Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

please help, unsupported slice timing
by Gregory Kirk 20 Sep '11

20 Sep '11

i am trying to run tracula on a large number of subjects, tracula dies quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data, the error actually comes from the data read function. the data is already in .nii format the error is 'unsupported slice timing pattern 5' this is diffusion data that is already in .nii format so the slice timing information is irrelevant, no slice timing correction is done on diffusion data, but the info was obviously encoded in the nifti header. what do i need to do to get this data to load, go edit the .nii header and 'remove' this info. i tried with the fsledithd function and just setting the 5 to 0 does not work, then i just get a 'read error' with no other information. this data is from a 1.5T siemens mobile scanner so the snr will be a little lower and the bval = 800 is lower so it is just the data that could use the helping hand of the spatial priors to find the tracts. i can run 500 of these if i can get this fixed, incarcerated psychopaths so an important data set. thank you Greg

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Re: [Freesurfer] FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 20 Sep '11

20 Sep '11

Hi Doug, No, we had the lh loaded in tksurfer, and when saving a point it showed up on the *left* in tkmedit (i.e., the right side). thanks ilana On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara <bweiland(a)med.umich.edu>wrote: > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, September 14, 2011 6:10 PM > To: Ilana Hairston > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit > > When you say on the "right hemi in tkmedit" do you mean on the right side > of the image (which is the left side of the brain)? > doug > > Ilana Hairston wrote: > > Hi there, > > We recently had a problem that tksurfer and tkmedit were flipped > > relative to each other. Basically, when saving a point in the left > > hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. > > Any ideas how this could have happened? > > Thanks > > ilana > > > > > > > > -- > >> ****************************** > >> Ilana Hairston ,PhD > >> Research Assistant Professor > >> 4250 Plymouth Rd. (rm 2439) > >> Psychiatry Department, Addiction Research Center University of > >> Michigan, Ann Arbor MI 48109-2700 > >> Tel: 734-232-0232; Mobile: 650-906-8449 > >> > >> ******************** > >> Reminder: Women do 66% of the work worldwide, earn 10% of the income, > >> and own 1% of the world's property > > > > > > > > ---------------------------------------------------------------------- > > -- > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 20 Sep '11

20 Sep '11

On Mon, Sep 19, 2011 at 15:20, R Edgar <freesurfer.rge(a)gmail.com> wrote: > Are you sure that there aren't per process limits which are set lower > than those? > > Richard I just checked, and no, there is no per process memory limit. Is there any way to get more information out from mri_ca_register than what is written in the logs? Lauge

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mris_calc problem
by Dabbs (Kevin) 19 Sep '11

19 Sep '11

I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error; ERROR 1 : mris_calc compute sym. pct. change (spc) problem? It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard? Thanks, Kevin Department of Neurology University of Wisconsin-Madison

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Is this normal when importing the annotations in tksurfer?
by Chen, Xu 19 Sep '11

19 Sep '11

Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer". "...... Found embedded color table in annotation. 8600 vertices did not have an annotation!" What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [Freesurfer] ICV differences from version 5.0 to 5.1
by Ed Gronenschild 19 Sep '11

19 Sep '11

Jon, The reason is that already in one step earlier in the pipeline, the nu-correct stage, a difference arises. See thread on "Differences in nu.mgz between v5.0.0 and v5.1.0" Cheers, Ed > 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

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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.

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