Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by Pedro Paulo de Magalhães Oliveira Junior 17 May '11

17 May '11

I'm having this error in the recon-all #-------------------------------------------- #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints?

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different V1 sizes for same subject in two different sessions
by Ritobrato Datta 17 May '11

17 May '11

Hello All, I have estimated V1 using Hinds and Fischl method for some subjects scanned on two different days. I've been going through the V1 surface area data for these. One thing that concerns me is that is seems that very different V1 sizes are reported for the same subject when scanned on different dates and each run through the cross sectional stream. I am trying to check the test-re-test values for these. Any idea why this is so and whats a better method to do the comparison ? Thanks Ri

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Re: [Freesurfer] Question about volumetric group analysis
by Michael Harms 17 May '11

17 May '11

For subcortical structures, you could consider using a covariate measure that itself includes subcortical gray matter. Not sure if the latest FS version has such a measure automatically constructed or not. In the past, we have used "whole brain volume" as a covariate for analysis of both cortical and subcortical structures, with "whole brain volume" defined as the volume contained within the pial surface (obtained using mris_volume) minus the volume of the lateral ventricles (contained within the aseg). cheers, -MH On Tue, 2011-05-17 at 10:19 -0300, Fernanda Palhano wrote: > Thanks, Michael. > > I have a follow up question. > If I understood, I should use the total cortical gray matter volume to > control for a global change > in cortical brain volume, so for exemple, if I'm interested in the > volume of parahippocampal gyrus, > I can normalize this way. And, once I have the measures for both the > hemispheres separately, I have to use the total cortical gray matter > of each one > to normalize? > But for other structures like hippocampus or amigdala it makes sense > to control using volume of gray matter? Or, I continue using the ICV? > > Thanks again, > > > On Tue, May 17, 2011 at 9:57 AM, Michael Harms > <mharms(a)conte.wustl.edu> wrote: > > Hi Fernanda, > The choice between ICV vs a measure of total "brain volume" or > total > cortical gray matter volume depends on whether you want to > control for > potential overall brain atrophy. Using ICV will control for > overall > "head size", but not for potential overall brain atrophy > (e.g., with > age, or related to dementia). Using total cortical gray > matter will > control for overall brain atrophy and thus would allow you to > say that > changes in a given structure were "above and beyond" any > existing global > atrophy. > > Personally, I find it more informative to control for > potential global > atrophy, and thus use total cortical gray matter rather than > ICV. After > all, if a structure is decreased in size, but the overall > brain is > decreased as well, you have not established anything regarding > the > specificity of that change to the structure of interest if you > use ICV > as the covariate. > > cheers, > -MH > > > On Tue, 2011-05-17 at 09:19 -0300, Fernanda Palhano wrote: > > Hello, > > > > I have two questions about volumetric analysis: > > First: Are the volume measures in the files aseg.stats or ? > > h.aparc.stats (Gray Matter Volume) already normalized by > ICV? Or > > should I divide > > all the structure volumes which I want to compare between > subjects by > > the ICV of each subject? > > Second: When comparing gray matter volumes the correct is > use the ICV > > or the total cortical gray matter volume to normalize? And > if I have > > to use the total cortical gray matter volume, how can I > obtain it? I > > know that this information is in the aseg.stats file, but I > was > > wondering if I can use asegstats2table to extract it. > > > > > > Thank you very much, > > > > Fernanda > > > > > _______________________________________________ > > 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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Question about volumetric group analysis
by Fernanda Palhano 17 May '11

17 May '11

Hello, I have two questions about volumetric analysis: First: Are the volume measures in the files aseg.stats or ?h.aparc.stats (Gray Matter Volume) already normalized by ICV? Or should I divide all the structure volumes which I want to compare between subjects by the ICV of each subject? Second: When comparing gray matter volumes the correct is use the ICV or the total cortical gray matter volume to normalize? And if I have to use the total cortical gray matter volume, how can I obtain it? I know that this information is in the aseg.stats file, but I was wondering if I can use asegstats2table to extract it. Thank you very much, Fernanda

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Segmentation Fault
by Chindhuri Selvadurai 17 May '11

17 May '11

Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command a while ago, and the command worked fine at that time. Do you have any idea what would be causing this error? The output is included below: Command: selxavg3-sess -analysis mandyrh3 -fwhm -s PBMCT15 Subjects Dir: /cluster/manoach/milton/subjects FreeSurfer v. Stable 5 Session: /autofs/cluster/manoach/milton/subjects/PBMCT15 ---------------- Fri May 13 12:21:58 EDT 2011 Run: 012 ---------------- Fri May 13 12:21:58 EDT 2011 Update not needed Fri May 13 12:21:58 EDT 2011 register-sess completed PBMCT15 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s PBMCT15 -d /autofs/cluster/manoach/milton/subjects -fsd bold -rlf task -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15 RunList: 012 ------- ************************** ----------- ------- Motion Correcting Run 012 ----------- ------- ************************** ----------- sess = PBMCT15 Fri May 13 12:21:58 EDT 2011 mc-afni2 --i 012/f.nii --t 012/template.nii --o 012/fmcpr.nii.gz --mcdat 012/fmcpr.mcdat /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_info --nframes --o /tmp/mriinfo.3377 012/template.nii log file is 012/fmcpr.nii.gz.mclog mcdat file is 012/fmcpr.mcdat tmp dir is 012/tmp.mc-afni2.3377 #@# -------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 012/template.nii 012/tmp.mc-afni2.3377/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from 012/template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998297, -0.0395807, 0.0428535) j_ras = (0.0411249, -0.998513, 0.0357732) k_ras = (0.0413739, 0.0374746, 0.998441) changing data type from short to float (noscale = 0)... writing to 012/tmp.mc-afni2.3377/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/manoach/milton/subjects/PBMCT15/bold mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float mri_convert 012/f.nii 012/tmp.mc-afni2.3377/invol.nii.gz -odt float Segmentation fault Thanks! Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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missing tutorial data for Longitudinal Processing - Tutorial
by Knut J Bjuland 17 May '11

17 May '11

Hi I am trying to follow the Longitudinal Processing - Tutorial but it appear that the tutorial data is missing at the server? Has the file been rename or moved to another place? Knut J Bjuland

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Re: [Freesurfer] freeview: creating ROIs, measuring volume
by Lynette Silva 16 May '11

16 May '11

Thanks Ruopeng, I tried tracing the outline with the freehand tool, and I also tried setting waypoints around the surface area of my ROI. What tools would you recommend? Thanks again! Lynette On Mon, May 16, 2011 at 3:46 PM, Ruopeng <rpwang(a)nmr.mgh.harvard.edu> wrote: > When you say tracing an ROI by hand in freeview, did you fill it or just > traced the outline? In any case, you will need to do this on each slice > by hand. However, there're various options and tools in freeview that > may help speed up the process dramatically. > > Ruopeng > > On 5/16/11 5:12 PM, Lynette Silva wrote: >> Hello All, >> >> I think I am missing a key step in creating an ROI in freeview. I have >> been tracing an ROI by hand in freeview, and saving as a label. Then I >> use mri_label2vol followed by mri_label_volume, and this works >> GREAT... except the output has far too few voxels to be the whole >> volume of my ROI. >> >> How can I select my ROI in three planes in freeview so that I can >> eventually get a volume output in mm^3? Someone here suggested I >> trace by hand on every slice in every view, but that can't be the way >> it's done, is it (please say it isn't)? >> >> Thanks! >> Lynette >> > > _______________________________________________ > 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. > > -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico

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freeview: creating ROIs, measuring volume
by Lynette Silva 16 May '11

16 May '11

Hello All, I think I am missing a key step in creating an ROI in freeview. I have been tracing an ROI by hand in freeview, and saving as a label. Then I use mri_label2vol followed by mri_label_volume, and this works GREAT... except the output has far too few voxels to be the whole volume of my ROI. How can I select my ROI in three planes in freeview so that I can eventually get a volume output in mm^3? Someone here suggested I trace by hand on every slice in every view, but that can't be the way it's done, is it (please say it isn't)? Thanks! Lynette -- Lynette M. Silva, M.S. Doctoral Candidate Department of Psychology University of New Mexico

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Re: [Freesurfer] mri_segstats error
by Douglas N Greve 16 May '11

16 May '11

yes, that is fine. doug Fernanda Palhano wrote: > Doug, > > I have another question about doing a volumetric group analysis. I > used the command: > asegstats2table --subjects V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 > V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 > V31 V32 --tablefile asegstats_new.txt --common-segs > To extract volume information for all my subjects. I'm interested in > use Left-Hippocampus and Right-Hippocampus to perform my group > analysis. Is it correct just import the columns data ( > Left-Hippocampus and Right-Hippocampus) in some statistical software? > > Thanks a lot, > Fernanda > > On Mon, May 16, 2011 at 4:25 PM, Fernanda Palhano > <nandapalhano(a)gmail.com <mailto:nandapalhano@gmail.com>> wrote: > > Doug, > > Actually, the file aseg.stats already exists. I think I only have > to use asegstats2table > <http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table> to > combine the stats from all my subjects. > > > Fernanda > > > On Mon, May 16, 2011 at 4:15 PM, Fernanda Palhano > <nandapalhano(a)gmail.com <mailto:nandapalhano@gmail.com>> wrote: > > Yes. > > [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] > fernandapalhano% ls > aseg.stats lh.aparc.a2009s.stats > lh.supramarg.stats rh.aparc.a2009s.stats wmparc.stats > lh.aparc.a2005s.stats lh.aparc.stats > rh.aparc.a2005s.stats rh.aparc.stats > > Fernanda > > > On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > wrote: > > does the stats directory exist? > doug > > Fernanda Palhano wrote: > > Hello, > > I'm trying to use mri_segstats to obtain some > subcortical volume stats. When running the command > line both in the tutorial data or in my own data, I > have the follow error: ERROR: could not open > stats/aseg.stats for writing > > [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial] > fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum > stats/aseg.stats --pv mri/norm.mgz --ctab-default > --excludeid 0 --brain-vol-from-seg --brainmask > mri/brainmask.mgz --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR > --etiv --subject 004 > Using defalt ctab > /Applications/freesurfer/FreeSurferColorLUT.txt > > $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 > greve Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum > stats/aseg.stats --pv mri/norm.mgz --ctab-default > --excludeid 0 --brain-vol-from-seg --brainmask > mri/brainmask.mgz --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR > --etiv --subject 004 > sysname Darwin > hostname Fernanda-Palhanos-Mac-Pro.local > machine i386 > user fernandapalhano > atlas_icv (eTIV) = 1792580 mm^3 (det: 1.086761 ) > ERROR: could not open stats/aseg.stats for writing > > Any ideas? > > Thanks, > Fernanda > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > -- 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

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Re: [Freesurfer] two questions
by Anderson Winkler 16 May '11

16 May '11

Hi Ilana, Normality isn't a requirement for FDR to work. However, if the distribution of your statistic isn't normal **under the null hypothesis**, neither follows t, F or any other well known parametrizable distribution, then you have to obtain p-values in a different way, not from the cdf/pdf of these distributions. Most likely you'd have to use permutations. But do you have any evidence that your cortical thickness measurements are not normal after regressing out your model? The histogram that appears in qdec window tells you the frequency of the statistics across space for all the vertices. This is not the same as the distribution of the residuals, nor of the statistic for each vertex if the same experiment were to be repeated many, many times. You could apply a normality test to each vertex using the residuals of the GLM. I wouldn't bother much with that, though. I see no reason why thickness measurements wouldn't be normal. All the best! Anderson On 05/16/2011 03:18 PM, Ilana Hairston wrote: > thanks! very helpful. > not to be argumentative, but if my Z distribution is not normal, is there meaning to FDR? > > > On May 16, 2011, at 2:08 PM, Anderson Winkler wrote: > >> Hi Ilana, >> >> I'll let the first question to the FS experts to answer. For the second: >> >>> 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? >> Even if the effect exists, your experiment wasn't able to detect it as >> significant, since nothing survived the multiple testing correction you >> used. Most scientific journals wouldn't accept conclusions based on >> non-significant results, despite how compelling the hypothesis might be. >> >>> 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. >> The p-values are in the files sig.mgh, in subdirectories of the qdec >> directory where the results of the analyses were stored. There are >> multiple ways to open and a suggestion is to convert to ASCII using the >> -c option of mris_convert, then open in Octave/Matlab with dlmread. >> >>> 3. Is there a way to set FDR separately for positive and negative values? >> The plain answer is no, because for the FDR procedure to work, it's >> necessary that the p-values under the null are uniformly distributed >> between 0 and 1 (from the definition of p-values). If you drop part of >> your distribution, then the p-values are no longer distributed like >> that. It turns out, however, that in some particular cases, part of the >> distribution does not actually exist (see Self& Liang, J Am. Stat >> Assoc, 1987 for some cases, particularly the Cases 5 and 7). A >> workaround is to divide the q by a constant that depends on the fraction >> of the distribution that known to be missing (e.g., for Case 5, instead >> of q=0.05, one could use q=0.025 to obtain the same 5% of false >> discoveries). However, these particular cases I believe don't apply to >> your scenario, so please, refrain from applying FDR separately only on >> positives or negatives. >> >> There is also a second reason for not applying FDR separately: for each >> set (positive and negative), the number of tests would be reduced, on >> average, by half, alleviating the multiple testing problem and making, >> on average, twice as easy for results to survive the threshold, >> inflating the amount of false discoveries, something undesired. >> >> Hope this helps! >> >> All the best, >> >> Anderson >> >> >> On 05/16/2011 09:53 AM, Ilana Hairston wrote: >>> Hi there, >>> First the simple question - is there a way to run mris_anatomical_stats on all my subjects at once generating a single output file? >>> >>> Second - actually comprised from several questions: when looking a the unthresholded group analysis on cortical thickness (in the averaged space), the distribution of negative and positive z values is not necessarily normal. i.e., the range of negative values maybe be 0 to -5, and the range of positive values 0 to +3. >>> 1. Is it legitimate toconclude from this that the regressor's overall effect is that it's associated with a thinner cortex (e.g., older subjects have a thinner cortex), eventhough most of the cortex does not survive FDR or multiple comparison correction? >>> 2. If yes, is there a way of exporting the distribution, or getting some numerical representation of the negative and positive values across the cortex, or within aparc annotations. >>> 3. Is there a way to set FDR separately for positive and negative values? >>> >>> thanks >>> ilana >>> >>> >>> >>> >>> >>> >>> Ilana Hairston >>> hairstonster(a)gmail.com >>> ************************* >>> Our ignorance is not so vast as our failure to use what we know. >>> —M. King Hubbert, peak oil prophet >>> >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Ilana Hairston > hairstonster(a)gmail.com > ************************* > Our ignorance is not so vast as our failure to use what we know. > —M. King Hubbert, peak oil prophet > > > > >

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Freesurfer May 2011