Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Re: [Freesurfer] talairaching functional data
by Joongnam Yang 04 Feb '05

04 Feb '05

Thanks, Doug, For some reason, mri_vol2vol is missing on my system. (everything else is there). Is there any way that I can download the binary alone from you without reinstalling everything...? Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 02/03/05 10:36 AM >>> You're better off using mri_vol2vol. There are lots of docs with --help, including how to convert a volume into talairach space. doug Joongnam Yang wrote: > > Hi, > > I ran "func2tal" with functional data (*.img) and got > > INFO: autodetected functype raw > ERROR: only selxavg, selavg, and sfa functypes are currently supported > > How can I change *.img functional data into the above functypes? > > Thanks. > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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error in the visualization of the parcellation
by Wan Park 03 Feb '05

03 Feb '05

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

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averaging brains over two sessions
by Margaret Duff 03 Feb '05

03 Feb '05

Hello, I am trying to reconstruct brains of patients who had one structural scan during each of 2 visits, a month apart. I averaged the two images together, but since they are from different visits, they look very badly lined up. It looks like there is one image and another image overlaid and shifted by a cm or so. These are clearly wrong and will not work but I was wondering if it was OK to run freesurfer with only one of the images, or if there was a way to line these two images up better so they can be combined? Thanks, Margaret

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talairaching functional data
by Joongnam Yang 03 Feb '05

03 Feb '05

Hi, I ran "func2tal" with functional data (*.img) and got INFO: autodetected functype raw ERROR: only selxavg, selavg, and sfa functypes are currently supported How can I change *.img functional data into the above functypes? Thanks. Nam.

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tcl/tk problem
by Don.Rojas＠UCHSC.edu 01 Feb '05

01 Feb '05

I'm having the same difficulty described with tksurfer and other commands described in a previous thread: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2005-January/000658 .html The error is the same for tksurfer and tkmedit: tksurfer: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory I also have recently upgraded to Fedora Core 3. The version of tcl/tk in Core 3 is 8.4.7-2, which is newer than the version described as successful for a Core 2 install. Has anyone using Core 3 worked around the problem yet? Don Rojas

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Mac OSX Installation Questions
by willcott＠pop.ruf.rice.edu 01 Feb '05

01 Feb '05

>Hello- > I am a new user of FreeSurfer. I am seeking a set of explicit >instruction for installing Mac OSX (10.3.7) binaries on a G4 >platform. I keep getting lost at the level of finding and using >minc_tools. Can anyone improve my knowledge base and attitude. > Thanks, Bob Willcott -- M. Robert Willcott 1807 Orchard Country Lane Houston, TX 77062 713.302.5148

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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

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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

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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 >

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