Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] volume of interest
by Douglas N Greve 18 Dec '12

18 Dec '12

I don't know that function. vox2ras0 is used when you have 0-based indices (as in C) and vox2ras1 is used when you have 1-based indices (as in matlab). doug On 12/18/2012 02:26 PM, octavian lie wrote: > Can I use your function xyzlab for this? If yes, I see that uses > vox2ras0 instead of vox2ras1. Please advise, > Octavian > > On Tue, Dec 18, 2012 at 11:52 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Use the matlab ind2sub command > doug > > > > On 12/18/2012 12:38 PM, octavian lie wrote: > > Dear Douglas, > > > How do I convert the index to its CRS correspondent? > I could think of using in matlab something like > ind=c+r*255+s* 255^2 > then using floor () to obtain c,r,s, but seems convoluted, is > there any code written on this that you can share? > Thank you again, > > Octavian. > > > > On Tue, Dec 18, 2012 at 11:06 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > If you load the volume in with MRIread > a = MRIread('yourvolume.mgz'); > a.vox2ras1 is the one-based vox2ras matrix which takes a > 1-based > column, row, slice and converts it to RAS. So you just need to > convert your indices to col, row, slice and apply this matrix. > > doug > > > > On 12/17/2012 06:53 PM, octavian lie wrote: > > Dear Douglas, > > Thank you very much for your input. > > 1. I generated the ind matrix as per your script, but > what I > wanted is to get a matrix with the RAS coordinates for the > pixels indexed in ind. Is there a way to do this? > > Thank you, > > Octavian > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

space of T1.mgz
by Mojdeh Zamyadi 18 Dec '12

18 Dec '12

Hi all, I want to segment the hippocampus into head/body/tail in itk SNAP using the hippocampus mask that I create from the result of recon-all segmentation. My question is, are the T1.mgz and aseg.mgz files in the native space of the image or in the atlas space? I know the voxel size is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), but I want to know if the original images are registered to a common atlas space or just resampled to a different voxel size. The reason I'm asking this, is because I'm doing a group study and I want to make sure all my subjects are in the same space so that the segmentation I do is accurate for all. Thanks for your help, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8

3 4

Re: [Freesurfer] volume of interest
by Douglas N Greve 18 Dec '12

18 Dec '12

Use the matlab ind2sub command doug On 12/18/2012 12:38 PM, octavian lie wrote: > Dear Douglas, > > > How do I convert the index to its CRS correspondent? > I could think of using in matlab something like > ind=c+r*255+s* 255^2 > then using floor () to obtain c,r,s, but seems convoluted, is there > any code written on this that you can share? > Thank you again, > > Octavian. > > > > On Tue, Dec 18, 2012 at 11:06 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > If you load the volume in with MRIread > a = MRIread('yourvolume.mgz'); > a.vox2ras1 is the one-based vox2ras matrix which takes a 1-based > column, row, slice and converts it to RAS. So you just need to > convert your indices to col, row, slice and apply this matrix. > > doug > > > > On 12/17/2012 06:53 PM, octavian lie wrote: > > Dear Douglas, > > Thank you very much for your input. > > 1. I generated the ind matrix as per your script, but what I > wanted is to get a matrix with the RAS coordinates for the > pixels indexed in ind. Is there a way to do this? > > Thank you, > > Octavian > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

"nu_estimate_np_and_em" error during recon-all
by Tudor Popescu 18 Dec '12

18 Dec '12

Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: *recon-all -subject M01 -i M01.nii.gz -all* After a few minutes, recon-all ended with the following message: *Assertion failed at line 827 in file templates/CachedArray.cc* *nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)* *nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)* *ERROR: nu_correct* *Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux* I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: - my PATH (listed below) does not seem to include two MNI installations * /home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games * - the version of FreeSurfer that I installed is the latest disk image available on the website (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see any dev version that would presumably include any missing libraries presumably implied by the above error - I tried updating the Xubuntu inside my VirtualBox, however it reports an insufficient space problem that from I can see does not have a trivial fix Advance thanks for any help! Tudor

2 1

vertices out of range after mris_label2annot
by Linda Douw 18 Dec '12

18 Dec '12

Hi experts, I have a bunch of custom-made labels (from the ConnectomeMapper software) that I want to put into a single annotation file. Therefore, I create a color-lookup table and use mris_label2annot as follows: mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a laus500_fixed_newest --l $LABEL_DIR/lh.bankssts_1.label --l $LABEL_DIR/lh.bankssts_2.label --l $LABEL_DIR/lh.bankssts_3.label ... etc for all labels Then, I try to load this annotation with tksurfer, but some errors come up (see below). What do these error messages mean? Could it have something to do with some vertices not having a label assigned to them? The annotation does look okay on tksurfer, but I run into problems later when using it, so I do need to work out why these errors come up. Thanks, Linda tksurfer fsaveragec lh inflated -annotation laus500_fixed_newest subject is fsaveragec hemi is lh surface is inflated surfer: current subjects dir: /cluster/neuromind/douw/scans/controls surfer: in dir with "scripts" in name surfer: session root data dir ($session) set to: surfer: /autofs/cluster/neuromind/douw checking for nofix files in 'inflated' Reading image info (/cluster/neuromind/douw/scans/controls/fsaveragec) Reading /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz surfer: Reading header info from /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz surfer: vertices=163842, faces=327680 reading colortable from annotation file... colortable with 502 entries read (originally /cluster/neuromind/douw/scans/lh_laus500_clut_new.txt) Found embedded color table in annotation. Warning: vertex 206 with annotation 100e251 - out of range! Warning: vertex 1280 with annotation 100e251 - out of range! Warning: vertex 2371 with annotation 100e251 - out of range! Warning: vertex 2372 with annotation 100e251 - out of range! Warning: vertex 5282 with annotation 100e251 - out of range! Warning: vertex 5283 with annotation 100e251 - out of range! Warning: vertex 5284 with annotation 100e251 - out of range! Warning: vertex 5285 with annotation 100e251 - out of range! Warning: vertex 6914 with annotation 100e251 - out of range! Warning: vertex 6915 with annotation 100e251 - out of range! Warning: vertex 9669 with annotation 100e251 - out of range! Warning: vertex 9670 with annotation 100e251 - out of range! Warning: vertex 9671 with annotation 100e251 - out of range! Warning: vertex 9672 with annotation 100e251 - out of range! Warning: vertex 9673 with annotation 100e251 - out of range! Warning: vertex 11176 with annotation 100e251 - out of range! Warning: vertex 11178 with annotation 100e251 - out of range! Warning: vertex 12962 with annotation 100e251 - out of range! Warning: vertex 12963 with annotation 100e251 - out of range! Warning: vertex 12964 with annotation 100e251 - out of range! Warning: vertex 12965 with annotation 100e251 - out of range! Warning: vertex 15365 with annotation 100e251 - out of range! Warning: vertex 21604 with annotation 100e251 - out of range! Warning: vertex 21605 with annotation 100e251 - out of range! Warning: vertex 21606 with annotation 100e251 - out of range! Warning: vertex 21607 with annotation 100e251 - out of range! Warning: vertex 21608 with annotation 100e251 - out of range! Warning: vertex 21609 with annotation 100e251 - out of range! Warning: vertex 21610 with annotation 100e251 - out of range! Warning: vertex 21611 with annotation 100e251 - out of range! Warning: vertex 21612 with annotation 100e251 - out of range! Warning: vertex 21613 with annotation 100e251 - out of range! Warning: vertex 21614 with annotation 100e251 - out of range! Warning: vertex 21615 with annotation 100e251 - out of range! Warning: vertex 21616 with annotation 100e251 - out of range! Warning: vertex 21617 with annotation 100e251 - out of range! Warning: vertex 21618 with annotation 100e251 - out of range! Warning: vertex 27939 with annotation 100e251 - out of range! Warning: vertex 27940 with annotation 100e251 - out of range! Warning: vertex 27941 with annotation 100e251 - out of range! Warning: vertex 27942 with annotation 100e251 - out of range! Warning: vertex 27943 with annotation 100e251 - out of range! Warning: vertex 27944 with annotation 100e251 - out of range! Warning: vertex 27945 with annotation 100e251 - out of range! Warning: vertex 27946 with annotation 100e251 - out of range! Warning: vertex 27947 with annotation 100e251 - out of range! Warning: vertex 28990 with annotation 100e251 - out of range! Warning: vertex 28991 with annotation 100e251 - out of range! Warning: vertex 31491 with annotation 100e251 - out of range! Warning: vertex 31493 with annotation 100e251 - out of range! Warning: vertex 31494 with annotation 100e251 - out of range! Warning: vertex 31495 with annotation 100e251 - out of range! Warning: vertex 31496 with annotation 100e251 - out of range! Warning: vertex 31497 with annotation 100e251 - out of range! Warning: vertex 39242 with annotation 100e251 - out of range! Warning: vertex 39243 with annotation 100e251 - out of range! Warning: vertex 39245 with annotation 100e251 - out of range! Warning: vertex 39246 with annotation 100e251 - out of range! Warning: vertex 39247 with annotation 100e251 - out of range! Warning: vertex 39248 with annotation 100e251 - out of range! Warning: vertex 39249 with annotation 100e251 - out of range! Warning: vertex 39250 with annotation 100e251 - out of range! Warning: vertex 39251 with annotation 100e251 - out of range! Warning: vertex 39252 with annotation 100e251 - out of range! Warning: vertex 39253 with annotation 100e251 - out of range! Warning: vertex 39254 with annotation 100e251 - out of range! Warning: vertex 39256 with annotation 100e251 - out of range! Warning: vertex 41896 with annotation 100e251 - out of range! Warning: vertex 41897 with annotation 100e251 - out of range! Warning: vertex 41898 with annotation 100e251 - out of range! Warning: vertex 43682 with annotation 100e251 - out of range! Warning: vertex 43683 with annotation 100e251 - out of range! Warning: vertex 43684 with annotation 100e251 - out of range! Warning: vertex 43685 with annotation 100e251 - out of range! Warning: vertex 52322 with annotation 100e251 - out of range! Warning: vertex 52324 with annotation 100e251 - out of range! Warning: vertex 52325 with annotation 100e251 - out of range! Warning: vertex 52326 with annotation 100e251 - out of range! Warning: vertex 52327 with annotation 100e251 - out of range! Warning: vertex 52328 with annotation 100e251 - out of range! Warning: vertex 52329 with annotation 100e251 - out of range! Warning: vertex 52330 with annotation 100e251 - out of range! Warning: vertex 52331 with annotation 100e251 - out of range! Warning: vertex 52332 with annotation 100e251 - out of range! Warning: vertex 52333 with annotation 100e251 - out of range! Warning: vertex 52334 with annotation 100e251 - out of range! Warning: vertex 52335 with annotation 100e251 - out of range! Warning: vertex 52336 with annotation 100e251 - out of range! Warning: vertex 61927 with annotation 100e251 - out of range! Warning: vertex 61928 with annotation 100e251 - out of range! Warning: vertex 61929 with annotation 100e251 - out of range! Warning: vertex 61930 with annotation 100e251 - out of range! Warning: vertex 61931 with annotation 100e251 - out of range! Warning: vertex 61932 with annotation 100e251 - out of range! Warning: vertex 61933 with annotation 100e251 - out of range! Warning: vertex 61934 with annotation 100e251 - out of range! Warning: vertex 61935 with annotation 100e251 - out of range! Warning: vertex 61936 with annotation 100e251 - out of range! Warning: vertex 61937 with annotation 100e251 - out of range! Warning: vertex 61938 with annotation 100e251 - out of range! Warning: vertex 63766 with annotation 100e251 - out of range! Warning: vertex 69130 with annotation 100e251 - out of range! Warning: vertex 69131 with annotation 100e251 - out of range! Warning: vertex 69132 with annotation 100e251 - out of range! Warning: vertex 69133 with annotation 100e251 - out of range! Warning: vertex 69134 with annotation 100e251 - out of range! Warning: vertex 69135 with annotation 100e251 - out of range! Warning: vertex 69136 with annotation 100e251 - out of range! Warning: vertex 69137 with annotation 100e251 - out of range! Warning: vertex 69138 with annotation 100e251 - out of range! Warning: vertex 69139 with annotation 100e251 - out of range! Warning: vertex 69140 with annotation 100e251 - out of range! Warning: vertex 69141 with annotation 100e251 - out of range! Warning: vertex 87857 with annotation 100e251 - out of range! Warning: vertex 87858 with annotation 100e251 - out of range! Warning: vertex 87859 with annotation 100e251 - out of range! Warning: vertex 87860 with annotation 100e251 - out of range! Warning: vertex 87861 with annotation 100e251 - out of range! Warning: vertex 87865 with annotation 100e251 - out of range! Warning: vertex 87866 with annotation 100e251 - out of range! Warning: vertex 87867 with annotation 100e251 - out of range! Warning: vertex 87868 with annotation 100e251 - out of range! Warning: vertex 87869 with annotation 100e251 - out of range! Warning: vertex 87870 with annotation 100e251 - out of range! Warning: vertex 87871 with annotation 100e251 - out of range! Warning: vertex 87872 with annotation 100e251 - out of range! Warning: vertex 87873 with annotation 100e251 - out of range! Warning: vertex 87874 with annotation 100e251 - out of range! Warning: vertex 87875 with annotation 100e251 - out of range! Warning: vertex 87876 with annotation 100e251 - out of range! Warning: vertex 87877 with annotation 100e251 - out of range! Warning: vertex 87878 with annotation 100e251 - out of range! Warning: vertex 87879 with annotation 100e251 - out of range! Warning: vertex 87880 with annotation 100e251 - out of range! Warning: vertex 87881 with annotation 100e251 - out of range! Warning: vertex 87882 with annotation 100e251 - out of range! Warning: vertex 87883 with annotation 100e251 - out of range! Warning: vertex 87884 with annotation 100e251 - out of range! Warning: vertex 87885 with annotation 100e251 - out of range! Warning: vertex 87886 with annotation 100e251 - out of range! Warning: vertex 87887 with annotation 100e251 - out of range! Warning: vertex 87888 with annotation 100e251 - out of range! Warning: vertex 87889 with annotation 100e251 - out of range! Warning: vertex 87892 with annotation 100e251 - out of range! Warning: vertex 87893 with annotation 100e251 - out of range! Warning: vertex 87894 with annotation 100e251 - out of range! Warning: vertex 87896 with annotation 100e251 - out of range! Warning: vertex 93844 with annotation 100e251 - out of range! Warning: vertex 93846 with annotation 100e251 - out of range! Warning: vertex 93847 with annotation 100e251 - out of range! Warning: vertex 93848 with annotation 100e251 - out of range! Warning: vertex 97060 with annotation 100e251 - out of range! Warning: vertex 97061 with annotation 100e251 - out of range! Warning: vertex 97062 with annotation 100e251 - out of range! Warning: vertex 97063 with annotation 100e251 - out of range! Warning: vertex 97064 with annotation 100e251 - out of range! Warning: vertex 97065 with annotation 100e251 - out of range! Warning: vertex 97066 with annotation 100e251 - out of range! Warning: vertex 97067 with annotation 100e251 - out of range! Warning: vertex 101384 with annotation 100e251 - out of range! Warning: vertex 101385 with annotation 100e251 - out of range! Warning: vertex 101386 with annotation 100e251 - out of range! Warning: vertex 101387 with annotation 100e251 - out of range! Warning: vertex 101388 with annotation 100e251 - out of range! Warning: vertex 112617 with annotation 100e251 - out of range! Warning: vertex 112618 with annotation 100e251 - out of range! Warning: vertex 112619 with annotation 100e251 - out of range! Warning: vertex 112620 with annotation 100e251 - out of range! Warning: vertex 112623 with annotation 100e251 - out of range! Warning: vertex 112624 with annotation 100e251 - out of range! Warning: vertex 112625 with annotation 100e251 - out of range! Warning: vertex 112626 with annotation 100e251 - out of range! Warning: vertex 112627 with annotation 100e251 - out of range! Warning: vertex 112628 with annotation 100e251 - out of range! Warning: vertex 112629 with annotation 100e251 - out of range! Warning: vertex 112630 with annotation 100e251 - out of range! Warning: vertex 112631 with annotation 100e251 - out of range! Warning: vertex 112632 with annotation 100e251 - out of range! Warning: vertex 112633 with annotation 100e251 - out of range! Warning: vertex 112634 with annotation 100e251 - out of range! Warning: vertex 112635 with annotation 100e251 - out of range! Warning: vertex 112636 with annotation 100e251 - out of range! Warning: vertex 112637 with annotation 100e251 - out of range! Warning: vertex 112638 with annotation 100e251 - out of range! Warning: vertex 112639 with annotation 100e251 - out of range! Warning: vertex 112640 with annotation 100e251 - out of range! Warning: vertex 112641 with annotation 100e251 - out of range! Warning: vertex 112642 with annotation 100e251 - out of range! Warning: vertex 126633 with annotation 100e251 - out of range! Warning: vertex 126634 with annotation 100e251 - out of range! Warning: vertex 126635 with annotation 100e251 - out of range! Warning: vertex 126636 with annotation 100e251 - out of range! Warning: vertex 126637 with annotation 100e251 - out of range! Warning: vertex 126638 with annotation 100e251 - out of range! Warning: vertex 126639 with annotation 100e251 - out of range! Warning: vertex 126640 with annotation 100e251 - out of range! Warning: vertex 126641 with annotation 100e251 - out of range! Warning: vertex 126642 with annotation 100e251 - out of range! Warning: vertex 126643 with annotation 100e251 - out of range! Warning: vertex 126644 with annotation 100e251 - out of range! Warning: vertex 126645 with annotation 100e251 - out of range! Warning: vertex 126646 with annotation 100e251 - out of range! Warning: vertex 126647 with annotation 100e251 - out of range! Warning: vertex 126648 with annotation 100e251 - out of range! Warning: vertex 126649 with annotation 100e251 - out of range! Warning: vertex 126650 with annotation 100e251 - out of range! Warning: vertex 126651 with annotation 100e251 - out of range! Warning: vertex 126652 with annotation 100e251 - out of range! Warning: vertex 129154 with annotation 100e251 - out of range! Warning: vertex 129155 with annotation 100e251 - out of range! Warning: vertex 129156 with annotation 100e251 - out of range! Warning: vertex 135944 with annotation 100e251 - out of range! Warning: vertex 135945 with annotation 100e251 - out of range! Warning: vertex 135952 with annotation 100e251 - out of range! Warning: vertex 135953 with annotation 100e251 - out of range! Warning: vertex 135954 with annotation 100e251 - out of range! Warning: vertex 135955 with annotation 100e251 - out of range! Warning: vertex 135956 with annotation 100e251 - out of range! Warning: vertex 135957 with annotation 100e251 - out of range! Warning: vertex 135958 with annotation 100e251 - out of range! Warning: vertex 135959 with annotation 100e251 - out of range! Warning: vertex 135960 with annotation 100e251 - out of range! Warning: vertex 135961 with annotation 100e251 - out of range! Warning: vertex 135962 with annotation 100e251 - out of range! Warning: vertex 135963 with annotation 100e251 - out of range! Warning: vertex 139275 with annotation 100e251 - out of range! Warning: vertex 139276 with annotation 100e251 - out of range! Warning: vertex 158680 with annotation 100e251 - out of range! Warning: vertex 158681 with annotation 100e251 - out of range! Warning: vertex 158682 with annotation 100e251 - out of range! Warning: vertex 158683 with annotation 100e251 - out of range! Warning: vertex 158684 with annotation 100e251 - out of range! Warning: vertex 158685 with annotation 100e251 - out of range! Warning: vertex 158692 with annotation 100e251 - out of range! Warning: vertex 158693 with annotation 100e251 - out of range! Warning: vertex 158694 with annotation 100e251 - out of range! Warning: vertex 158695 with annotation 100e251 - out of range! Warning: vertex 158696 with annotation 100e251 - out of range! Warning: vertex 158697 with annotation 100e251 - out of range! Warning: vertex 158698 with annotation 100e251 - out of range! Warning: vertex 158699 with annotation 100e251 - out of range! Warning: vertex 158700 with annotation 100e251 - out of range! Warning: vertex 158701 with annotation 100e251 - out of range! Warning: vertex 158702 with annotation 100e251 - out of range! Warning: vertex 158703 with annotation 100e251 - out of range! Warning: vertex 158704 with annotation 100e251 - out of range! Warning: vertex 158705 with annotation 100e251 - out of range! Warning: vertex 158706 with annotation 100e251 - out of range! Warning: vertex 158707 with annotation 100e251 - out of range! Warning: vertex 158708 with annotation 100e251 - out of range! Warning: vertex 158709 with annotation 100e251 - out of range! Warning: vertex 158710 with annotation 100e251 - out of range! Warning: vertex 158711 with annotation 100e251 - out of range! Warning: vertex 158712 with annotation 100e251 - out of range! Warning: vertex 158713 with annotation 100e251 - out of range! Warning: vertex 158714 with annotation 100e251 - out of range! Warning: vertex 158715 with annotation 100e251 - out of range! Warning: vertex 158716 with annotation 100e251 - out of range! Warning: vertex 158717 with annotation 100e251 - out of range! Warning: vertex 158718 with annotation 100e251 - out of range! Warning: vertex 158722 with annotation 100e251 - out of range! Warning: vertex 158723 with annotation 100e251 - out of range! Warning: vertex 158724 with annotation 100e251 - out of range! Warning: vertex 158725 with annotation 100e251 - out of range! Warning: vertex 158726 with annotation 100e251 - out of range! Warning: vertex 158727 with annotation 100e251 - out of range!

2 1

Info change size nii
by Andrea Tateo 18 Dec '12

18 Dec '12

Hello FS experts, I have a problem to solve. I have a binary image.nii to estimate the segmentation of freesurfer. His size is 70,30,70 but format nii includes other information: resolution, origin, ... so, when I convert image.nii to image.mgz, I see an image of size256, 256, 256, (256 slides for orientation). I need to have the image.nii of size 256,256,256 voxels. there is a FreeSurfer's command which allows me to convert to image.nii with size 256 256 256 (if I convert image.nii to image.mgz, the image.mgz has size 256, 256,256) Thank you very much Andrea

2 1

Error from mri_concat while using QDEC
by Tudor Popescu 18 Dec '12

18 Dec '12

Hello everyone, I tried doing the QDEC group analysis tutorial, however after doing everything as instructed in the tutorial, when pressing Analyze I get the error message: *Error in Analyze: command failed: mri_concat /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh (..)* ..even though those files are all accessible there! I pasted that same mri_concat manually into the terminal, however no output is produced at the command prompt, nor any files are created. In previous attempts, I used to also get this error *" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in SUBJECTS_DIR "* *Syntax error: Bad fd number"* after following the sh/bash workaround from this <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h…>previous thread, I no longer get that error, however get stuck with the error mentioned above. My SUBJECTS_DIR already contains a copy of the default subjects folder. Debug info below. Any help greatly appreciated! Tudor -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/virtualuser/freesurfer FSFAST_HOME /home/virtualuser/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects MNI_DIR /home/virtualuser/freesurfer/mni

2 1

Some beginner questions on cortical thickness analyses
by Tudor Popescu 18 Dec '12

18 Dec '12

Dear all, I have some questions I could not find an answer to myself, I'd really appreciate it if anyone could help out. 1) How should recon-all be used to process all subjects' data (i.e. obtain the surface for each subject) before taking it to QDEC (or command prompt) for a group thickness analysis? The QDEC tutorial mentions a separate tutorial for the recon-all preprocessing part, but it is not at all clear which one that is. Is there more to it than just typing "recon-all --i file.nii –i file.dcm –subject bert –all" for each subject (assuming NIFTI structurals)? 2) Is mri_glmfit FreeSurfer's equivalent of the randomise command in FSL, i.e. it does nonparametric permutation-based inference based on the given design matrix and produces statistical maps? Or are there differences between the two in how the GLM is applied? 3) Freeview and tksurfer seem to overlap in scope - when would you use one rather than the other? Does it have to do with viewing structurals vs statistically-generated maps? 4) I see that points on reconall-generated surfaces are always referred to in tutorials as vertices rather than voxels. Since both represent the "unit of space", what exactly is the difference between them? Many thanks in advance! Tudor

2 1

volume of interest
by octavian lie 18 Dec '12

18 Dec '12

Dear All, I have created a volume of interest in itksnap and imported it in FS as a .mgz volume filled binary mask. How can I: 1. export it from FS in matlab and generate a .mat array containing only the volume pixels within the volume (intensity 1) ? 2. Is there a way to generate a 3D surface mesh of the boundary of the volume of interest, as, for example, with the brain pial surface? If not, is there a way to import into FS formats such as VTK, STL or BYU meshes? Thank you, Octavian

2 3

Order of recommended reconstructions - CPs and skullstripping
by Thomas Fink 18 Dec '12

18 Dec '12

Dear experts, In the recommended reconstructions ( http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) it is stated that one should do CPs first and than do skullstripping. Why is that? However the recon-all after CPs (recon-all -autorecon2-cp -autorecon3 -subjid) includes less (or later) stages from the autorecon process (only stages 12-31) than the recon-all after skullstripping (recon-all -autorecon2 -autorecon3 -subjid) (stages 6-31) does. Wouldn't this indicate that skullstripping should be done before applying CPs? Best regards Thomas

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer