Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

how to read lh.avg_thickness data ?
by tulu＠ms36.hinet.net 11 Mar '12

11 Mar '12

Dear FS experts, is it possible to read cortical thickness data from lh.avg_thickness data into matlab for further process ? which tool I need to use ? sincerely yours Jung Lung Hsu

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How to access information in gamma.mgh and gammavar.mgh?
by Knut J Bjuland 10 Mar '12

10 Mar '12

Dear Sirs/Madams How to access information in gamma.mgh and gammavar.mgh? Which command should I use? Since it not explained in the tutorial. I want to use it to calculate effective population size? How large population size is needed to demonstrate a deviation between to population in cortical thickness? Best regards Knut J

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error in eating individual label values of area
by Kristine Beate Walhovd 09 Mar '12

09 Mar '12

Hi, I am trying to get the individual data points for a label I´ve made for an effect site on area. After making the label, I try to go to group and marked graphed vertices avg. It then just gives me this error message (pasted below)- this has happened on different boxes and w/ different effects. Is there some reason why I can´t do this on area? I am truly grateful for any idea on how to fix this! best, kristine element "error110" already exists in ".fsgdf-0.gwPlot" element "error110" already exists in ".fsgdf-0.gwPlot" while executing "$gw element create error$nClass$nErrorIndex -data $lBar -color $color -symbol splus -label "" -pixels 5" (procedure "FsgdfPlot_PlotData" line 91) invoked from within "FsgdfPlot_PlotData $iID" (procedure "FsgdfPlot_EndPointList" line 5) invoked from within "FsgdfPlot_EndPointList $gGDFID " (procedure "GDF_SendCurrentPoints" line 23) invoked from within "GDF_SendCurrentPoints" (procedure "GDF_PlotAvgMarkedVerts" line 4) invoked from within "GDF_PlotAvgMarkedVerts " invoked from within ".w.fwMenuBar.mbwTools.mw.cmw14 invoke active" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke active]" (procedure "tk::MenuInvoke" line 47) invoked from within "tk::MenuInvoke .w.fwMenuBar.mbwTools.mw.cmw14 1" (command bound to event) -- Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway

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Re: [Freesurfer] Fwd: Total WM and GM Vol in FS 5.0.0
by Bruce Fischl 09 Mar '12

09 Mar '12

Hi Dhinakaran. I think we include this in one of the stats files. Allison or Doug would know. cheers Bruce On Fri, 9 Mar 2012, Dhinakaran Chinappen wrote: > Hi Prof. Fischl and Dr.Greve, > I was wondering if you all got this email below? I sent in to the FS > listserv early yesterday. > > Would really appreciate your help on this matter of total WM and total GM. > > Much thanks, > Dhinakaran. > > > ---------- Forwarded message ---------- > From: Dhinakaran Chinappen <dchinapp(a)seas.upenn.edu> > Date: Thu, Mar 8, 2012 at 1:20 PM > Subject: Total WM and GM Vol in FS 5.0.0 > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Cc: Professor Lynnae Schwartz <schwartzl1(a)email.chop.edu> > > > Hi all, > I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical > GM and WM were made available in the final output files. > > What is the best way to calculate total gray matter volume (cortical and > subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are > there commands to calculate total cortical and total subcortical volumes of > GM separately? > > As for total white matter, is using the sum of the volumes of > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered > acceptable practice? Or should I go to the command line and use > mris_wm_volume? > > Thanks in advance for the clarification, > Dhinakaran. > > > > -- > > > >

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GLM for volume
by Linda Zhang 09 Mar '12

09 Mar '12

Dear all, In mris_preproc, I see that there's an option to choose volume for --meas, would this change anything in the subsequent GLM processes (mri_surf2surf, mri_glmfit)? I'm following the tutorial for group analysis, but I haven't seen any mention of measures apart from thickness, so is this even a valid question? For mri_surf2surf and mri_glmfit, what are the other options for areas apart from --cortex? Cheers, Linda

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DTI analysis: freesurfer vs DTI studio
by Ayaz, Muhammad 09 Mar '12

09 Mar '12

Dear All, I am new to freesurfer DTI analysis. Can anybody explain what is the advantage of using freesurfer for DTI analysis over DTI studio? Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Group comparison
by Allie Rosen 09 Mar '12

09 Mar '12

Hi All, I am trying to compare controls to patients. There is an interaction between group and age (i.e. the aging pattern is different for both groups). I did an interaction contrast and this was significant in the same areas that were significant in the original comparison. I can't switch to a DOSS model (because the slopes are different). Interestingly, I'm getting some areas increasing with age as well, but I'm not sure if these results are valid since some may argue I can't compare the group thicknesses if there is this interaction. There aren't topologic errors in my samples either. Given all this, I'm at a bit of a loss in terms of figuring out how to compare thicknesses between the groups. Can it still be done? Thank you, Allison

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save custom made path on surface as label
by Erhan Genc 09 Mar '12

09 Mar '12

Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: genc(a)mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-ge…

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tkregister2 error
by Daniel Preciado 09 Mar '12

09 Mar '12

Dear list, I'm having problems with the tkregister2 command, I input the following command: tkregister2 --mov ~/Desktop/input/*_d/mri/rawavg.mgz --noedit --s *_d --regheader --reg ~/Desktop/input/*_d/mri/register.dat Where I'm setting the directory of my subjects, and I get the following output /Desktop/input/*_d/mri/register.dat /usr/local/freesurfer/tktools/tkregister2.bin: No match. However, when I try a similar command with the sample data from bert (And after adjusting the subject folder settings) It works fine. I ran out of ideas on how to fix it, does anybody have any clue of what can I do? Thanks a lot for your help Regards

2 1

dimension mismatch in fieldsign-sess
by Greg Burgess 08 Mar '12

08 Mar '12

Hi freesurfers, I'm getting an error that I don't know how to track down. Running the following command: fieldsign-sess -a rtopy.self.lh -sphere -s CP10021_v5 I get the following error: reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Complex Reshaping 7208 Ripping Zeros ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. Rot (rad): 0 0 surfer: compute_fieldsign() As suggested in previous posts, I've tried running: recon-all -s CP10021_v5 -make all -dontrun recon-all -vno-check -s CP10021_v5 but no issues are reported, and I can't find any issues in the log files or output. Can anyone suggest a next step? Thanks, --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

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Freesurfer March 2012