Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

long_mris_slopes/long_qdec_table command not found
by Peter Bohn 20 Jun '13

20 Jun '13

Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter

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subj: Undefined variable.
by Knut J Bjuland 20 Jun '13

20 Jun '13

Hi Strange error in tracula 5.1. When I use a dmric file that have worked before I now get subj: Undefined variable. I may have uppgrade tcsh. Is there any fix to get tracula-preproc to use the id from dmric files Knut J

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Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
by Martin Reuter 20 Jun '13

20 Jun '13

Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter(a)gmx.de> wrote: >Hi Martin, > >thanks a lot fort he quick reply! When I type freesurfer into the >window it shows me v5.0.0 as the version. Sorry for my prior mistake >concerning the version’s name. All other commands I use run perfectly >fine. > >Thanks once again! > >Best regards > >Peter > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 05:21:39 -0400 >To: bohn-peter(a)gmx.de >CC: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Hi Peter, >can you run any free surfer command at all? Looks to me that you did >not source free surfer. What happens if you typefreesurferinto the >terminal window? It should print the version. >Best, Martin >On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter(a)gmx.de> wrote: > > >Dear Freesurfer experts, > >I was trying to run some longitudinal analysis but whenever I want to >use the commands “long_mris_slopes” or “long_qdec_table” I just get >“command not found” as an answer. When I try to look up a package that >might include the command, by typing “cnf long_mris_slopes”, >I also just get “command not found” as an answer. We are currently >using version v 1.313.2.6. > >Does anyone of you know if the two commands that I would like to run, >are included in this version? Where would I have to look for the >additional package if it exists? Or am I by any chance just typing the >commands incorrect? > >Many thanks for the help! > >Sincerely yours > >Peter_______________________________________________Freesurfer mailing >listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >---------------------------------Dr. Martin ReuterAssistant in >Neuroscience - Massachusetts General Hospital >Instructor in Neurology - Harvard Medical School >MGH / HMS / MIT > >A.A.Martinos Center for Biomedical Imaging >149 Thirteenth Street, Suite 2301 >Charlestown, MA 02129 > >Phone: +1-617-724-5652 >Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.eduWeb : >http://reuter.mit.edu > > > > >_______________________________________________ >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. -- Sent from my phone, please excuse brevity.

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error in lme_mass_fit using matlab tools
by Catherine Bois 20 Jun '13

20 Jun '13

Hi, Thank you for your response. I am actually using two random effects (time and intercepts), and have fixed my design matrix to incorporate this. We are actually running R2011b Matlab, however I just realised that we do not have the Statistics toolbox. Could this be what is causing the errors? Is the Statistics toolbox freely available to download? Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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error --qdec long
by Catherine Bois 20 Jun '13

20 Jun '13

Dear Freesurfer experts, I am trying to prepare my data for linear mixed modeling using the matlab add ons, with this command mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh However I keep getting this error message ERROR: flag --qdec-long not recognized I am using version 5.3 and read on the release notes that qdec-long only works with unix input text files (\n newline). I thought that was the format of my textfile, and also confused as to why the wrong format of the file would make the flag unrecognized as opposed to the textfile...I was also wondering whether the -long table needs to be "shrunk" to cross-sectional format as it does in the two stage model? I have attached an excerpt of my textfile qdec, would greatly appreciate help in establishing whether it is somehow the format of the textfile that is the problem? Thank you very much for your help, Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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export the ROIs in 'Desikan-Killiany' cortical atlas
by Yang, Daniel 20 Jun '13

20 Jun '13

Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas) Would it be a good fit? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Longitudinal processing
by Linn Mittlestein 19 Jun '13

19 Jun '13

Dear Freesurfer group. I am having some concerns about Freesurfer and the different steps. I have used version 5.0 for the cross-sectional timepoints, and I am now using version 5.3 for the longitudinal processing. I am doing therefore the several different steps involved in longitudinal processing, for example -base, -long runs and now for the lme analysis with matlab also the smoothing steps etc. I am very concerned however because looking at the brain masks after these steps have been done (ie the cross-sectional runs), they look much worse than they did before the longitudinal editing began; large chunks of surfaces are missing. Has anybody else reported this problem? Could it be because the longitudinal steps are now being done with version 5.3 as opposed to 5? Surely this should not have such a large effect on the brainmasks, as to completely "deform" them? Kind Regards, Linn

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mri_convert segmentation fault in bash
by Caspar M. Schwiedrzik 19 Jun '13

19 Jun '13

Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar

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mri_convert and flips
by Ray, Siddharth 19 Jun '13

19 Jun '13

Hi all, I have some of my subjects with their A/P and L/R labels flipped and using mri_convert convert command to make them right. I was little concerned that I am just providing command with -in_ourientation and -out_orientation info to get the right labeled images, is this anyway going to change my actual image data/pixel values? Please let me know. Thanks, -Siddharth

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Re: [Freesurfer] check orientation
by Bruce Fischl 19 Jun '13

19 Jun '13

Hi Brigitte, could you cc the list so that others can answer? I'm not sure what qualifies as "turned around" in FSL. They may have some preferred oreintation. In general we don't, and as long as the direction cosines are preserved (i.e. avoid analyze format!) you should be fine Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote: > Dear Bruce, > thank you very much! > Please excuse a (potentially naive) follow-up question (as we didn't use > external markers): So if in FSL some raw T1 data are found to be "turned > around", is it something that Freesurfer "takes care of" at a certain point > in the analysis or would you suggest to swap/correct the data after checking > w/ FSL and then analyze them with Freesurfer? > > Thanks again and kind regards! > Brigitte > > > 2013/6/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Brigette, > > not sure how you could do this except visually. Bring the images > up and verify that the directions that we specify are correct > (although of course this isn't possible for L/R unless you have > some type of external fiducial marker like a vitamin E tablet) > > cheers > Bruce > On Wed, 19 Jun 2013, Brigitte Dahmen wrote: > > Dear Freesurfer experts, > > is there a command in Freesurfer to check for > correct orientation (LAS vs. > PSR) of T1 images (similar to "fslhd" in FSL)? > > Thank you very much! > Brigitte > > > > > 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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Freesurfer June 2013