Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

WM/Pial surfs Problem with SPGRs from 3T GE
by Thomas Fink 27 Jul '12

27 Jul '12

Hey Experts, As you can see from the picture, the autorecon does not work properly (for WM/Pial surfs) with my files: Especially in the temporal lobes. I am working with the SPGR files of a 3T GE Machine. Is there any way to optimize the autorecon results for SPGRs? (Except the lavish application of CPs.) Best regards Thomas On Mon, Jul 23, 2012 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Questions about correction over 2 hemispheres and MCC > (Reem Jan) > 2. More than two time-points in longitudinal base = Memory > allocation error? (Liz Bowman) > 3. Re: Talairach registration (Mojdeh Zamyadi) > 4. Subcortical segmentations (Jordan Pierce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Jul 2012 21:12:44 +0000 > From: Reem Jan <r.jan(a)auckland.ac.nz> > Subject: Re: [Freesurfer] Questions about correction over 2 > hemispheres and MCC > To: "Watson, Christopher" <Christopher.Watson(a)childrens.harvard.edu> > Cc: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > 3375B664D4A0834FB7D0C15D590A9EF11825DBC1(a)FMHS-MBX1.fmhs.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, J?rgen and Chris > > Thank you for elaborating further. I've gone with a Bonferroni correction > as I had a limited number of tests (a-priori hypothesis). But just out of > interest Chris, you mentioned you found correlations between subcortical > structures, do you have a reference I could look at? The tool that J?rgen > suggested requires we enter a correlation coefficient, so I wondered if I > could use published values or whether I'd need to calculate my own (if so, > could you please recommend a way of doing that in Freesurfer or FSL?) > > Many thanks in advance > > Kind regards > Reem > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of J?rgen H?nggi > Sent: Sunday, 22 July 2012 7:47 p.m. > To: Watson, Christopher > Cc: Freesurfer Mailinglist > Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres > and MCC > > Hi Chris > > Yes there are such tools. Bonferroni oder Sidak test that take into > account the correlated measures. Here you can find these tools > > http://www.quantitativeskills.com/sisa/calculations/bonfer.htm > > Cheers > J?rgen > > > On [DATE], "Watson, Christopher" <[ADDRESS]> wrote: > > > What about, for example, the correlations I've seen in a cohort of > subjects. > > > > In 158 subjects aged 10-19 (both controls and patients), the > > correlation between L & R thalamus is 0.91, and the correlations > > between L & R of caudate, putamen, pallidum, hippocampus, and amygdala > were all 0.75 or higher. > > > > I would think that a Bonferroni correction would be incredibly > > conservative and, in my opinion, just plain wrong because true > > significant diff's would be missed. Is there any principled way of > > dealing with multiple tests that are correlated? > > > > Thanks, > > Chris > > ________________________________________ > > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > > Sent: Saturday, July 21, 2012 12:01 PM > > To: Watson, Christopher > > Cc: Douglas N Greve; freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Questions about correction over 2 > > hemispheres and MCC > > > > Hi Chris, > > > > bonferroni will be overly conservative in that case, but we rarely > > really know the true covariance structure of the data, so we would > > rather err on the side of being conservative. > > > > cheers > > Bruce > > On Fri, 20 Jul 2012, Watson, Christopher > > wrote: > > > >> Hi Doug et al, > >> > >> The 2nd question is something I've wondered about. Doesn't a > >> Bonferroni correction assume that the measures are independent? > >> If so, I think in the case of subcortical structures, it is incorrect > >> to use this method, as e.g. the putamen and pallidal volumes are not > >> independent of one another. > >> If not, and it is acceptable to use when there are dependencies > >> between measures, how do you calculate the FWE? It wouldn't be equal > >> to alpha/n, unless I am misunderstanding something. > >> > >> Thanks, > >> Chris > >> ________________________________________ > >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu > >> [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve > >> [greve(a)nmr.mgh.harvard.edu] > >> Sent: Friday, July 20, 2012 2:38 PM > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] Questions about correction over 2 > >> hemispheres and MCC > >> > >> Hi Reem, it looks like you've done everything correctly (sorry for > >> the null result). As for your second, question, I don't think there > >> is a way other than Bonferroni. You can try FDR, but it makes the > >> interpretation a little messy. > >> doug > >> > >> On 07/19/2012 07:59 PM, Reem Jan wrote: > >>> > >>> Hi Doug > >>> > >>> I hope it?s okay that I double check I?m doing the correction over 2 > >>> hemispheres correctly and ask a question regarding correction for > >>> multiple comparisons. I will briefly describe what I have done: > >>> > >>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20). > >>> > >>> 1.I ran a surface thickness study: > >>> > >>> ?For the ?mri_glmfit? command, I used DOSS and specified a contrast > >>> of > >>> +1 -1 0 (Controls > MA) > >>> > >>> ?I ran a pre-cached simulation with the following command: > >>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos > >>> > >>> ?This simulation should only have corrected for the left hemisphere > >>> as I understand it. My cluster summary text file showed me that a > >>> cluster survived in the insula. I interpreted this as ?controls had > >>> higher grey matter thickness in this cluster located in the insula > >>> than drug addicts?. However, this was only corrected over the left > >>> hemisphere (when I ran the same simulation in the right hemisphere, > >>> nothing survived multiple comparison correction). > >>> > >>> ?I now wanted to correct the lh results for 2 hemispheres. From the > >>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2 > >>> ways, are both of these correct and give the same result? > >>> > >>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 > >>> spaces --no-sim csdbase > >>> > >>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos > >>> --cwpvalthresh 0.025 > >>> > >>> ?No clusters survived the Bonferroni correction over both hemispheres. > >>> So I assume I can no longer report this result? > >>> > >>> 2.I ran a subcortical volume study: > >>> > >>> ?I used SPSS to perform the statistical analysis on each of 14 > >>> subcortical structures (left and right). Is there a good way to > >>> correct for multiple comparisons, apart from Bonferroni, which would > >>> be very conservative? > >>> > >>> Many thanks for your advice. > >>> > >>> Kind regards > >>> > >>> Reem > >>> > >>> *Reem Jan*** > >>> > >>> BPharm (Hons), RegPharmNZ > >>> > >>> PhD Student / Pharmacist > >>> > >>> School of Pharmacy, Faculty of Medical & Health Sciences, The > >>> University of Auckland, Private Bag 92019, Auckland, New Zealand. > >>> > >>> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 > >>> > >>> F: +64 9 367 7192 > >>> > >>> *From:*freesurfer-bounces@nmr.mgh.harvard.edu > >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of > >>> *Douglas Greve > >>> *Sent:* Friday, 20 July 2012 11:52 a.m. > >>> *To:* freesurfer(a)nmr.mgh.harvard.edu > >>> *Subject:* Re: [Freesurfer] slice-by-slice predictors > >>> > >>> Sorry, not possible. > >>> > >>> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote: > >>> > >>> Hi! > >>> Is it possible to have slice-by-slice predictors in Freesurfer, and > >>> if so, how? > >>> Thanks, > >>> Caspar > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@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 > >> > >> -- > >> 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. > >> > >> > >> _______________________________________________ > >> 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 > > > > ---------------------------------------------------------------------------- > J?rgen H?nggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > > ---------------------------------------------------------------------------- > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 2 > Date: Mon, 23 Jul 2012 10:21:33 +1000 > From: Liz Bowman <ea_bowman(a)hotmail.com> > Subject: [Freesurfer] More than two time-points in longitudinal base = > Memory allocation error? > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SNT135-W17F702D9DC415BB91613828CDD0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hello, > I have several patients scans taken over multiple time points (up to nine > time points in some patients). I thought I might be able to use these to > create a base template for longitudinal processing, however the process > fails and exits with errors if I try to create a base with more than two > time points from a patient. > This is a sample of the error log of the most recent attempt, with three > timepoints: > Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- > diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. > transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: > 0.00156813 < 0.01 :-) > Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- > diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) > malloc: *** mmap(size=262144) failed (error code=12)*** error: can't > allocate region*** set a breakpoint in malloc_error_break to > debugMRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice > Cannot allocate memoryDarwin 550D-UOM88670.local 10.8.0 Darwin Kernel > Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 > For more details, see the log file > /Applications/freesurfer/subjects/KSx3/scripts/recon-all.logTo report a > problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > I would be grateful for any advice. > Regards, > EA Bowman > > >

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CSF and brain volume quantification.
by Matthew Goldfinger 27 Jul '12

27 Jul '12

Dearest gurus of all things Freesurfer, I am looking for a simple way to quantify the amount of CSF, the total volume of brain matter (excluding ventricular space if possible) and, as a check on these two, the total intracranial area. Essentially I need a way to compare how much room there is for the brain to move around and deform. Any ideas on how best to achieve these goals would be most appreciated. Best, Matthew

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FreeSurfer TrackVis Transforms
by Trietsch, Rayna 27 Jul '12

27 Jul '12

Hi, I would like to follow the workflow for the FreeSurfer TrackVis Transforms (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms) but I'm not sure how to get started. The first step is to load the trk data and divide the trk coordinates from the file by the voxel_size in the header. How do I do that? Is this done in matlab? Is there a way to export the trk coordinates into matlab? If anyone could help me get started with this, that would be great. Thanks. ~Rayna~

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Re: [Freesurfer] tracula -bedp - path
by Anastasia Yendiki 26 Jul '12

26 Jul '12

Hi Keith - This seems to be a different problem here, since all the bedpostx outputs are there and are loaded in without a problem. The error occurs after that. What's the size of your images? Does the mask file look normal? Thanks, a.y On Thu, 26 Jul 2012, Keith Yoder wrote: > Hi, > > Was there any resolution to this issue? I'm having a similar problem > running trac-all on a Linux cluster. > > I think bedpostx works if I call it directly from the command line twice. > The first time, bedpostx_postproc.sh doesn't seem to work and the > *samples.nii.gz files are only created if I rerun bedpostx. However, > trac-all...-path fails. I've attached the trac-all-path output and pasted > the relevant section below: > > Creating output directory/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dpath/lh.cst_AS_av > g33_mni_flt > Loading DWIs from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/dwi.nii.gz > Loading mask from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/diff/aparc+ > aseg_mask.flt.nii.gz > Loading BEDPOST parameter samples from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri.bedpostX > Loading segmentation map from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/mni/aparc+a > seg.nii.gz > Loading b-values from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvals > Loading gradients from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvecs > Segmentation fault (core dumped) > > Here are the contents of the subjects bedpostX directory: > > bvals > bvecs > commands.txt > diff_slices > dyads1_dispersion.nii.gz > dyads1.nii.gz > dyads2_dispersion.nii.gz > dyads2.nii.gz > logs > mean_dsamples.nii.gz > mean_f1samples.nii.gz > mean_f2samples.nii.gz > mean_ph1samples.nii.gz > mean_ph2samples.nii.gz > mean_S0samples.nii.gz > mean_th1samples.nii.gz > mean_th2samples.nii.gz > merged_f1samples.nii.gz > merged_f2samples.nii.gz > merged_ph1samples.nii.gz > merged_ph2samples.nii.gz > merged_th1samples.nii.gz > merged_th2samples.nii.gz > monitor > nodif_brain_mask.nii.gz > xfms > > Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and > trac-all.log for the subject. Let me know if there is any other information > you need. > > Thanks in advance, > Keith > -- > Keith YoderPhD Candidate, Integrative Neuroscience > Social Cognitive Neuroscience Laboratory > The University of Chicago > 5846 S. University Avenue, Kelly 312 > Chicago, IL 60637 > Phone: 574-215-9678 > kjyoder(a)uchicago.edu > > > > > On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Judit, > > 1. If you can run bedpostx directly then you should do: > bedpostx /usr/local/freesurfer/subjects/C001/dmri > > Note that this dmri directory and the one you tried to run > bedpostx_single_slice.sh on are different, so I'm not sure which > location is the right one where your data is, but in any case > you don't need to run bedpostx_single_slice.sh. > > 2. The error seems to occur either when it's reading the bvecs > file, or right after that when it's accessing the bedpostx > outputs. So I'd try to look those for that subject and see if > everything is ok. > > Hope this helps, > a.y > > On Fri, 7 Oct 2011, Judit Haasz wrote: > > > Hi, > > I ran into 2 problems related to tracula. > > 1. trac-all -bedp command exits with following > message. > > WARN: Running FSL's bedbost locally - this might > take a while > >> > WARN: It is recommended to run this step on a > cluster > >> > bedpostx_seychelles > /usr/local/freesurfer/subjects/C001/dmri > >> > subjectdir is > /usr/local/freesurfer/subjects/C001/dmri > >> > Making bedpostx directory structure > >> > Queuing preprocessing stages > >> > [: 223: NONE: unexpected operator > >> > [: 314: NONE: unexpected operator > >> > [: 327: xbedpostx_pre: unexpected operator > >> > [: 486: x: unexpected operator > >> > [: 486: -le: argument expected > >> > Queuing parallel processing stage > >> > [: 223: NONE: unexpected operator > >> > [: 327: xbedpostx: unexpected operator > >> > [: 486: x53: unexpected operator > >> > 0 slices processed > >> > Queuing post processing stage > >> > [: 223: NONE: unexpected operator > >> > [: 314: NONE: unexpected operator > >> > [: 327: xbedpostx_post: unexpected operator > >> > [: 486: x: unexpected operator > >> > [: 486: -le: argument expected > >> > > > This problem has been posted in May and June. > bedpostx from command line > runs perfectly and that is how I have been running > it so far. One of u > suggested to try the following: > > /usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffu > sion_tutorial/dtisubjects2005/subj_523/dmri > 2 1 1000 1250 25 1 0 > > then I got: > > ** ERROR (nifti_image_read): failed to find header > filefor'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ > dmr > i/data_slice_0000' > **ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisub > jects2 > 005/subj_523/dmri/data_slice_0000): bad header info > ERROR: failed to openfile/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ > dmri > /data_slice_0000 > ERROR: Could not openimage/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523 > /dmri > /data_slice_0000 > Image Exception : #22 :: Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 > 3/dmri > /data_slice_0000 > > An exception has been thrown > Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 > 3/dmri > /data_slice_0000Trace: read_volume4DROI. > > Done > > Can u suggest a reason behind all this? This happens > on Linux machine > (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM > Version: Java > 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM > mixed mode). > On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz > 6-core Intel Xeon > processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp > runs well. > > My other question is: > trac-all -path exists with error (in case of a > single subject): > > Loading DWIsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /dwi.nii.gz > Loading maskfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dlab > el/diff/aparc+aseg_mask.bbr.nii.gz > Loading BEDPOST parameter samplesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > .bedpostX > Loading segmentation mapfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dlab > el/mni/aparc+aseg.nii.gz > Loading b-valuesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /bvals > Loading gradientsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /bvecs > Segmentation fault > Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar > 18 18:42:20 UTC 2011 > x86_64 GNU/Linux > > trac-paths exited with ERRORS at Fri Oct 7 10:21:20 > CEST 2011 > > thanks for help. > Judit > > > > > > _______________________________________________ > 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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Trouble downloading tutorial data
by Vy Dinh 26 Jul '12

26 Jul '12

Dear surfers, I'm having trouble downloading the longitudinal data form the website. This is the command I used: curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz Error message: curl: (56) FTP response reading failed Am I typing the filename in wrong? Also, I tested the command to download another file and it work, but not for the longitudinal data. Thanks, Vy

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Re: [Freesurfer] stats
by Douglas N Greve 26 Jul '12

26 Jul '12

Hi Viola, I have a different work flow for you. When you run FDR, it will change the "Min" value under "Threshold". Go to a terminal and cd to the contrast directory of your qdec output folder, then run the commands below. It is assumed below that the threshold you want to use is 3.37. You should replace that with the threshold found by FDR. The files with the "337" can be named anything. I just put "337" to make them unique. doug cd QDECOUTPUTDIR/CONTRAST mri_surfcluster --in sig.mgh --thmin 3.37 --subject fsaverage --hemi lh \ --sum cluster.337.summary.dat --ocn cluster.337.seg.mgh \ --annot aparc --oannot ./cluster.337.seg.annot mri_segstats --seg cluster.337.seg.mgh --excludeid 0 --i ../y.mgh \ --sumwf cluster.337.wf.dat cluster.337.wf.dat will be a text table with number of rows equal to the number of subjects and number of columns equal to the number of clusters. To see which cluster is which, run tksurfer fsaverage lh inflated -annot ./cluster.337.seg.annot -curv -gray Each cluster will have a color and a number. On 07/24/2012 02:52 AM, Oertel, Viola wrote: > Okay. And how I do the clusterwise correction? In which window does it appear? > > Viola > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Gesendet: Dienstag, 24. Juli 2012 04:06 > Bis: Oertel, Viola; free surfer > Betreff: Re: [Freesurfer] stats > > Neither of these tables is the one you want. Those are tables of > standard freesurfer ROIs and are unrelated to your map-based analysis. > You will need to do the cluster-wise correction for multiple comparisons > using the voxel-wise threshold that FDR found. Set the cwp (cluster-wise > p-value) threshold to 1 so that you get all of the clusters. When you do > the clusterwise correction, it will produce a file with the values you want. > doug > > On 7/23/12 2:44 AM, Oertel, Viola wrote: >> Hi Doug, >> I did the correction for multiple comparisons (FDR 0,05). Then, I have seen significant clusters in the map. After that, I run the generate tables stat (or so on) button and got two tables with thickness values. But I don't know which one of the tables is the right one because this step produced two files: >> >> >> lh.aparc.a2005s.thickness.stats and >> lh.aparc.thickness.stats >> >> May you tell me which one is the right, and are these results only the significant areas, or all computed once? >> >> >> Thanks, >> Viola >> >> ________________________________________ >> Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Gesendet: Freitag, 20. Juli 2012 21:26 >> Bis: Oertel, Viola; Freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: AW: [Freesurfer] stats >> >> Hi Viola, those stats tables are unrelated to your map-based exploratory >> analysis. If you have clusters in your map, you should run the >> correction for multiple comparisons. This will give you significant >> clusters. It will also produce a table of mean thicknesses in each >> cluster for each subject which you can then import to SPSS. >> doug >> >> On 07/19/2012 04:35 PM, Oertel, Viola wrote: >>> Yes. I did the contrast pat. vs. cont and see some significant regions on the display. After that, I did this "generate" stats table. My idea was to put this scores into SPSS and run the inferential statistics there. But I am not sure which table I have to use. What I want to use are the thickness values of each participant of all significant regions which I can see on the template. >>> Currently, I am not sure what kind of regions the tables show? Are that all regions, only the significant ones of the specific contrast I compute? I have seen that both tables show different regions. But I currently don't how the selection works. >>> >>> May you help with that? >>> >>> Thanks and best regards, >>> >>> Viola >>> >>> ________________________________________ >>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 19. Juli 2012 17:30 >>> Bis: freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] stats >>> >>> Those stats tables just gives statistics (means, standard deviations) >>> for thickness in different regions. They do not have inferential >>> statistics. Have you run an analysis on patients vs controls? >>> doug >>> >>> On 07/19/2012 09:27 AM, Oertel, Viola wrote: >>>> Dear Doug, >>>> >>>> I have a question: when I create the stats tables, there are two tables: >>>> >>>> lh.aparc.a2005s.thickness.stats and >>>> >>>> lh.aparc.thickness.stats >>>> >>>> which one is the right one if I want to get the thickness values of >>>> the significant clusters from the main effect (pat. / controls)? >>>> >>>> Thanks and best regards, >>>> >>>> Viola >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >> -- >> 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 > > -- 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

1 0

Surface number of vertices mismatch
by Pablo Polosecki 26 Jul '12

26 Jul '12

Dear List, I am trying to show my results on Caret's F99 atlas, in Caret. For this I already managed to take my anatomical (white, pial etc) surfaces and register them to F99 in Caret, which works fine. I am trying now to get my functional p-map (initially a nifti volume) into Caret too to overlay them on my anatomical surface together with the atlas information. For this my plan s the followign 1-Convert my nifti p-map volume into a surface using mri_vol2surf 2-Convert the resulting surface into caret surface using caret_command tools. 3-Apply to the resulting surface the same transformation I applied to my anatomical surfaces to have them all in register with Caret's F99 atlas. It seems like step 1 works fine, but when I try to run step too, Caret complains that my anatomical surface doesn't have the same number of vertices as my functional surface. Indeed, when opening the anatomical surface in maltab with read_surf, it seems to have exactly twice the number of vertices that my functional surface has (I cannot open it with read_surf for some reason but I see the number when I open it with a text editor or when I look at the output of mri_vol2surf). Would anyone have a suggestion as to why this is the way it is and how I could have my 2 surfaces have the same number of nodes? Thank you very much, Pablo

4 7

FW: bringing surfaces from different subjects into the same space in matlab
by Rebelo Ferreira Marques Jose Pedro 26 Jul '12

26 Jul '12

Dear freesurfer experts, I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct: I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces. At that moment my different subjects surfaces had different number of vertices and I would like to average them together. Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data. Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface. I then created a new paint surface where only those vertices were taken into account. Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas? Is there a better way to do this? Thanks in advance, Jose Marques

3 2

CSF segmentation and cortical ribbon
by Christopher Coello 26 Jul '12

26 Jul '12

Dear Freesurfer users, I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels. Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned. My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ? Thanks a lot in advance, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516 -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

2 5

recon-all error
by Yigal Agam 25 Jul '12

25 Jul '12

Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-000015-000001.dcm -mail etanski(a)nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/manoach/dod/subjects/DODASD012/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz sysname Linux hostname compute-0-88 machine x86_64 user etanski input ./tmp.mri_nu_correct.mni.14699/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14699/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading ./tmp.mri_nu_correct.mni.14699/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.14699/nu2.mnc ./tmp.mri_nu_correct.mni.14699/nu2.mnc mul Linux compute-0-88 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DODASD012 exited with ERRORS at Wed Jul 25 12:27:28 EDT 2012 For more details, see the log file /autofs/cluster/manoach/dod/subjects/DODASD012/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any suggestions? Thanks, Yigal

2 1

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Freesurfer July 2012