Re: [Freesurfer] error in the visualization of the parcellation
Can you send me the annotation file? On Thu, 3 Feb 2005, Wan Park wrote: 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 -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
Hi Margaret, mri_motion_correct calls the mni rigid body alignment code. Use it as: mri_motion_correct... cheers, Bruce p.s. you still are probably better off just using one volume. There's no difference in processing, but more manual intervention will probably be needed. On Thu, 3 Feb 2005, Margaret Duff wrote: Hi, Both images are from here on the old bay 2 scanner, they just occurred 1 month apart. Could you describe a little for me how to use mri_motion_correct and how it differs from setup structural scans in csurf? I checked the wiki, but it did not have tons of info. Also, what are the major differences in using only one scan as opposed to two for the reconstruction? Thanks for your help, Margaret On Wed, 2 Feb 2005, Bruce Fischl wrote: Hi Margaret, what are you using to align them? If they are from different sites, then they may not be possible to really align, due to differences in shims, read-out directions and bandwidth. Reconning with a single image is certainly doable (we've done hundreds), but is more labor intensive. cheers, Bruce On Wed, 2 Feb 2005, Margaret Duff wrote: 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 ___ 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] 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
Re: [Freesurfer] averaging brains over two sessions
The best thing is to follow the instructions in recon-all -help. recon-all will automatically use mri_motion_correct2. Basically, you just need to put your two scans in mri/orig/001 and mri/orig/002. However, if there is an artifact (as Ev suggests), then you'll have to use just one of the scans. doug Margaret Duff wrote: > > Hi, Both images are from here on the old bay 2 scanner, they just > occurred 1 month apart. Could you describe a little for me how to use > mri_motion_correct and how it differs from setup structural scans in > csurf? I checked the wiki, but it did not have tons of info. Also, what > are the major differences in using only one scan as opposed to two for the > reconstruction? Thanks for your help, Margaret > > On Wed, 2 Feb 2005, Bruce Fischl > wrote: > > > Hi Margaret, > > > > what are you using to align them? If they are from different sites, then > > they may not be possible to really align, due to differences in shims, > > read-out directions and bandwidth. Reconning with a single image is > > certainly doable (we've done hundreds), but is more labor intensive. > > > > cheers, > > Bruce > > > > On Wed, > > 2 Feb 2005, Margaret Duff wrote: > > > > > 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 > > > > > > ___ > > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] averaging brains over two sessions
Hi, Both images are from here on the old bay 2 scanner, they just occurred 1 month apart. Could you describe a little for me how to use mri_motion_correct and how it differs from setup structural scans in csurf? I checked the wiki, but it did not have tons of info. Also, what are the major differences in using only one scan as opposed to two for the reconstruction? Thanks for your help, Margaret On Wed, 2 Feb 2005, Bruce Fischl wrote: > Hi Margaret, > > what are you using to align them? If they are from different sites, then > they may not be possible to really align, due to differences in shims, > read-out directions and bandwidth. Reconning with a single image is > certainly doable (we've done hundreds), but is more labor intensive. > > cheers, > Bruce > > On Wed, > 2 Feb 2005, Margaret Duff wrote: > > > 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 > > > > ___ > > 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
Re: [Freesurfer] talairaching functional data
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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
