Freesurfer November 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
73 discussions

64 vs 32
by Sasha Wolosin 17 Nov '05

17 Nov '05

Dear all, I have run several subjects on a 64-bit machine using the stable release. I recently installed the 32-bit stable version on a 32-bit machine. I noticed that running stage1 on the 32-bit version took much longer than running stage1 on the 64-bit machine (several hours, actually). So I looked at the recon-all scripts for each version and I noticed that they were different. The 32-bit version includes the extra steps DoGCAReg, DoCANormalize, DoCAReg, and DoCALabel. Does anyone know why this is? Below are the stage1 lists for each version. Thanks, Sasha 32-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoGCAReg = 1; set DoCANormalize = 1; set DoCAReg = 1; set DoCALabel = 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw 64-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: mris_ca_label 32vs64 (Satrajit Ghosh)
by Sasha Wolosin 17 Nov '05

17 Nov '05

Dear all, I have also noticed a discrepancy between the stable 32 and the stable 64. The FreeSurferEnv.csh files are quite different. Why is that? Are there any other differences? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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mris_ca_label 32vs64
by Satrajit Ghosh 17 Nov '05

17 Nov '05

I'm noticing some discrepancies between the 64 bit and the 32 bit version of mris_ca_label. I've shown the output from the 64 bit version and the 32 bit version operating on the same subject. I'm using are the dev versions for centos from the download site. To note: 1. In the 64 bit version I get the following output during the process: GCSANclassify: could not find GCS for node 0! Numerical result out of range The 32 bit version does not generate this error on either on th 64 bit machine or a 32 bit machine. 2. The numerical values listed for changed and examined are different. This could well be the case if there was some random element being used. Thanks, Satra ******************** 64 bit output *********************** [satra@sweetsixteen subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.64/subjects/average/lh.SpeechLabAtlas02.gcs.. . 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: 12146 changed, 161370 examined... 001: 2766 changed, 44430 examined... 002: 867 changed, 13696 examined... 003: 356 changed, 4560 examined... 004: 174 changed, 2006 examined... 005: 99 changed, 984 examined... 006: 56 changed, 525 examined... 007: 35 changed, 299 examined... 008: 20 changed, 197 examined... 009: 13 changed, 110 examined... 010: 4 changed, 90 examined... 011: 4 changed, 22 examined... 012: 0 changed, 11 examined... 000: 296 total segments, 236 labels (2598 vertices) changed 001: 76 total segments, 16 labels (103 vertices) changed 002: 60 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 95 changed) writing output to lh-aparc.annot... classification took 1 minutes and 29 seconds. reading atlas from /speechlab/software/freesurfer.64/subjects/average/rh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... GCSANclassify: could not find GCS for node 0! Numerical result out of range GCSANclassify: could not find GCS for node 0! Numerical result out of range GCSANclassify: could not find GCS for node 0! Numerical result out of range relabeling using gibbs priors... 000: 10608 changed, 158433 examined... 001: 2326 changed, 38991 examined... 002: 725 changed, 11759 examined... 003: 307 changed, 3966 examined... 004: 150 changed, 1744 examined... 005: 51 changed, 827 examined... 006: 26 changed, 287 examined... 007: 12 changed, 146 examined... 008: 11 changed, 79 examined... 009: 11 changed, 54 examined... 010: 7 changed, 56 examined... 011: 6 changed, 38 examined... 012: 4 changed, 30 examined... 013: 2 changed, 21 examined... 014: 5 changed, 10 examined... 015: 0 changed, 17 examined... 000: 233 total segments, 174 labels (2403 vertices) changed 001: 72 total segments, 14 labels (54 vertices) changed 002: 58 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 91 changed) writing output to rh-aparc.annot... classification took 1 minutes and 21 seconds. *********************** 32 bit output on 64 bit machine ******** [satra@sweetsixteen subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.32/subjects/average/lh.SpeechLabAtlas02.gcs.. . 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: 12079 changed, 161370 examined... 001: 2690 changed, 44278 examined... 002: 810 changed, 13380 examined... 003: 361 changed, 4352 examined... 004: 178 changed, 2025 examined... 005: 105 changed, 1038 examined... 006: 69 changed, 608 examined... 007: 44 changed, 381 examined... 008: 26 changed, 233 examined... 009: 18 changed, 162 examined... 010: 7 changed, 106 examined... 011: 3 changed, 48 examined... 012: 2 changed, 21 examined... 013: 1 changed, 12 examined... 014: 0 changed, 5 examined... 000: 293 total segments, 234 labels (2674 vertices) changed 001: 78 total segments, 19 labels (100 vertices) changed 002: 59 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 86 changed) writing output to lh-aparc.annot... classification took 1 minutes and 52 seconds. reading atlas from /speechlab/software/freesurfer.32/subjects/average/rh.SpeechLabAtlas02.gcs.. . 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: 10576 changed, 158433 examined... 001: 2384 changed, 38916 examined... 002: 683 changed, 11993 examined... 003: 313 changed, 3870 examined... 004: 164 changed, 1744 examined... 005: 94 changed, 929 examined... 006: 49 changed, 502 examined... 007: 20 changed, 286 examined... 008: 13 changed, 114 examined... 009: 7 changed, 75 examined... 010: 5 changed, 44 examined... 011: 4 changed, 27 examined... 012: 3 changed, 20 examined... 013: 4 changed, 19 examined... 014: 2 changed, 20 examined... 015: 3 changed, 14 examined... 016: 3 changed, 20 examined... 017: 1 changed, 16 examined... 018: 0 changed, 7 examined... 000: 230 total segments, 173 labels (2273 vertices) changed 001: 66 total segments, 9 labels (28 vertices) changed 002: 57 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 83 changed) writing output to rh-aparc.annot... classification took 1 minutes and 42 seconds. *********************** 32 bit output on 32 bit machine ******************* [satra@four subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.32/subjects/average/lh.SpeechLabAtlas02.gcs.. . 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: 12040 changed, 161370 examined... 001: 2723 changed, 44275 examined... 002: 794 changed, 13548 examined... 003: 348 changed, 4370 examined... 004: 185 changed, 1950 examined... 005: 101 changed, 1035 examined... 006: 76 changed, 607 examined... 007: 39 changed, 422 examined... 008: 25 changed, 223 examined... 009: 13 changed, 126 examined... 010: 5 changed, 65 examined... 011: 3 changed, 27 examined... 012: 4 changed, 20 examined... 013: 1 changed, 22 examined... 014: 2 changed, 5 examined... 015: 2 changed, 11 examined... 016: 2 changed, 10 examined... 017: 1 changed, 9 examined... 018: 0 changed, 9 examined... 000: 288 total segments, 226 labels (2311 vertices) changed 001: 79 total segments, 17 labels (109 vertices) changed 002: 62 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 104 changed) writing output to lh-aparc.annot... classification took 3 minutes and 8 seconds. reading atlas from /speechlab/software/freesurfer.32/subjects/average/rh.SpeechLabAtlas02.gcs.. . 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: 10629 changed, 158433 examined... 001: 2376 changed, 39027 examined... 002: 729 changed, 12097 examined... 003: 325 changed, 4004 examined... 004: 183 changed, 1848 examined... 005: 91 changed, 982 examined... 006: 51 changed, 512 examined... 007: 38 changed, 284 examined... 008: 22 changed, 205 examined... 009: 12 changed, 133 examined... 010: 3 changed, 74 examined... 011: 3 changed, 16 examined... 012: 2 changed, 16 examined... 013: 2 changed, 10 examined... 014: 2 changed, 12 examined... 015: 2 changed, 10 examined... 016: 2 changed, 10 examined... 017: 3 changed, 12 examined... 018: 1 changed, 16 examined... 019: 0 changed, 7 examined... 000: 230 total segments, 173 labels (2426 vertices) changed 001: 65 total segments, 9 labels (61 vertices) changed 002: 56 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 83 changed) writing output to rh-aparc.annot... classification took 3 minutes and 5 seconds.

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atlas and coordinate
by Antao Du 16 Nov '05

16 Nov '05

Hi, I processed a bunch of data using the version of 2004 freesurfer. what is the atlas and the coordinate file for each locations used in mris_anatomical_stats? Thanks, Antao

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tkmedit
by Sasha Wolosin 16 Nov '05

16 Nov '05

Dear all, My brains appear too bright after skull stripping, so I tried to fix this with the following command: tkmedit 2316_corffe brain -mm-main 0 255 But the --mm-main option did not have an effect unless I set the max to be lower than the actual max (which was about 170 in this case) The brightness/contrast gui in the tkmedit menu does not allow me to increase the max either. I am using the stable release for x86_64 machines. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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T1 volume problem
by Michele Perry 15 Nov '05

15 Nov '05

Hi, I am having problems with the dev version of Freesurfer. I realized after viewing the aseg that there was a skullstrip problem that I hadn't noticed when I checked the brain volume between -autorecon1 and -autorecon2. When I open brain.mgz and T1.mgz in tkmedit, they look identical (i.e. I can't see skull in the T1). Any idea what went wrong? Michele

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Re: [Freesurfer] labels
by Sasha Wolosin 14 Nov '05

14 Nov '05

great, thanks Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] labels
by Sasha Wolosin 14 Nov '05

14 Nov '05

If the atlas is not included, how am I able to run mris_ca_label? Is the atlas you are referring to different from the ?h.atlas2002_simple.gcs file found in /freesurfer/average? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] labels
by Sasha Wolosin 14 Nov '05

14 Nov '05

so for the stable release should I run both mris_ca_label and mris_anatomical_stats? I'm not sure I understand how to use mris_anatomical_stats to get all the information- is it necessary to specify a surface file? Also, can I view the thickness map of an individual subject? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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freesurfer + fsl
by Don Hagler 14 Nov '05

14 Nov '05

I had a similar problem running Linux RedHat E4. It seems that fsl and freesurfer have incompatible versions of tcltktix. One solution is to always run freesurfer and fsl from different terminal windows. Peter Soros wrote: Wed, 02 Nov 2005 15:19:19 -0800 Hi All, I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 10.4.2) - thanks for the OS X release! Unfortunately, fsl doesn't work after the installation of Freesurfer. This is the error message I get when I try to open the fsl GUI: Error in startup script: no suitable image found. Did find: /Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown fi le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 19) FSL was installed in the recommended directory /usr/local/fsl/ and worked well before. Any help to get FSL working again is highly appreciated!! Peter

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Freesurfer November 2005