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16 participants
30084 discussions

list of normals to triangle vertices
by Krieger, Donald N. 13 Oct '15

13 Oct '15

Hi everyone, I need to create the vector normal to the surface at each "white" vertex. I would like to end up with 7 fields in each entry: 1 Vertex number 2-4 RAS coordinates 5-7 RAS components of the normal vector pointed from ctx --> wm mri_annotation2label gets me the first 4. I just don't want to reinvent the wheel getting the normal. If there's a way to get freesurfer to kick out the normals, that would be best. Here are naïve questions that arise out of this problem: 1. Is there a simple way to identify which vertices are "nearest neighbors" other than measuring and sorting the distances between each and all the others i.e. which ones form a triangle? I understand to use the normalized average of the 6 triangles which include the vertex. 2. Is there a simple way to identify the order of the sides of each triangle so that their cross product is ordered correctly to produce ctx --> wm? Thanks for your help with this. Don

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DEPRECATED warning in Freesurfers
by Peter Wendorff 13 Oct '15

13 Oct '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I'm working with freesurfer as a software developer in a cloud project. My task is to enable control of freesurfer via network (e.g. REST interfaces). That works fine so far, but I stumbled over the following pearl deprecated warning: "Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer//mni/bin/sharpen_volume line 153." Which has been printed to the log files repeatingly. I'm not a pearl expert, but I think, it's due to a more up to date pearl version used here, that deprecated the usage of ? delimiters for patterns without explicit operator. Using / as a delimiter works fine. I changed that locally to (new line 153): ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; (the original code here was): ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; I'm not sure this is the best solution. It's even not strictly necessary to change this - it's only a warning that's thrown; but I think, it's useful. How can I submit this as a patch? Is it enough to report here? What to do? regards Peter Wendorff P.S.: For referene the header parameters of my sharpen_volume for revision comparison: #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author: bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header - ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGTa5kACgkQi8ffXNvWmYSCUQCghMg1EffqfeJK4PSfo20uF8/J H0MAnjJc0WbHPf5gLDUw70K8fnQPjS+L =g+6e -----END PGP SIGNATURE-----

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Re: [Freesurfer] LME toolbox for longitudinal FA volume maps ?
by Matthieu Vanhoutte 13 Oct '15

13 Oct '15

Dear experts, Could anyone please help me ? My group has small size (7 subjects) with non equally spaced different timepoints (from 2 up to 4). Best regards, Matthieu Le 30 sept. 2015 13:57, "Matthieu Vanhoutte" <matthieuvanhoutte(a)gmail.com> a écrit : > Hi Martin, > > Thank you for helping ! > > 1) What should I use for the parameter estimation: "mass univariate" or Novel > mass-univariate tools (spatiotemporal models)" ? > > 2) I have one group of subjects with different timepoints (non equally > spaced and different numbers of timepoints), and would like to see the > significant change of FA according to time. Will LME study allow me to get > this change and how to define contrast to assess it ? Are the results of > this longitudinal study directionals, i.e. is it possible to establish an > increase or decrease of FA in significant regions according to time ? > > 3) Should the covariates (age, gender...) be demeaned or centered ? > > 4) Has the accurate time variable to be in years absolutely or could it > be also in days ? > > > Best regards, > > Matthieu > > > 2015-09-29 17:11 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: > >> Hi Matthieu, >> >> use lme_mass_fit_vw and the y is a simple vector. I would mask the image >> before doing this and only pass the brain voxels (to increase speed and >> reduce comparisons). >> >> Best, Martin >> >> >> On 09/29/2015 10:43 AM, Matthieu Vanhoutte wrote: >> >> Hi Martin, >> >> I understand for the multiple comparisons problem. But if I consider a >> voxel-by-voxel analysis just as hippocampal volume (lme_fit_FS for >> estimation), how could I consider a correction for multiple comparisons in >> this univariate case ? >> >> Shouldn't I use the lme_mass_fit or lme_mass_fit_vw functions in my mass >> univariate case ? If yes, how do I have to format my 3D FA volume as input >> of the LME toolbox ? >> >> Best regards, >> >> Matthieu >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> 2015-09-29 16:34 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >> >>> Hi Matthieu, >>> >>> yes, multiple comparisons are a problem for any mass univariate >>> approach. You can use the FDR2 correction (in the lme matlab tools) which >>> is less conservative than standard FDR. You can also work in specific ROI's >>> and average there, to reduce the number of comparisons. >>> >>> Best, Martin >>> >>> >>> On 09/29/2015 09:11 AM, Matthieu Vanhoutte wrote: >>> >>> Hi Martin, >>> >>> Thank you for your answer. >>> >>> However, I would like to consider FA maps as a mass-univariate problem >>> and not a univariate voxel-by-voxel as hippocampal volume. Indeed, my >>> voxels aren't independant, are they ? So, how to correct for multiple >>> comparisons then ? >>> >>> Best regards, >>> >>> Matthieu >>> >>> 2015-09-29 15:04 GMT+02:00 Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Matthieu, >>>> >>>> if all your images are perfectly registered, you can do LME on a >>>> voxel-by-voxel basis, just as if you had hippocampal volume or any other >>>> ROI measure. >>>> >>>> Best, Martin >>>> >>>> >>>> On 09/29/2015 06:46 AM, Matthieu Vanhoutte wrote: >>>> >>>> Dear experts, >>>> >>>> I would like to know if it is possible to make a longitudinal study >>>> with LME toolbox from volume FA maps registered in a common space ? >>>> >>>> I don't have T1 images so the recon-all process couldn't be processed. >>>> But if I put my 3D FA volume of dim = [nx,ny,nz] in a 1D nx*ny*nz voxels >>>> format, could it be in good way for LME ? >>>> >>>> Thanks for helping ! >>>> >>>> Best regards, >>>> >>>> Matthieu >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> -- >>>> Martin Reuter, PhD >>>> Assistant Professor of Radiology, Harvard Medical School >>>> Assistant Professor of Neurology, Harvard Medical School >>>> A.A.Martinos Center for Biomedical Imaging >>>> Massachusetts General Hospital >>>> Research Affiliate, CSAIL, MIT >>>> Phone: +1-617-724-5652 >>>> Web : 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. >>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Martin Reuter, PhD >>> Assistant Professor of Radiology, Harvard Medical School >>> Assistant Professor of Neurology, Harvard Medical School >>> A.A.Martinos Center for Biomedical Imaging >>> Massachusetts General Hospital >>> Research Affiliate, CSAIL, MIT >>> Phone: +1-617-724-5652 >>> Web : 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. >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, PhD >> Assistant Professor of Radiology, Harvard Medical School >> Assistant Professor of Neurology, Harvard Medical School >> A.A.Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Research Affiliate, CSAIL, MIT >> Phone: +1-617-724-5652 >> Web : 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. >> >> >

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error with .lta files in longitudinal
by Justin McKee 12 Oct '15

12 Oct '15

Hi, I’ve not idea why a few of my longitudinal runs have started to fail. It’s saying there’s a problem with the .lta files, >From “bugr” script FREESURFER_HOME: /opt/fmrib/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 I ‘ve lost the exact command line but it would have been recon-all –long ACT_364_12M ACT_364_3scan_base -all The error message is mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz ltaReadFile(/home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta Linux jalapeno12.fmrib.ox.ac.uk 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ACT_364_12M.long.ACT_364_3scan_base exited with ERRORS at Mon Oct 12 18:16:19 BST 2015 I’m a bit confused because /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ Has a full complement of.lta files including the one mentioned in the error message.. Obviously it’s taken a while to get to this stage so I’m loathe to re-run the –base and –long again, as I had made extensive edits to the ACT_364_3scan_base brain mask file and ran autorecon-pial and don’t want to loose those if possible, or indeed do them again and get the same mistake at this stage. Have attached the recon-all.log file Any help gratefully received! Cheers Justin Dr Justin McKee Clinical Research Fellow in Multiple Sclerosis Nuffield Department of Clinical Neuroscience University of Oxford

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high resolution data using recon-all
by Yun Wang 12 Oct '15

12 Oct '15

Hi All, I have 7T high resolution data 0.625mm. Is it appropriate to process the data using recon-all ? If not, any idea? Thanks! Yun Wang

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Error: cannot determine file type
by will brown 12 Oct '15

12 Oct '15

Hi all, Am receiving the below error, I haven't used this scan before but have never had issues with .dcm. Sorry I'm not sure what sort of scanner they are from. Any help would be appreciated. Cheers, Will /usr/local/freesurfer/subjects/YU mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz ERROR: cannot determine file type for /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s YU exited with ERRORS at Mon Oct 12 21:21:24 NZDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] longitudinal stream: adding a time point
by Martin Reuter 11 Oct '15

11 Oct '15

Hi Ruthi, that is possible in several ways. The question is what images do you want to map and for what purposes. For easy transfer of control points or edits, it should be OK, or external data that you created and want to take along (fMRI or other images). But if you plan to map images that are part of the stream and then further process it, that may be problematic (again because of potential biases that may sneak in). So to go from old base to new you can a) register the base images (e.g. norm.mgz) and then use the transform to map stuff (I think this would do the trick: mri_robust_register --mov <oldnorm.mgz> --dst <newnorm.mgz> --lta old2new.lta --mapmov old2new.mgz --sat 6 you can then use mri_convert or vol2vol to map stuff using the lta (make sure to use nearest neighbor interpolation for label maps and cubic interpolation for images). In mri_convert -rt cubic or -rt nearest b) you can concatenate the existing transform from a cross sectional to the old base (actually the inverse) with the new transform from that time point to the new base. The problem here is (although it should not matter much) that you again need to select a specific time point and that is again a potential source of bias. Also if you accidentally select a time point with motion artifacts or other problems this could be unstable. So I recommend option a). Best Martin > On Oct 11, 2015, at 6:20 AM, Adam, Ruth <Ruth.Adam(a)med.uni-muenchen.de> wrote: > > Thank you Martin! > In that case, is there an easy way to register volumes marked on the old 2 time-points base to a new 3 time-points base? > Have a nice week. > > Best, > ruthi > > Message: 3 > Date: Thu, 8 Oct 2015 20:18:47 +0200 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] longitudinal stream: adding a time point > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <4599EF79-C8D8-4448-ADE3-3941CAA18D41(a)nmr.mgh.harvard.edu <mailto:4599EF79-C8D8-4448-ADE3-3941CAA18D41@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="us-ascii" > > Hi Ruthi, > > it is possible to add time points retrospectively without re-creating the base. However this will likely induce a processing bias, as the 3rd time point is treated differently from the first two. How big that is going to be nobody knows (it depends on your data and on the number of time points). The more time points are in the base, the less of a problem it should be, but with only 2, adding a 3rd may not be good. > > Here is how you can do it > recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all > but I recommend against it. If you do, you definitely need to describe this in the publication as it is not the standard procedure. You should also run several cases (maybe ones that did not need edits) separately with 3 time points in the base and test for differences. > > The re-creation of the base is the biggest problem in unbiased longitudinal processing, but necessary to ensure all time points undergo exactly the same treatment. > > Best, Martin > >> On Oct 8, 2015, at 4:40 PM, Adam, Ruth <Ruth.Adam(a)med.uni-muenchen.de <mailto:Ruth.Adam@med.uni-muenchen.de>> wrote: >> >> Dear all, >> >> We have run recon-all longitudinal stream on two time points and now have an additional time point we would like to integrate. >> Since edits and analysis were already done using the 2 time points template, we would like to avoid creation of a new template (by combining all time points) and instead register the third time point to the pre-existing template. >> What is the best way to do so? Is there a way to force recon-all to use a specific template? >> >> Many thanks! >> >> Best, >> ruthi

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repeated measures ANOVA using the FSGD file
by pablo najt 10 Oct '15

10 Oct '15

Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many subjects within family_1, same for family_2 and so on... I also want to include gender as a covariate. In short my question is:For my design in repeated measures do I need to define all my groups for each discrete variable as how we do it for glm?For example if I want to have variables GROUP + GENDER + FAMILY.Should i do it as follows?class HC_Female_Family1class PT_Female_Family1class HC_Male_Family2class HC_Female_Family2...... Many thanks,Pablo

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A potential problem in qdec
by chenhf_uestc 09 Oct '15

09 Oct '15

Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but there was an error (acctached error.png) that puzzled me for a long time. I and my colleague help me to check all the files but do not find where is the error. I performed the same analyses on other computers, there was the same error. However, if I remove the files gender.levels, group.levels and fsid.levels (I means that I just keep the qdec.table.dat), it works. I can design, display and finally obtain the results. Could anyone give me some suggestions? Any help would be greatly appreciate. Best, Feng

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Automaticky: Jan Sanda is out of the office (příchod 09.11.2015)
by Jan.Sanda＠fnmotol.cz 09 Oct '15

09 Oct '15

Jsem mimo kancelář do 09.11.2015. Poznámka: Toto je automatická odpověď na vaši zprávu "[Freesurfer] PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback" odeslanou dne 10.10.2015 0:58:09. Toto je jediné oznámení, které obdržíte v době nepřítomnosti této osoby.

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