Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] tkmedit bus error
by Gonzalo Rojas Costa 19 Sep '11

19 Sep '11

Hi Carolina: And did you tested the tksurfer command ?... for example: tksurfer CORBIC_vol01 rh pial Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile > Message: 4 > Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] tkmedit bus error > To: Carolina Valencia <cvalencia(a)linkdx.com.co> > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > > Hi Carolina, > > does this happen every time? Can you run freeview on the volumes and see > if it can display them properly? > > cheers > Bruce > On Thu, 15 Sep 2011, Carolina Valencia > wrote: > >> Hi FSusers >> >> I run recon-all in a patient without problems, but when I tried to view it in tkmedit, an error pops up. >> >> I appreciate your help! >> >> Best regards, >> Carolina >> >> recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT 2011 >> done >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error >> cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz >> $FREESURFER_HOME/FreeSurferColorLUT.txt >> Bus error

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question about the vertex index?
by orangekic 19 Sep '11

19 Sep '11

Hello, I am wondering if there are 163842 vertices in fsaverage, will the vertex number be from 0 to 163841 or 1 to 163842 in the label file? Best, KIC

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recon-all steps necessary to get aseg.nii
by Jeff Eriksen 19 Sep '11

19 Sep '11

I would like to run FreeSurfer just up to the point it creates the aseg file, and no further. I believe this would be steps 1 through 11. Is there any way other than making a copy of the recon-all script and removing everything after step 11. Not sure I know exactly where this is. -Jeff

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Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 19 Sep '11

19 Sep '11

Hi Bruce, I run it on our local cluster and there is plenty of memory. Here is the memory print out from top: Mem: 18479108k total, 7724396k used, 10754712k free, 369152k buffers Swap: 72019344k total, 1475720k used, 70543624k free, 6322748k cached There is also plenty of disk space. Best, Lauge On Sun, Sep 18, 2011 at 04:52, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Lauge > How much ram do yo have? Gzip need a lot > Bruce > > > > On Sep 17, 2011, at 3:30 PM, Lauge Emil Borch Laurs S0rensen > <lauges(a)diku.dk> wrote: > > Lauge > > 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.

2 1

unsupported slice timing pattern 5 ?
by Gregory Kirk 18 Sep '11

18 Sep '11

hi, started working with a new data set to tracula proc. right off the bat it dies on mri_convert with unsupported slice timing pattern 5 if i simply do mri_convert data.nii.gz dwi_orig.nii.gz it dies with same, it's from a siemens 1.5 mobile scanner. somebody else converted this data to .nii. don't really understand what this is ? basically it's just copying a .nii file, what could it be doing with slice timing ? thanks

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tkmedit bus error
by Carolina Valencia 18 Sep '11

18 Sep '11

Hi FSusers I run recon-all in a patient without problems, but when I tried to view it in tkmedit, an error pops up. I appreciate your help! Best regards, Carolina recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT 2011 done cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Bus error cvalencia-Precision-WorkStation-T3400:~> tkmedit CORBIC_vol01 brainmask.mgz -aux T1.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Bus error

2 1

ICV differences from version 5.0 to 5.1
by Koller, Jonathan 16 Sep '11

16 Sep '11

Hi, We have noticed differences in Talairach registration (and therefore ICV estimates) in some of our subjects from version 5.0 to version 5.1. Please see the attached document. There are 4 subjects, each row represents the same subject, same input images, same recon-all options (-all) between versions. The bottom of the second page has a table with the ICV values for these subjects across versions. Have there been any changes to the Talairach registration step from 5.0 to 5.1 that would account for these differences? Thanks, Jon

1 0

mri_surf2vol
by Peter Savadjiev 16 Sep '11

16 Sep '11

Hi, I am trying to convert the "curv" surfaces to a volume, using the mri_surf2vol command in the following manner: cd subjects/subjid mri_surf2vol --surf curv --hemi lh --template ./mri/orig.mgz --outvol /tmp/curv.mgz --surfval ./surf/lh.curv --fillribbon --volregidentity subjid I get the following output: gdiagno = -1 Using identity matrix for registration Cannot find orig.mgz, trying orig/COR files instead... mri_read(): couldn't determine type of file subjects/subjid/mri/orig mri_surf2vol ERROR: reading subjects/subjid/mri/orig header Could you please tell me what is wrong with the command? In particular, the file orig.mgz does exist at the specified path, so I don't understand why "cannot find orig.mgz"? The file can be visualized without problems, so the file is not corrupted. Thank you

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Colours for significant clusters
by Antonella Kis 16 Sep '11

16 Sep '11

Hi, Based on Group Analysis tutorial by loading the cluster annotation in tksurfer you can visualize all clusters, regardless of significance. Then changing the label mode to "Outline" by hitting the outline button and loading the cluster p-value overlay I can see all the significant clusters coloured in blue and having a different colour for the outline. I wonder if there is a way so I can make all the significant clusters blue without having any outline. If I change the outline mod the clusters will show different colours (the same as the outline colour). Thank you. Antonella

2 1

distance scale bar on tksurfer
by Yang Liu 16 Sep '11

16 Sep '11

Hi, I want to get a distance scale bar on tksurfer's window. I can get a very dark bar on the black background, but I can't see any text around it. I guess it is because the text is also black, which is buried under the black background. Is there a way to change the text color? Thanks, Yang

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