 0.520 0.162 0.0418.611 1.256 S_occipital_anterior 8169 4643 9060 1.971 +- 0.606 0.185 0.061 142.550 19.432 G_frontal_superior 806483904 1.868 +- 0.652 0.170 0.054 11.111 1.823 S_cingulate-Marginalis_part 761454869 1.961 +- 0.665 0.145 0.0377.589 0.992 S_subparietal 2634 1496 3645 2.456 +- 0.629 0.205 0.076 62.685 6.930 G_temporal_inferior 385173500 2.845 +- 0.535 0.133 0.0414.932 0.410 G_temp_sup-Planum_tempolale 946577 1356 2.365 +- 0.443 0.172 0.0409.745 1.653 S_temporal_inferior 2556 1766 2644 1.539 +- 0.548 0.174 0.045 35.471 6.396 S_parieto_occipital 1608945 2243 2.355 +- 0.613 0.154 0.035 12.523 2.516 Lat_Fissure-post_sgt 2976 1816 4799 2.656 +- 0.539 0.209 0.061 67.117 7.108 G_occipit-temp_lat-Or_fusiform 91 42 56 1.341 +- 0.194 0.141 0.0260.851 0.105 S_paracentral 2519 1720 3436 2.049 +- 1.045 0.152 0.040 26.893 5.123 S_calcarine 365212345 1.644 +- 0.419 0.128 0.0152.299 0.248 S_collateral_transverse_post 1247714 1541 2.183 +- 0.494 0.165 0.036 12.002 2.265 S_occipito-temporal_lateral 3489 2058 3863 1.885 +- 0.594 0.175 0.049 48.747 6.589 S_cingulate-Main_part 1792 1174 2649 2.327 +- 1.109 0.179 0.041 38.026 2.807 G_occipit-temp_med-Lingual_part 1340746 1715 2.317 +- 0.546 0.177 0.061 22.078 3.527 G_temp_sup-Lateral_aspect 3040 1843 3431 1.874 +- 0.487 0.147 0.031 28.439 3.845 S_frontal_superior 1638893 2173 2.380 +- 0.695 0.159 0.045 24.985 3.034 G_cingulate-Main_part 637336867 2.556 +- 0.682 0.171 0.064 14.747 1.730 G_subcentral 214102226 2.234 +- 0.679 0.080 0.0170.636 0.115 S_subcentral_post 1509817 2192 2.657 +- 0.733 0.162 0.058 26.524 3.281 G_temp_sup-G_temp_transv_and_interm_S 811432 1032 2.336 +- 0.799 0.143 0.041 10.138 1.131 S_pericallosal 1438720 1688 2.373 +- 0.619 0.127 0.050 16.264 2.842 G_temp_sup-Planum_polare 1561943 2367 2.519 +- 0.422 0.151 0.040 15.352 2.301
[Freesurfer] Parcellation
Hello, I need to parcellate the brain in standard areas (eg. prefrontal, occipital, temporal, etc.). I have a MAC and I did the parcellation with the new binaries that Kevin Teich sent me. What I have is a multicolor brain painted in tiny pieces. Is this correct? What I am interested is to calculate the gray matter volume (with mris_anatimical_stats) of some standard areas. How can I do this? Thank you very much! Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parcellation II
cheers! i did exactly the same thing with another brain but this time i obtained this which looks much better: inline: parcellation2.tiff (i am sending this again in a smaller size to avoid the mediator) i guess this is correct. now, how can i use this areas to calculate the gray matter volume of these standard areas? thanks! wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] new tkmedit and tksurfer
I am supposed to have libtiff, glut, tclkt, tix and blt installed, but I still receive this message: for volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished for surface: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished Curiously, I did not have this problems before the new binaries. Do you think that may be a line or it is more about env? thanks! wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI align
I think I need to do the MNI align. Could someone teach me how to do this? Thanks, Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error in the visualization of the parcellation
hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 16263 examined... 003:473 changed, 5771 examined... 004:281 changed, 2658 examined... 005:157 changed, 1570 examined... 006: 69 changed, 848 examined... 007: 34 changed, 397 examined... 008: 19 changed, 211 examined... 009: 9 changed, 120 examined... 010: 8 changed, 47 examined... 011: 8 changed, 49 examined... 012: 2 changed, 44 examined... 013: 0 changed, 11 examined... 000: 538 total segments, 417 labels (5917 vertices) changed 001: 158 total segments, 44 labels (399 vertices) changed 002: 116 total segments, 2 labels (13 vertices) changed 003: 114 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot... writing colortable into annotation file... classification took 4 minutes and 49 seconds. i tried to see it and wrote: tksurfer 22970 rh inflated en then file> label> import annot> /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot but i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% tksurfer 22970 rh inflated surfer: current subjects dir: /usr/local/freesurfer_package/freesurfer/subjects surfer: not in scripts dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer_package/freesurfer/subjects surfer: /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/T1/COR-.info INFO: Src volume /tmp/mritotal_4912/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_4912/orig_8_dxyz.mnc cannot be found. ncopen: filename /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc: Invalid dimension id or name miopen: MINC package entry point Error opening /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc mincRead(): error reading volume from file /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc surfer: vertices=169800, faces=339596 surfer: using interface /usr/local/freesurfer_package/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer_package/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[11526]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error [ogden:freesurfer_package/freesurfer/subjects] wpark% could you please help me with this? thanks, wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to seed points 2
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 32018 98977240 22065520831%/ -- recon-all exited with errors at Wed Jan 26 16:07:52 EST 2005 what could be the problem? thanks a lot. wan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] how to seed points
when i try to create the surface, i receive this message: /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ponscall.dat /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/wm /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ponscall.dat... reading input volume...done. searching for cutting planes...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; /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 2435 (min = 350, max = 1400), aspect = 0.88 (min = 0.10, max = 0.75) 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, 1400) area[0] = 2001 (min = 350, max = 1400), aspect = 0.99 (min = 0.10, max = 0.75) 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. /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not find corpus callosum 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 find_cutting_plane:seed point not in structure! Searching neighborhood... could you please teach me how to solve the problem? thanks, wan park___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to visualize the parcellation
hi, after doing: recon-all -stage4b -subjid 40032 -hemi lh recon-all -stage4b -subjid 40032 -hemi rh, i did: parcellate_subject 40032 and it seems to have finished without problems. now, how can i visualize the different areas? thanks, wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] parcellation
Hi, I am want to parcellate my brains, but when I put parcellate_subject alone, I receive the following message; tcsh: CSURF_DIR: Undefined variable What should I do? Second question: Let's say my subject is called bert What's the complete line I should right to do it? Thanks a lot, Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Parcellation 2
Thanks for the previous help! Now I have this problem: setenv CSURF_DIR $FREESURFER_HOME [ash:local/freesurfer_package/freesurfer] wpark% cd subjects [ash:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 40032 reading atlas from /usr/local/freesurfer_package/freesurfer/average/ lh.atlas2002_simple.gcs... reading color table from GCSA file MRISreadVertexPosition(sphere.reg): could not open file /usr/local/freesurfer_package/freesurfer/subjects/40032/su rf/lh.sphere.reg No such file or directory mris_ca_label: could not read annot file sphere.reg for 40032 No such file or directory 40032 is my subject. what could be the problem? thanks, wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] question
I want to calculate the gray matter volume in certain areas (eg. cortical area 39). What should I do? Thanks, Wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI auto talairaching
could you please tell me how to do auto talairaching with the MINC? thanks wan ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
