Freesurfer

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30088 discussions

White matter intensity normalisation
by Charlotte Bernard 12 Mar '12

12 Mar '12

Dear Freesurfer users, I run FS on my 670 subjects. All the scans were acquired on a 1.5T Philips scan. I noticed that my values in the WM are near 100-110 but not exactly 110. I think it is a problem! Is it link to the 1.5T? How can I fix it? I joined my log file of QA tools: could you help me to undertand the output? wm-anat-snr results: SNR: Anatomical signal-to-noise ratio in white matter mWM: Mean white matter intensity value stdWM: Standard deviation of white matter intensity value voxWM: Total number of white matter voxels in eroded mask SubjID SNR mWM stdWM voxWM 1 13,37* 104,18 7,79* 24181 <------ 2 14,79* 105,90 7,16* 22148 <------ 3 13,57* 104,75 7,72* 37341 <------ 4 12,67* 104,18 8,22* 29311 <------ 5 14,36* 105,44 7,34* 48083 <------ 6 11,40* 103,92 9,11* 47704 <------ 7 14,52* 104,71 7,21* 25706 <------ 8 9,92 101,42 10,22 40187 9 11,31* 104,28 9,22* 22967 <------ 10 11,61* 102,92 8,86* 19850 <------ 11 14,78* 105,05 7,11* 26607 <------ 12 11,36* 105,33 9,27* 15465 <------ 13 11,30* 103,69 9,18* 34685 <------ 14 11,73* 105,20 8,97* 40471 <------ 15 11,92* 104,04 8,73* 13777 <------ 16 9,46 102,04 10,79 30314 17 12,60* 106,40 8,44* 38432 <------ I thought it can help me to quickly identify the subjects who didn't work for this step. For example, the subject n°8 has a problem? Thanks, Charlotte

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Buckner Tutorial data set
by Ahmed, F, Me <fahmed＠sun.ac.za> 12 Mar '12

12 Mar '12

Hello Freesurfer experts, I'm trying to extract the data from the tutorial dataset "buckner_data-tutorial_subjs.tar.gz" by typing this command "tar -xvzf buckner_data-tutorial_subjs.tar.gz" and after it finished, I got this error message: tar: buckner_data/tutorial_subjs/130: Cannot create symlink to `group_analysis_tutorial/130': Operation not supported buckner_data/buckner_public_distribution.README.txt tar: buckner_data/tutorial_subjs/fbert-feat/fbert.gfeat/.files: Directory renamed before its status could be extracted tar: buckner_data/tutorial_subjs/fbert-feat/fbert1.feat/.files: Directory renamed before its status could be extracted tar: buckner_data/tutorial_subjs/fbert-feat/fbert2.feat/.files: Directory renamed before its status could be extracted tar: Error exit delayed from previous errors [root@localhost EONCS]# Can someone please explain to me why this happened and what I can do to fix this? Thank you and Kind Regards, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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aseg.mgz doe not look as good after Longitudinal Processing on 5.1
by Brain Apprentice 12 Mar '12

12 Mar '12

Hi Surfers, I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good for the most part, the aseg segmentation are often looking much much worse. I have attached a sample screen grab to show you what I mean. The images on top are of the Longitudinal Processed axial and sagittal views. The images on bottom are of the same subject before the Longitudinal Processing has occurred. It is possible I am doing something wrong. I just thought I would throw it out to the experts to see if they are having similar experiences. Thanks very much, B.A.

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read and write thickness file ?
by tulu＠ms36.hinet.net 11 Mar '12

11 Mar '12

Dear FS experts, I would like to read cortical thickness data from lh.thickness.fwhm10.fsaverage.mgh file and do some calculation. then save the result as thickness file. which matlab script should I use ? sincerely yours Jung-Lung, Hsu

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Re: [Freesurfer] How to access information in gamma.mgh and gammavar.mgh?
by Douglas Greve 11 Mar '12

11 Mar '12

It's a "volume" files with about 160000 values. If you know which vertex you want, you can load it into matlab with MRIread.m On 3/11/12 1:44 PM, Knut J Bjuland wrote: > Hi Doug > > Could you please explain how I can extract the standard deviation in > > rstd.mgh? Should I use mri_info or matlab? > > Knut J > > > > On 10. mars 2012 23:17, Douglas Greve wrote: >> Hi Knut, you will need the effect size which is gamma/rstd where rstd is >> the the standard deviation of the noise which is stored in rstd.mgh in >> the glm directory. >> doug >> >> On 3/10/12 10:35 AM, Knut J Bjuland wrote: >>> 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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> 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. >> >> >> > >

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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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